Starting phenix.real_space_refine on Thu Mar 21 13:11:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sof_10273/03_2024/6sof_10273.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sof_10273/03_2024/6sof_10273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sof_10273/03_2024/6sof_10273.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sof_10273/03_2024/6sof_10273.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sof_10273/03_2024/6sof_10273.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sof_10273/03_2024/6sof_10273.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.154 sd= 1.821 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 128 5.16 5 C 9966 2.51 5 N 2707 2.21 5 O 2968 1.98 5 H 14564 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 24": "OE1" <-> "OE2" Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 363": "OE1" <-> "OE2" Residue "A TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 643": "OE1" <-> "OE2" Residue "A GLU 663": "OE1" <-> "OE2" Residue "B GLU 760": "OE1" <-> "OE2" Residue "B GLU 834": "OE1" <-> "OE2" Residue "B TYR 852": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 907": "OD1" <-> "OD2" Residue "C GLU 6": "OE1" <-> "OE2" Residue "C PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C GLU 239": "OE1" <-> "OE2" Residue "C TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 287": "OE1" <-> "OE2" Residue "C GLU 318": "OE1" <-> "OE2" Residue "C GLU 329": "OE1" <-> "OE2" Residue "C TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 509": "OE1" <-> "OE2" Residue "C TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 591": "OD1" <-> "OD2" Residue "C GLU 697": "OE1" <-> "OE2" Residue "D GLU 766": "OE1" <-> "OE2" Residue "D TYR 845": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 849": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 908": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "K TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30333 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 11127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 11127 Classifications: {'peptide': 719} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 678} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2532 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 152} Chain: "C" Number of atoms: 11118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 11118 Classifications: {'peptide': 719} Link IDs: {'PTRANS': 40, 'TRANS': 678} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2508 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 9, 'TRANS': 152} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 286 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 471 Classifications: {'peptide': 30} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "E" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 299 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "F" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 471 Classifications: {'peptide': 30} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "K" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 292 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 471 Classifications: {'peptide': 30} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "I" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 292 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 466 Classifications: {'peptide': 30} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 28} Time building chain proxies: 12.65, per 1000 atoms: 0.42 Number of scatterers: 30333 At special positions: 0 Unit cell: (118.72, 142.04, 166.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 128 16.00 O 2968 8.00 N 2707 7.00 C 9966 6.00 H 14564 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=49, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 182 " distance=2.04 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.04 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.02 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.05 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.02 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.02 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.04 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 304 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS C 524 " distance=2.03 Simple disulfide: pdb=" SG CYS A 647 " - pdb=" SG CYS B 860 " distance=2.04 Simple disulfide: pdb=" SG CYS A 682 " - pdb=" SG CYS A 685 " distance=2.03 Simple disulfide: pdb=" SG CYS A 683 " - pdb=" SG CYS C 683 " distance=2.03 Simple disulfide: pdb=" SG CYS B 786 " - pdb=" SG CYS B 795 " distance=2.02 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS C 26 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 159 " - pdb=" SG CYS C 182 " distance=2.02 Simple disulfide: pdb=" SG CYS C 192 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS C 196 " - pdb=" SG CYS C 207 " distance=2.03 Simple disulfide: pdb=" SG CYS C 208 " - pdb=" SG CYS C 216 " distance=2.04 Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS C 225 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 241 " - pdb=" SG CYS C 253 " distance=2.03 Simple disulfide: pdb=" SG CYS C 259 " - pdb=" SG CYS C 284 " distance=2.04 Simple disulfide: pdb=" SG CYS C 266 " - pdb=" SG CYS C 274 " distance=2.02 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 304 " - pdb=" SG CYS C 308 " distance=2.04 Simple disulfide: pdb=" SG CYS C 312 " - pdb=" SG CYS C 333 " distance=2.04 Simple disulfide: pdb=" SG CYS C 435 " - pdb=" SG CYS C 468 " distance=2.03 Simple disulfide: pdb=" SG CYS C 647 " - pdb=" SG CYS D 860 " distance=2.03 Simple disulfide: pdb=" SG CYS C 682 " - pdb=" SG CYS C 685 " distance=2.03 Simple disulfide: pdb=" SG CYS D 786 " - pdb=" SG CYS D 795 " distance=2.04 Simple disulfide: pdb=" SG CYS G 6 " - pdb=" SG CYS G 11 " distance=2.04 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 11 " distance=2.04 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS F 7 " distance=2.03 Simple disulfide: pdb=" SG CYS E 20 " - pdb=" SG CYS F 19 " distance=2.04 Simple disulfide: pdb=" SG CYS K 6 " - pdb=" SG CYS K 11 " distance=2.04 Simple disulfide: pdb=" SG CYS K 7 " - pdb=" SG CYS L 7 " distance=2.03 Simple disulfide: pdb=" SG CYS K 20 " - pdb=" SG CYS L 19 " distance=2.03 Simple disulfide: pdb=" SG CYS I 6 " - pdb=" SG CYS I 11 " distance=2.05 Simple disulfide: pdb=" SG CYS I 7 " - pdb=" SG CYS J 7 " distance=2.04 Simple disulfide: pdb=" SG CYS I 20 " - pdb=" SG CYS J 19 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 22.82 Conformation dependent library (CDL) restraints added in 3.1 seconds 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3700 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 30 sheets defined 15.7% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 removed outlier: 3.654A pdb=" N ARG A 19 " --> pdb=" O ASN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 47 Processing helix chain 'A' and resid 193 through 198 removed outlier: 4.117A pdb=" N SER A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 264 Processing helix chain 'A' and resid 323 through 331 removed outlier: 3.610A pdb=" N ALA A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 358 Processing helix chain 'A' and resid 435 through 445 Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 689 through 691 No H-bonds generated for 'chain 'A' and resid 689 through 691' Processing helix chain 'A' and resid 692 through 714 removed outlier: 3.910A pdb=" N PHE A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 870 Processing helix chain 'C' and resid 16 through 24 removed outlier: 3.559A pdb=" N ARG C 19 " --> pdb=" O ASN C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 49 removed outlier: 3.676A pdb=" N PHE C 46 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU C 49 " --> pdb=" O ASP C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 153 Processing helix chain 'C' and resid 193 through 197 removed outlier: 3.803A pdb=" N LYS C 197 " --> pdb=" O THR C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 265 Processing helix chain 'C' and resid 323 through 329 Processing helix chain 'C' and resid 350 through 358 Processing helix chain 'C' and resid 435 through 447 removed outlier: 3.854A pdb=" N ILE C 439 " --> pdb=" O CYS C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 452 Processing helix chain 'C' and resid 496 through 498 No H-bonds generated for 'chain 'C' and resid 496 through 498' Processing helix chain 'C' and resid 691 through 714 removed outlier: 3.741A pdb=" N GLU C 695 " --> pdb=" O GLN C 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 808 through 813 removed outlier: 4.137A pdb=" N ASP D 812 " --> pdb=" O GLU D 808 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 870 Processing helix chain 'G' and resid 2 through 7 Processing helix chain 'G' and resid 13 through 18 Processing helix chain 'H' and resid 8 through 20 removed outlier: 4.247A pdb=" N GLY H 20 " --> pdb=" O TYR H 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 7 Processing helix chain 'F' and resid 7 through 20 Processing helix chain 'K' and resid 2 through 7 Processing helix chain 'K' and resid 12 through 18 Processing helix chain 'L' and resid 9 through 20 Processing helix chain 'I' and resid 3 through 9 removed outlier: 3.714A pdb=" N SER I 9 " --> pdb=" O GLN I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 20 removed outlier: 3.639A pdb=" N LEU I 16 " --> pdb=" O SER I 12 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASN I 18 " --> pdb=" O TYR I 14 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR I 19 " --> pdb=" O GLN I 15 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS I 20 " --> pdb=" O LEU I 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 20 removed outlier: 4.006A pdb=" N VAL J 12 " --> pdb=" O GLY J 8 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N CYS J 19 " --> pdb=" O LEU J 15 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 13 removed outlier: 9.488A pdb=" N VAL A 7 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 12.500A pdb=" N HIS A 32 " --> pdb=" O VAL A 7 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N GLN A 34 " --> pdb=" O PRO A 9 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N MET A 11 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N LEU A 36 " --> pdb=" O MET A 11 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE A 13 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N MET A 38 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE A 29 " --> pdb=" O MET A 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 13 removed outlier: 9.488A pdb=" N VAL A 7 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 12.500A pdb=" N HIS A 32 " --> pdb=" O VAL A 7 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N GLN A 34 " --> pdb=" O PRO A 9 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N MET A 11 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N LEU A 36 " --> pdb=" O MET A 11 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE A 13 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N MET A 38 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE A 64 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 65 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU A 93 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 removed outlier: 3.609A pdb=" N THR A 172 " --> pdb=" O VAL A 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.507A pdb=" N ASN A 215 " --> pdb=" O VAL A 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 231 through 233 removed outlier: 3.894A pdb=" N PHE A 231 " --> pdb=" O VAL A 238 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 246 through 248 Processing sheet with id=AA7, first strand: chain 'A' and resid 278 through 280 Processing sheet with id=AA8, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AA9, first strand: chain 'A' and resid 387 through 388 removed outlier: 3.556A pdb=" N ILE A 388 " --> pdb=" O THR A 420 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 398 through 401 removed outlier: 7.792A pdb=" N PHE A 427 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N TYR A 401 " --> pdb=" O PHE A 427 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 477 through 480 Processing sheet with id=AB3, first strand: chain 'A' and resid 533 through 534 removed outlier: 3.953A pdb=" N GLY A 502 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 604 through 605 removed outlier: 4.514A pdb=" N VAL A 604 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 612 " --> pdb=" O VAL A 604 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 760 through 762 removed outlier: 4.160A pdb=" N GLU B 760 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 630 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL B 762 " --> pdb=" O TYR A 628 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR A 628 " --> pdb=" O VAL B 762 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AB7, first strand: chain 'C' and resid 11 through 13 removed outlier: 7.736A pdb=" N LEU C 61 " --> pdb=" O HIS C 32 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLN C 34 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU C 63 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU C 36 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ARG C 65 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET C 38 " --> pdb=" O ARG C 65 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 93 through 96 removed outlier: 3.961A pdb=" N TYR C 144 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 212 through 216 removed outlier: 5.922A pdb=" N LEU C 213 " --> pdb=" O CYS C 228 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N CYS C 228 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASN C 215 " --> pdb=" O VAL C 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 245 through 247 Processing sheet with id=AC2, first strand: chain 'C' and resid 278 through 280 removed outlier: 3.519A pdb=" N ILE C 285 " --> pdb=" O VAL C 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 319 through 321 Processing sheet with id=AC4, first strand: chain 'C' and resid 335 through 336 removed outlier: 3.600A pdb=" N ILE C 364 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 402 through 403 removed outlier: 7.223A pdb=" N ALA C 402 " --> pdb=" O HIS C 429 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 471 through 472 removed outlier: 7.184A pdb=" N GLU C 471 " --> pdb=" O LYS C 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 475 through 480 removed outlier: 3.563A pdb=" N ARG C 479 " --> pdb=" O LEU C 486 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 533 through 534 removed outlier: 3.932A pdb=" N GLY C 502 " --> pdb=" O LEU C 569 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 602 through 604 removed outlier: 3.721A pdb=" N LYS C 614 " --> pdb=" O ILE C 602 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE C 611 " --> pdb=" O ILE D 770 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE D 770 " --> pdb=" O ILE C 611 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 779 through 780 removed outlier: 3.712A pdb=" N TYR D 779 " --> pdb=" O ALA D 803 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 820 through 823 removed outlier: 3.644A pdb=" N VAL D 827 " --> pdb=" O PHE D 823 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 880 through 884 removed outlier: 3.875A pdb=" N VAL D 884 " --> pdb=" O THR D 901 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR D 901 " --> pdb=" O VAL D 884 " (cutoff:3.500A) 253 hydrogen bonds defined for protein. 663 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.65 Time building geometry restraints manager: 23.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 14562 1.03 - 1.24: 2059 1.24 - 1.44: 5035 1.44 - 1.65: 8915 1.65 - 1.85: 150 Bond restraints: 30721 Sorted by residual: bond pdb=" CB CYS B 786 " pdb=" SG CYS B 786 " ideal model delta sigma weight residual 1.808 1.748 0.060 3.30e-02 9.18e+02 3.26e+00 bond pdb=" C VAL B 911 " pdb=" N PRO B 912 " ideal model delta sigma weight residual 1.339 1.399 -0.059 3.40e-02 8.65e+02 3.05e+00 bond pdb=" CG ARG A 577 " pdb=" CD ARG A 577 " ideal model delta sigma weight residual 1.520 1.469 0.051 3.00e-02 1.11e+03 2.90e+00 bond pdb=" CB ASN C 337 " pdb=" CG ASN C 337 " ideal model delta sigma weight residual 1.516 1.554 -0.038 2.50e-02 1.60e+03 2.34e+00 bond pdb=" N ILE G 10 " pdb=" CA ILE G 10 " ideal model delta sigma weight residual 1.474 1.451 0.024 1.57e-02 4.06e+03 2.29e+00 ... (remaining 30716 not shown) Histogram of bond angle deviations from ideal: 70.31 - 83.07: 6 83.07 - 95.83: 0 95.83 - 108.59: 11287 108.59 - 121.35: 36782 121.35 - 134.11: 7098 Bond angle restraints: 55173 Sorted by residual: angle pdb=" C GLN C 276 " pdb=" CA GLN C 276 " pdb=" HA GLN C 276 " ideal model delta sigma weight residual 109.00 70.31 38.69 3.00e+00 1.11e-01 1.66e+02 angle pdb=" CB CYS C 288 " pdb=" CA CYS C 288 " pdb=" HA CYS C 288 " ideal model delta sigma weight residual 109.00 71.81 37.19 3.00e+00 1.11e-01 1.54e+02 angle pdb=" C CYS C 288 " pdb=" CA CYS C 288 " pdb=" HA CYS C 288 " ideal model delta sigma weight residual 109.00 73.02 35.98 3.00e+00 1.11e-01 1.44e+02 angle pdb=" N GLN C 276 " pdb=" CA GLN C 276 " pdb=" HA GLN C 276 " ideal model delta sigma weight residual 110.00 75.10 34.90 3.00e+00 1.11e-01 1.35e+02 angle pdb=" N CYS C 288 " pdb=" CA CYS C 288 " pdb=" HA CYS C 288 " ideal model delta sigma weight residual 110.00 75.62 34.38 3.00e+00 1.11e-01 1.31e+02 ... (remaining 55168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 13001 17.91 - 35.83: 1324 35.83 - 53.74: 393 53.74 - 71.66: 114 71.66 - 89.57: 39 Dihedral angle restraints: 14871 sinusoidal: 7971 harmonic: 6900 Sorted by residual: dihedral pdb=" CB CYS I 6 " pdb=" SG CYS I 6 " pdb=" SG CYS I 11 " pdb=" CB CYS I 11 " ideal model delta sinusoidal sigma weight residual -86.00 0.66 -86.66 1 1.00e+01 1.00e-02 9.04e+01 dihedral pdb=" CB CYS E 7 " pdb=" SG CYS E 7 " pdb=" SG CYS F 7 " pdb=" CB CYS F 7 " ideal model delta sinusoidal sigma weight residual -86.00 -170.30 84.30 1 1.00e+01 1.00e-02 8.65e+01 dihedral pdb=" CB CYS A 196 " pdb=" SG CYS A 196 " pdb=" SG CYS A 207 " pdb=" CB CYS A 207 " ideal model delta sinusoidal sigma weight residual 93.00 10.56 82.44 1 1.00e+01 1.00e-02 8.34e+01 ... (remaining 14868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1886 0.059 - 0.119: 407 0.119 - 0.178: 70 0.178 - 0.238: 1 0.238 - 0.297: 1 Chirality restraints: 2365 Sorted by residual: chirality pdb=" CA GLN C 276 " pdb=" N GLN C 276 " pdb=" C GLN C 276 " pdb=" CB GLN C 276 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CA CYS B 786 " pdb=" N CYS B 786 " pdb=" C CYS B 786 " pdb=" CB CYS B 786 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.76e-01 chirality pdb=" CA CYS C 288 " pdb=" N CYS C 288 " pdb=" C CYS C 288 " pdb=" CB CYS C 288 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.85e-01 ... (remaining 2362 not shown) Planarity restraints: 4709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 622 " 0.046 2.00e-02 2.50e+03 8.26e-02 1.02e+02 pdb=" CG ASN A 622 " -0.096 2.00e-02 2.50e+03 pdb=" OD1 ASN A 622 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 622 " 0.140 2.00e-02 2.50e+03 pdb="HD21 ASN A 622 " 0.017 2.00e-02 2.50e+03 pdb="HD22 ASN A 622 " -0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 668 " -0.041 2.00e-02 2.50e+03 4.84e-02 3.52e+01 pdb=" CD GLN A 668 " 0.045 2.00e-02 2.50e+03 pdb=" OE1 GLN A 668 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 GLN A 668 " 0.071 2.00e-02 2.50e+03 pdb="HE21 GLN A 668 " 0.001 2.00e-02 2.50e+03 pdb="HE22 GLN A 668 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 295 " -0.021 2.00e-02 2.50e+03 3.78e-02 2.15e+01 pdb=" CG ASN A 295 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN A 295 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 295 " -0.066 2.00e-02 2.50e+03 pdb="HD21 ASN A 295 " -0.003 2.00e-02 2.50e+03 pdb="HD22 ASN A 295 " 0.044 2.00e-02 2.50e+03 ... (remaining 4706 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 3058 2.22 - 2.81: 65440 2.81 - 3.41: 79486 3.41 - 4.00: 102587 4.00 - 4.60: 153751 Nonbonded interactions: 404322 Sorted by model distance: nonbonded pdb=" H GLN C 276 " pdb=" HA GLN C 276 " model vdw 1.624 1.816 nonbonded pdb=" H CYS C 288 " pdb=" HA CYS C 288 " model vdw 1.625 1.816 nonbonded pdb=" O HIS C 247 " pdb=" H CYS C 284 " model vdw 1.645 1.850 nonbonded pdb=" OD1 ASN C 255 " pdb=" H PHE C 258 " model vdw 1.657 1.850 nonbonded pdb=" O PRO C 432 " pdb=" H GLY C 463 " model vdw 1.660 1.850 ... (remaining 404317 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CG or name ND1 or name CD2 or name CE1 or name NE2 or name HA or name HB2 \ or name HB3 or name HD2 or name HE1 or name HE2)) or resid 2 through 266 or (re \ sid 267 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name CE or name NZ or name H or name HA )) or (resid 268 and (name N or n \ ame CA or name C or name O or name CB or name CG or name OD1 or name ND2 or name \ H or name HA )) or resid 269 or (resid 270 through 271 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD or name NE or name CZ or nam \ e NH1 or name NH2 or name H or name HA )) or resid 272 through 287 or (resid 288 \ and (name N or name CA or name C or name O or name CB or name SG or name H or n \ ame HA )) or resid 289 through 420 or (resid 421 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 422 through 691 or (resi \ d 692 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 693 through 719)) selection = (chain 'C' and (resid 1 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2 or name CD1 or name H or name HA ) \ ) or (resid 14 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA )) \ or resid 15 through 369 or (resid 370 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name CD1 or name H or name HA )) or resi \ d 371 through 387 or (resid 388 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 389 through 624 or (resid 625 and (name N \ or name CA or name C or name O or name CB or name CG1 or name CG2 or name CD1 o \ r name H or name HA )) or resid 626 through 716 or (resid 717 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 718 through \ 719)) } ncs_group { reference = (chain 'B' and (resid 756 through 813 or (resid 814 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 815 through 914 or (r \ esid 915 and (name N or name CA or name C or name O or name CB or name CG1 or na \ me CG2 or name CD1 or name H or name HA )) or resid 916 or (resid 917 and (name \ N or name CA or name C or name CB or name CG or name CD or name CE or name NZ or \ name H or name HA )))) selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 3 through 9 or (resid 10 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 11 th \ rough 20 or (resid 21 and (name N or name CA or name C or name CB or name CG or \ name OD1 or name ND2 or name H or name HA )))) selection = (chain 'G' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 3 through 21)) selection = (chain 'I' and (resid 1 through 9 or (resid 10 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 11 through 20 or (resid 21 \ and (name N or name CA or name C or name CB or name CG or name OD1 or name ND2 \ or name H or name HA )))) selection = (chain 'K' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 3 through 20 or (resid 21 and (name N \ or name CA or name C or name CB or name CG or name OD1 or name ND2 or name H or \ name HA )))) } ncs_group { reference = (chain 'F' and (resid 1 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB or name OG1 or name CG2 or name H or name HA )) or resid 2 \ 8 through 30)) selection = (chain 'H' and (resid 1 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB or name OG1 or name CG2 or name H or name HA )) or resid 2 \ 8 through 30)) selection = chain 'J' selection = (chain 'L' and (resid 1 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB or name OG1 or name CG2 or name H or name HA )) or resid 2 \ 8 through 30)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.440 Extract box with map and model: 6.410 Check model and map are aligned: 0.440 Set scattering table: 0.290 Process input model: 88.560 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 16157 Z= 0.382 Angle : 0.932 8.476 21917 Z= 0.497 Chirality : 0.050 0.297 2365 Planarity : 0.007 0.107 2857 Dihedral : 14.587 89.574 5973 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.66 % Favored : 82.34 % Rotamer: Outliers : 0.62 % Allowed : 10.98 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.47 (0.15), residues: 1942 helix: -2.83 (0.24), residues: 257 sheet: -4.35 (0.28), residues: 177 loop : -4.06 (0.13), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 183 HIS 0.022 0.003 HIS A 263 PHE 0.017 0.003 PHE C 64 TYR 0.024 0.003 TYR K 14 ARG 0.029 0.002 ARG D 774 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASN G 21 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Evaluate side-chains 522 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 511 time to evaluate : 2.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.7989 (mmm-85) cc_final: 0.7769 (mpt-90) REVERT: A 96 PHE cc_start: 0.7854 (t80) cc_final: 0.7618 (t80) REVERT: A 120 GLU cc_start: 0.8377 (tt0) cc_final: 0.8085 (tt0) REVERT: A 123 ASN cc_start: 0.8574 (m-40) cc_final: 0.8236 (p0) REVERT: A 329 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8362 (mt-10) REVERT: A 355 GLU cc_start: 0.8855 (tt0) cc_final: 0.8337 (tp30) REVERT: A 368 LEU cc_start: 0.8171 (tp) cc_final: 0.7883 (tp) REVERT: B 869 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8491 (mm-30) REVERT: C 14 ARG cc_start: 0.6180 (ptp-170) cc_final: 0.5809 (mtm180) REVERT: C 123 ASN cc_start: 0.9030 (m110) cc_final: 0.8595 (t0) REVERT: C 245 TYR cc_start: 0.8445 (m-80) cc_final: 0.7870 (m-80) REVERT: C 372 ARG cc_start: 0.8188 (mtp180) cc_final: 0.7944 (mtt90) REVERT: C 373 SER cc_start: 0.9239 (m) cc_final: 0.8679 (p) REVERT: C 404 ASP cc_start: 0.8909 (m-30) cc_final: 0.8676 (m-30) REVERT: C 406 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7579 (mm110) REVERT: C 553 MET cc_start: 0.7550 (ptp) cc_final: 0.7262 (ptm) REVERT: C 575 GLU cc_start: 0.7180 (pm20) cc_final: 0.6660 (pm20) REVERT: C 609 SER cc_start: 0.8967 (p) cc_final: 0.8690 (t) REVERT: C 614 LYS cc_start: 0.9149 (mtmt) cc_final: 0.8792 (mtpp) REVERT: D 781 ILE cc_start: 0.7622 (mp) cc_final: 0.7370 (mm) REVERT: G 14 TYR cc_start: 0.8197 (t80) cc_final: 0.7876 (t80) REVERT: F 18 VAL cc_start: 0.9057 (t) cc_final: 0.8776 (t) REVERT: J 3 ASN cc_start: 0.5014 (m110) cc_final: 0.4603 (p0) outliers start: 11 outliers final: 4 residues processed: 517 average time/residue: 0.6621 time to fit residues: 480.0686 Evaluate side-chains 377 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 373 time to evaluate : 2.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.0020 chunk 147 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 chunk 176 optimal weight: 6.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN A 78 ASN A 148 ASN A 189 GLN A 230 ASN A 247 HIS A 295 ASN A 298 ASN A 405 ASN A 406 GLN ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 ASN ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 788 GLN B 894 ASN C 21 HIS C 78 ASN C 418 ASN ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 546 GLN C 589 GLN C 594 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 894 ASN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 GLN ** L 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 ASN J 10 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16157 Z= 0.239 Angle : 0.703 6.354 21917 Z= 0.380 Chirality : 0.045 0.313 2365 Planarity : 0.007 0.095 2857 Dihedral : 8.106 73.431 2155 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.25 % Favored : 82.75 % Rotamer: Outliers : 0.28 % Allowed : 2.25 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.06 (0.15), residues: 1942 helix: -2.28 (0.27), residues: 261 sheet: -4.09 (0.29), residues: 193 loop : -3.81 (0.13), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 183 HIS 0.019 0.002 HIS D 829 PHE 0.027 0.002 PHE D 866 TYR 0.020 0.002 TYR C 430 ARG 0.006 0.001 ARG A 409 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASN G 21 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Evaluate side-chains 456 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 451 time to evaluate : 2.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.8528 (pp) cc_final: 0.8318 (pp) REVERT: A 96 PHE cc_start: 0.7794 (t80) cc_final: 0.7495 (t80) REVERT: A 120 GLU cc_start: 0.8500 (tt0) cc_final: 0.8034 (tt0) REVERT: A 329 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8206 (mt-10) REVERT: A 355 GLU cc_start: 0.8824 (tt0) cc_final: 0.8277 (tp30) REVERT: A 419 LEU cc_start: 0.8963 (tt) cc_final: 0.8715 (tp) REVERT: A 430 TYR cc_start: 0.8654 (m-80) cc_final: 0.8404 (m-80) REVERT: A 507 TYR cc_start: 0.8794 (p90) cc_final: 0.8198 (p90) REVERT: A 547 ASN cc_start: 0.8569 (p0) cc_final: 0.8294 (p0) REVERT: B 779 TYR cc_start: 0.6729 (m-10) cc_final: 0.6397 (m-10) REVERT: C 14 ARG cc_start: 0.5906 (ptp-170) cc_final: 0.5495 (mtm180) REVERT: C 123 ASN cc_start: 0.9001 (m110) cc_final: 0.8466 (t0) REVERT: C 208 CYS cc_start: 0.0655 (m) cc_final: -0.0050 (m) REVERT: C 245 TYR cc_start: 0.8469 (m-80) cc_final: 0.7901 (m-80) REVERT: C 373 SER cc_start: 0.9116 (m) cc_final: 0.8265 (p) REVERT: C 406 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7442 (mm-40) REVERT: C 453 GLU cc_start: 0.7987 (mp0) cc_final: 0.7734 (mp0) REVERT: C 533 ASP cc_start: 0.8558 (p0) cc_final: 0.8350 (p0) REVERT: C 656 ARG cc_start: 0.8496 (mmp-170) cc_final: 0.8234 (mmp-170) REVERT: C 695 GLU cc_start: 0.8640 (mp0) cc_final: 0.8432 (mp0) REVERT: G 14 TYR cc_start: 0.8221 (t80) cc_final: 0.7932 (t80) REVERT: H 24 PHE cc_start: 0.5682 (p90) cc_final: 0.5152 (p90) REVERT: E 4 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8701 (mt-10) outliers start: 5 outliers final: 0 residues processed: 452 average time/residue: 0.6503 time to fit residues: 417.2691 Evaluate side-chains 370 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 0.0980 chunk 146 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 176 optimal weight: 7.9990 chunk 190 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 141 optimal weight: 0.3980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 881 ASN E 5 GLN ** L 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 10 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16157 Z= 0.178 Angle : 0.643 7.821 21917 Z= 0.346 Chirality : 0.045 0.321 2365 Planarity : 0.005 0.093 2857 Dihedral : 7.687 70.623 2155 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.68 % Favored : 85.32 % Rotamer: Outliers : 0.11 % Allowed : 1.91 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.71 (0.16), residues: 1942 helix: -1.83 (0.29), residues: 262 sheet: -3.79 (0.31), residues: 188 loop : -3.61 (0.14), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 183 HIS 0.011 0.001 HIS D 829 PHE 0.021 0.001 PHE D 866 TYR 0.012 0.001 TYR A 401 ARG 0.007 0.000 ARG C 576 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASN G 21 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Evaluate side-chains 433 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 431 time to evaluate : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8005 (mt0) cc_final: 0.7704 (mt0) REVERT: A 36 LEU cc_start: 0.8557 (pp) cc_final: 0.8322 (pp) REVERT: A 96 PHE cc_start: 0.7857 (t80) cc_final: 0.7520 (t80) REVERT: A 120 GLU cc_start: 0.8384 (tt0) cc_final: 0.7916 (tt0) REVERT: A 329 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8235 (mt-10) REVERT: A 419 LEU cc_start: 0.8915 (tt) cc_final: 0.8703 (tp) REVERT: A 430 TYR cc_start: 0.8619 (m-80) cc_final: 0.8279 (m-80) REVERT: A 507 TYR cc_start: 0.8740 (p90) cc_final: 0.8369 (p90) REVERT: A 574 ASP cc_start: 0.8403 (t70) cc_final: 0.8150 (t0) REVERT: A 709 LEU cc_start: 0.8167 (tt) cc_final: 0.7922 (tt) REVERT: B 779 TYR cc_start: 0.6686 (m-10) cc_final: 0.6339 (m-10) REVERT: C 245 TYR cc_start: 0.8407 (m-80) cc_final: 0.7857 (m-80) REVERT: C 362 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7940 (mt-10) REVERT: C 372 ARG cc_start: 0.8428 (mtt180) cc_final: 0.8195 (mtt90) REVERT: C 373 SER cc_start: 0.9164 (m) cc_final: 0.8619 (t) REVERT: C 406 GLN cc_start: 0.8143 (mm-40) cc_final: 0.7731 (mm-40) REVERT: C 656 ARG cc_start: 0.8444 (mmp-170) cc_final: 0.8216 (mmp-170) REVERT: C 695 GLU cc_start: 0.8632 (mp0) cc_final: 0.8388 (mp0) REVERT: C 707 ASP cc_start: 0.8677 (m-30) cc_final: 0.8406 (m-30) REVERT: G 14 TYR cc_start: 0.8199 (t80) cc_final: 0.7916 (t80) REVERT: E 4 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8671 (mt-10) outliers start: 2 outliers final: 0 residues processed: 432 average time/residue: 0.6702 time to fit residues: 413.8110 Evaluate side-chains 361 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 174 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 177 optimal weight: 0.9980 chunk 187 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 HIS C 21 HIS C 78 ASN C 100 HIS C 111 ASN ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN ** C 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 GLN ** L 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 16157 Z= 0.314 Angle : 0.708 10.300 21917 Z= 0.383 Chirality : 0.045 0.315 2365 Planarity : 0.006 0.093 2857 Dihedral : 7.720 65.952 2155 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 22.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.74 % Favored : 81.26 % Rotamer: Outliers : 0.11 % Allowed : 2.82 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.79 (0.16), residues: 1942 helix: -1.82 (0.29), residues: 266 sheet: -3.89 (0.30), residues: 190 loop : -3.68 (0.13), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 658 HIS 0.011 0.002 HIS D 829 PHE 0.020 0.002 PHE C 96 TYR 0.018 0.002 TYR K 14 ARG 0.008 0.001 ARG C 576 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASN G 21 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Evaluate side-chains 408 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 406 time to evaluate : 2.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.8686 (pp) cc_final: 0.8483 (pp) REVERT: A 120 GLU cc_start: 0.8246 (tt0) cc_final: 0.7932 (tt0) REVERT: A 135 ARG cc_start: 0.8408 (mtm-85) cc_final: 0.7552 (mtm180) REVERT: A 278 VAL cc_start: 0.8748 (m) cc_final: 0.8451 (t) REVERT: A 329 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8198 (mt-10) REVERT: A 430 TYR cc_start: 0.8704 (m-80) cc_final: 0.8460 (m-80) REVERT: A 530 THR cc_start: 0.9114 (m) cc_final: 0.8887 (p) REVERT: A 574 ASP cc_start: 0.8502 (t70) cc_final: 0.8282 (t0) REVERT: A 709 LEU cc_start: 0.8270 (tt) cc_final: 0.8034 (tt) REVERT: C 208 CYS cc_start: 0.0689 (m) cc_final: -0.0007 (m) REVERT: C 245 TYR cc_start: 0.8496 (m-80) cc_final: 0.8007 (m-80) REVERT: C 362 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7950 (mm-30) REVERT: C 373 SER cc_start: 0.9307 (m) cc_final: 0.8840 (t) REVERT: C 507 TYR cc_start: 0.8904 (p90) cc_final: 0.8700 (p90) REVERT: C 556 LEU cc_start: 0.9152 (mp) cc_final: 0.8750 (mp) REVERT: C 656 ARG cc_start: 0.8518 (mmp-170) cc_final: 0.8282 (mmp-170) REVERT: C 695 GLU cc_start: 0.8660 (mp0) cc_final: 0.8445 (mp0) REVERT: C 711 ASN cc_start: 0.8552 (t0) cc_final: 0.8260 (m-40) REVERT: G 14 TYR cc_start: 0.8409 (t80) cc_final: 0.8140 (t80) REVERT: E 4 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8870 (mt-10) REVERT: J 3 ASN cc_start: 0.5073 (m-40) cc_final: 0.4523 (p0) outliers start: 2 outliers final: 0 residues processed: 408 average time/residue: 0.6397 time to fit residues: 374.1615 Evaluate side-chains 332 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 156 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 139 optimal weight: 0.1980 chunk 77 optimal weight: 0.8980 chunk 160 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN C 100 HIS ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 ASN ** C 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 820 HIS ** L 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 10 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16157 Z= 0.277 Angle : 0.680 11.191 21917 Z= 0.366 Chirality : 0.045 0.320 2365 Planarity : 0.006 0.091 2857 Dihedral : 7.688 66.660 2155 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 22.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.87 % Favored : 82.13 % Rotamer: Outliers : 0.06 % Allowed : 1.35 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.69 (0.16), residues: 1942 helix: -1.56 (0.30), residues: 260 sheet: -3.87 (0.30), residues: 194 loop : -3.62 (0.14), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 658 HIS 0.010 0.002 HIS A 263 PHE 0.023 0.002 PHE D 866 TYR 0.017 0.002 TYR B 849 ARG 0.007 0.001 ARG C 576 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASN G 21 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Evaluate side-chains 404 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 403 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.8470 (pp) cc_final: 0.8229 (pp) REVERT: A 120 GLU cc_start: 0.8329 (tt0) cc_final: 0.7998 (tt0) REVERT: A 278 VAL cc_start: 0.8825 (m) cc_final: 0.8445 (t) REVERT: A 329 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8219 (mt-10) REVERT: A 430 TYR cc_start: 0.8721 (m-80) cc_final: 0.8449 (m-80) REVERT: A 438 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8374 (tp30) REVERT: A 547 ASN cc_start: 0.8839 (p0) cc_final: 0.8560 (p0) REVERT: A 709 LEU cc_start: 0.8162 (tt) cc_final: 0.7954 (tt) REVERT: C 245 TYR cc_start: 0.8485 (m-80) cc_final: 0.8021 (m-80) REVERT: C 362 GLU cc_start: 0.8416 (mt-10) cc_final: 0.7980 (mm-30) REVERT: C 373 SER cc_start: 0.9280 (m) cc_final: 0.8523 (p) REVERT: C 656 ARG cc_start: 0.8576 (mmp-170) cc_final: 0.8330 (mmp-170) REVERT: C 695 GLU cc_start: 0.8672 (mp0) cc_final: 0.8456 (mp0) REVERT: G 14 TYR cc_start: 0.8367 (t80) cc_final: 0.8088 (t80) REVERT: E 4 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8875 (mt-10) REVERT: F 13 GLU cc_start: 0.8989 (mp0) cc_final: 0.8719 (mp0) REVERT: J 3 ASN cc_start: 0.5220 (m-40) cc_final: 0.4728 (p0) outliers start: 1 outliers final: 1 residues processed: 403 average time/residue: 0.6470 time to fit residues: 374.8872 Evaluate side-chains 338 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 337 time to evaluate : 2.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 63 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 155 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN C 32 HIS C 78 ASN ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 10 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16157 Z= 0.229 Angle : 0.635 9.495 21917 Z= 0.342 Chirality : 0.044 0.324 2365 Planarity : 0.005 0.091 2857 Dihedral : 7.446 65.377 2155 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 20.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.18 % Favored : 81.82 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.54 (0.16), residues: 1942 helix: -1.28 (0.31), residues: 260 sheet: -3.74 (0.30), residues: 198 loop : -3.55 (0.14), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 658 HIS 0.009 0.001 HIS A 263 PHE 0.027 0.002 PHE A 76 TYR 0.015 0.001 TYR A 646 ARG 0.006 0.000 ARG C 576 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASN G 21 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Evaluate side-chains 402 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 402 time to evaluate : 2.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.6917 (mtt180) cc_final: 0.6568 (mtt-85) REVERT: A 36 LEU cc_start: 0.8482 (pp) cc_final: 0.8181 (pp) REVERT: A 96 PHE cc_start: 0.7749 (t80) cc_final: 0.7412 (t80) REVERT: A 120 GLU cc_start: 0.8329 (tt0) cc_final: 0.7768 (tt0) REVERT: A 278 VAL cc_start: 0.8736 (m) cc_final: 0.8396 (t) REVERT: A 329 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8163 (mt-10) REVERT: A 355 GLU cc_start: 0.8899 (tt0) cc_final: 0.8430 (tp30) REVERT: A 438 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8375 (tp30) REVERT: A 507 TYR cc_start: 0.8779 (p90) cc_final: 0.8229 (p90) REVERT: A 547 ASN cc_start: 0.8911 (p0) cc_final: 0.8620 (p0) REVERT: A 709 LEU cc_start: 0.8244 (tt) cc_final: 0.8015 (tt) REVERT: C 14 ARG cc_start: 0.6293 (ptp-170) cc_final: 0.5895 (mtm180) REVERT: C 245 TYR cc_start: 0.8507 (m-80) cc_final: 0.8030 (m-80) REVERT: C 355 GLU cc_start: 0.8485 (tt0) cc_final: 0.8185 (tt0) REVERT: C 362 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7984 (mm-30) REVERT: C 373 SER cc_start: 0.9268 (m) cc_final: 0.8720 (p) REVERT: C 435 CYS cc_start: 0.4349 (m) cc_final: 0.3048 (m) REVERT: C 438 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7482 (mt-10) REVERT: C 656 ARG cc_start: 0.8606 (mmp-170) cc_final: 0.8375 (mmp-170) REVERT: C 711 ASN cc_start: 0.8487 (t0) cc_final: 0.8175 (m110) REVERT: G 14 TYR cc_start: 0.8339 (t80) cc_final: 0.8073 (t80) REVERT: E 4 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8883 (mt-10) REVERT: F 13 GLU cc_start: 0.9069 (mp0) cc_final: 0.8867 (mp0) REVERT: J 3 ASN cc_start: 0.5194 (m-40) cc_final: 0.4848 (p0) outliers start: 0 outliers final: 0 residues processed: 402 average time/residue: 0.6593 time to fit residues: 382.2042 Evaluate side-chains 340 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 2.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 180 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 104 optimal weight: 0.4980 chunk 186 optimal weight: 0.9980 chunk 117 optimal weight: 0.0970 chunk 113 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 115 optimal weight: 0.2980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 10 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.183 16157 Z= 0.214 Angle : 0.619 12.215 21917 Z= 0.329 Chirality : 0.045 0.331 2365 Planarity : 0.005 0.090 2857 Dihedral : 7.220 64.836 2155 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.62 % Favored : 85.38 % Rotamer: Outliers : 0.06 % Allowed : 0.84 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.26 (0.17), residues: 1942 helix: -1.02 (0.31), residues: 259 sheet: -3.60 (0.30), residues: 204 loop : -3.35 (0.14), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 414 HIS 0.009 0.001 HIS A 263 PHE 0.039 0.002 PHE C 642 TYR 0.011 0.001 TYR A 646 ARG 0.030 0.001 ARG D 863 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASN G 21 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Evaluate side-chains 406 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 405 time to evaluate : 2.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.6797 (mtt180) cc_final: 0.6459 (mtt-85) REVERT: A 85 SER cc_start: 0.7340 (t) cc_final: 0.5497 (t) REVERT: A 96 PHE cc_start: 0.7729 (t80) cc_final: 0.7342 (t80) REVERT: A 120 GLU cc_start: 0.8304 (tt0) cc_final: 0.7890 (tt0) REVERT: A 329 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8201 (mt-10) REVERT: A 430 TYR cc_start: 0.8765 (m-10) cc_final: 0.8555 (m-80) REVERT: A 438 GLU cc_start: 0.8810 (tp30) cc_final: 0.8581 (tp30) REVERT: A 505 LEU cc_start: 0.9183 (tp) cc_final: 0.8980 (tp) REVERT: A 507 TYR cc_start: 0.8731 (p90) cc_final: 0.8213 (p90) REVERT: A 547 ASN cc_start: 0.8869 (p0) cc_final: 0.8559 (p0) REVERT: A 709 LEU cc_start: 0.8117 (tt) cc_final: 0.7906 (tt) REVERT: C 14 ARG cc_start: 0.6217 (ptp-170) cc_final: 0.5937 (mtm180) REVERT: C 245 TYR cc_start: 0.8468 (m-80) cc_final: 0.7994 (m-80) REVERT: C 355 GLU cc_start: 0.8377 (tt0) cc_final: 0.8097 (tt0) REVERT: C 362 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8007 (mm-30) REVERT: C 373 SER cc_start: 0.9303 (m) cc_final: 0.8611 (p) REVERT: C 656 ARG cc_start: 0.8575 (mmp-170) cc_final: 0.8343 (mmp-170) REVERT: G 14 TYR cc_start: 0.8344 (t80) cc_final: 0.8070 (t80) REVERT: E 4 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8813 (mt-10) REVERT: J 3 ASN cc_start: 0.5325 (m-40) cc_final: 0.4982 (p0) outliers start: 1 outliers final: 1 residues processed: 405 average time/residue: 0.6652 time to fit residues: 389.5240 Evaluate side-chains 346 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 345 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 74 optimal weight: 1.9990 chunk 111 optimal weight: 0.0060 chunk 56 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 127 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN C 280 HIS ** C 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 10 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.126 16157 Z= 0.210 Angle : 0.611 11.687 21917 Z= 0.328 Chirality : 0.045 0.429 2365 Planarity : 0.005 0.092 2857 Dihedral : 7.097 64.232 2155 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.32 % Favored : 83.68 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.22 (0.17), residues: 1942 helix: -0.94 (0.31), residues: 256 sheet: -3.56 (0.29), residues: 209 loop : -3.33 (0.14), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 658 HIS 0.018 0.001 HIS D 829 PHE 0.021 0.001 PHE A 76 TYR 0.011 0.001 TYR E 19 ARG 0.012 0.000 ARG D 863 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASN G 21 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Evaluate side-chains 397 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 397 time to evaluate : 2.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.6831 (mtt180) cc_final: 0.6571 (mtt180) REVERT: A 120 GLU cc_start: 0.8288 (tt0) cc_final: 0.7994 (tt0) REVERT: A 329 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8241 (mt-10) REVERT: A 507 TYR cc_start: 0.8745 (p90) cc_final: 0.8246 (p90) REVERT: A 709 LEU cc_start: 0.8235 (tt) cc_final: 0.8001 (tt) REVERT: C 14 ARG cc_start: 0.6210 (ptp-170) cc_final: 0.5943 (mtm180) REVERT: C 245 TYR cc_start: 0.8449 (m-80) cc_final: 0.7946 (m-80) REVERT: C 355 GLU cc_start: 0.8426 (tt0) cc_final: 0.8158 (tt0) REVERT: C 362 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7996 (mm-30) REVERT: C 372 ARG cc_start: 0.8539 (mtt180) cc_final: 0.8339 (mtt90) REVERT: C 435 CYS cc_start: 0.4683 (m) cc_final: 0.3140 (m) REVERT: C 438 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7492 (mt-10) REVERT: C 656 ARG cc_start: 0.8615 (mmp-170) cc_final: 0.8398 (mmp-170) REVERT: C 711 ASN cc_start: 0.8480 (t0) cc_final: 0.8162 (m110) REVERT: G 14 TYR cc_start: 0.8379 (t80) cc_final: 0.8107 (t80) REVERT: E 4 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8804 (mt-10) REVERT: J 3 ASN cc_start: 0.5365 (m-40) cc_final: 0.4993 (p0) outliers start: 0 outliers final: 0 residues processed: 397 average time/residue: 0.6429 time to fit residues: 368.0201 Evaluate side-chains 346 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 5.9990 chunk 174 optimal weight: 0.9990 chunk 179 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 136 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 114 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN ** C 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 10 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 16157 Z= 0.176 Angle : 0.585 9.628 21917 Z= 0.314 Chirality : 0.044 0.370 2365 Planarity : 0.005 0.092 2857 Dihedral : 6.875 63.369 2155 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.68 % Favored : 85.32 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.09 (0.17), residues: 1942 helix: -0.99 (0.31), residues: 273 sheet: -3.44 (0.29), residues: 210 loop : -3.22 (0.15), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 658 HIS 0.010 0.001 HIS D 829 PHE 0.021 0.001 PHE A 76 TYR 0.011 0.001 TYR E 19 ARG 0.008 0.000 ARG D 863 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASN G 21 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Evaluate side-chains 393 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 2.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLU cc_start: 0.7881 (tp30) cc_final: 0.7605 (tp30) REVERT: A 14 ARG cc_start: 0.6623 (mtt180) cc_final: 0.6302 (mtt180) REVERT: A 120 GLU cc_start: 0.8253 (tt0) cc_final: 0.7960 (tt0) REVERT: A 329 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8206 (mt-10) REVERT: A 355 GLU cc_start: 0.8857 (tt0) cc_final: 0.8518 (tp30) REVERT: A 438 GLU cc_start: 0.8782 (tp30) cc_final: 0.8554 (tp30) REVERT: A 505 LEU cc_start: 0.9192 (tp) cc_final: 0.8981 (tp) REVERT: A 507 TYR cc_start: 0.8734 (p90) cc_final: 0.8260 (p90) REVERT: A 593 THR cc_start: 0.6952 (m) cc_final: 0.6749 (m) REVERT: C 14 ARG cc_start: 0.6211 (ptp-170) cc_final: 0.5860 (mtm180) REVERT: C 178 PHE cc_start: 0.8099 (m-80) cc_final: 0.7506 (m-80) REVERT: C 245 TYR cc_start: 0.8445 (m-80) cc_final: 0.7925 (m-80) REVERT: C 362 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7976 (mm-30) REVERT: C 435 CYS cc_start: 0.4837 (m) cc_final: 0.3100 (m) REVERT: C 438 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7448 (mt-10) REVERT: C 656 ARG cc_start: 0.8587 (mmp-170) cc_final: 0.8366 (mmp-170) REVERT: C 711 ASN cc_start: 0.8437 (t0) cc_final: 0.8186 (m110) REVERT: G 14 TYR cc_start: 0.8371 (t80) cc_final: 0.8092 (t80) REVERT: J 3 ASN cc_start: 0.5597 (m-40) cc_final: 0.5189 (p0) outliers start: 0 outliers final: 0 residues processed: 393 average time/residue: 0.6592 time to fit residues: 373.7324 Evaluate side-chains 346 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 2.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 184 optimal weight: 0.4980 chunk 112 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 193 optimal weight: 4.9990 chunk 177 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN C 295 ASN ** C 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 10 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16157 Z= 0.203 Angle : 0.613 9.479 21917 Z= 0.329 Chirality : 0.044 0.359 2365 Planarity : 0.005 0.092 2857 Dihedral : 7.026 62.541 2155 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.89 % Favored : 83.11 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.17), residues: 1942 helix: -0.98 (0.31), residues: 268 sheet: -3.26 (0.31), residues: 205 loop : -3.23 (0.15), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 658 HIS 0.009 0.001 HIS D 829 PHE 0.020 0.001 PHE A 76 TYR 0.013 0.001 TYR A 646 ARG 0.006 0.001 ARG D 863 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASN G 21 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Evaluate side-chains 394 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 394 time to evaluate : 2.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLU cc_start: 0.7901 (tp30) cc_final: 0.7479 (tp30) REVERT: A 14 ARG cc_start: 0.6901 (mtt180) cc_final: 0.6408 (mtt180) REVERT: A 120 GLU cc_start: 0.8252 (tt0) cc_final: 0.7978 (tt0) REVERT: A 329 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8263 (mt-10) REVERT: A 355 GLU cc_start: 0.8882 (tt0) cc_final: 0.8561 (tp30) REVERT: A 438 GLU cc_start: 0.8805 (tp30) cc_final: 0.8495 (tp30) REVERT: A 505 LEU cc_start: 0.9162 (tp) cc_final: 0.8907 (tp) REVERT: A 507 TYR cc_start: 0.8744 (p90) cc_final: 0.8195 (p90) REVERT: A 709 LEU cc_start: 0.8079 (tt) cc_final: 0.7876 (tt) REVERT: C 14 ARG cc_start: 0.6320 (ptp-170) cc_final: 0.5868 (mtm180) REVERT: C 245 TYR cc_start: 0.8440 (m-80) cc_final: 0.7927 (m-80) REVERT: C 362 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7987 (mm-30) REVERT: C 373 SER cc_start: 0.9178 (m) cc_final: 0.8615 (t) REVERT: C 435 CYS cc_start: 0.5011 (m) cc_final: 0.3237 (m) REVERT: C 438 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7505 (mt-10) REVERT: C 711 ASN cc_start: 0.8498 (t0) cc_final: 0.8208 (m110) REVERT: G 14 TYR cc_start: 0.8509 (t80) cc_final: 0.8175 (t80) REVERT: E 4 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8819 (mt-10) REVERT: J 3 ASN cc_start: 0.5624 (m-40) cc_final: 0.5227 (p0) outliers start: 0 outliers final: 0 residues processed: 394 average time/residue: 0.6412 time to fit residues: 362.7326 Evaluate side-chains 346 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 154 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 158 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 0.0050 chunk 135 optimal weight: 0.8980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN ** C 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 10 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.105009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.090109 restraints weight = 185235.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.093926 restraints weight = 99073.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.096471 restraints weight = 59994.640| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.5433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 16157 Z= 0.161 Angle : 0.587 9.465 21917 Z= 0.312 Chirality : 0.044 0.345 2365 Planarity : 0.005 0.091 2857 Dihedral : 6.766 61.778 2155 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.90 % Favored : 86.10 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.17), residues: 1942 helix: -0.80 (0.31), residues: 267 sheet: -3.12 (0.32), residues: 204 loop : -3.11 (0.15), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 658 HIS 0.008 0.001 HIS A 263 PHE 0.019 0.001 PHE A 76 TYR 0.011 0.001 TYR C 277 ARG 0.005 0.000 ARG D 863 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7836.33 seconds wall clock time: 138 minutes 41.89 seconds (8321.89 seconds total)