Starting phenix.real_space_refine on Sun Mar 17 15:29:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl7_25193/03_2024/7sl7_25193_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl7_25193/03_2024/7sl7_25193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl7_25193/03_2024/7sl7_25193.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl7_25193/03_2024/7sl7_25193.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl7_25193/03_2024/7sl7_25193_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl7_25193/03_2024/7sl7_25193_neut.pdb" } resolution = 3.1 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3460 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 124 5.16 5 C 9350 2.51 5 N 2524 2.21 5 O 2734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 6": "OE1" <-> "OE2" Residue "A TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "A PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 239": "OE1" <-> "OE2" Residue "B GLU 287": "OE1" <-> "OE2" Residue "B PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 13": "OE1" <-> "OE2" Residue "H GLU 13": "OE1" <-> "OE2" Residue "H GLU 21": "OE1" <-> "OE2" Residue "F TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 17": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14732 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 819, 6623 Classifications: {'peptide': 819} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 773} Chain breaks: 6 Chain: "B" Number of atoms: 6623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 819, 6623 Classifications: {'peptide': 819} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 773} Chain breaks: 6 Chain: "G" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 214 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "H" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 214 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "I" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 200 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "J" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 200 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "C" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 165 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "D" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 165 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "E" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 164 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "F" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 164 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Time building chain proxies: 7.71, per 1000 atoms: 0.52 Number of scatterers: 14732 At special positions: 0 Unit cell: (120.35, 130.31, 173.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 124 16.00 O 2734 8.00 N 2524 7.00 C 9350 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 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 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 649 " - pdb=" SG CYS A 862 " distance=2.03 Simple disulfide: pdb=" SG CYS A 788 " - pdb=" SG CYS A 797 " distance=2.04 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 862 " distance=2.03 Simple disulfide: pdb=" SG CYS B 788 " - pdb=" SG CYS B 797 " distance=2.04 Simple disulfide: pdb=" SG CYS G 7 " - pdb=" SG CYS C 7 " distance=2.03 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS C 20 " distance=2.03 Simple disulfide: pdb=" SG CYS H 7 " - pdb=" SG CYS D 7 " distance=2.03 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS D 20 " distance=2.03 Simple disulfide: pdb=" SG CYS I 7 " - pdb=" SG CYS E 7 " distance=2.03 Simple disulfide: pdb=" SG CYS I 19 " - pdb=" SG CYS E 20 " distance=2.03 Simple disulfide: pdb=" SG CYS J 7 " - pdb=" SG CYS F 7 " distance=2.03 Simple disulfide: pdb=" SG CYS J 19 " - pdb=" SG CYS F 20 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 11 " distance=2.03 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 11 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 11 " distance=2.03 Simple disulfide: pdb=" SG CYS F 6 " - pdb=" SG CYS F 11 " 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: 4.59 Conformation dependent library (CDL) restraints added in 2.7 seconds 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3440 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 33 sheets defined 19.5% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 17 through 24 removed outlier: 3.788A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU A 22 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU A 24 " --> pdb=" O HIS A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.755A pdb=" N PHE A 46 " --> pdb=" O PRO A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 137 removed outlier: 3.740A pdb=" N ILE A 136 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.731A pdb=" N ASP A 142 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 314 through 318 removed outlier: 3.679A pdb=" N GLU A 318 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.577A pdb=" N GLU A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 358 removed outlier: 3.758A pdb=" N ALA A 356 " --> pdb=" O ALA A 352 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.543A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.555A pdb=" N ARG A 451 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLN A 452 " --> pdb=" O LYS A 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 448 through 452' 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 640 through 646 removed outlier: 4.002A pdb=" N LEU A 646 " --> pdb=" O LEU A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 716 removed outlier: 3.659A pdb=" N ILE A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 872 Processing helix chain 'B' and resid 17 through 24 removed outlier: 3.839A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU B 22 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU B 24 " --> pdb=" O HIS B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.741A pdb=" N PHE B 46 " --> pdb=" O PRO B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 137 removed outlier: 3.746A pdb=" N ILE B 136 " --> pdb=" O ASP B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 removed outlier: 3.730A pdb=" N ASP B 142 " --> pdb=" O SER B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 256 through 268 Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.584A pdb=" N GLU B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 358 removed outlier: 3.727A pdb=" N ALA B 356 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN B 357 " --> pdb=" O GLU B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.569A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 removed outlier: 3.558A pdb=" N ARG B 451 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLN B 452 " --> pdb=" O LYS B 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 448 through 452' Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 640 through 646 removed outlier: 3.999A pdb=" N LEU B 646 " --> pdb=" O LEU B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 716 removed outlier: 3.630A pdb=" N ILE B 694 " --> pdb=" O THR B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 872 Processing helix chain 'G' and resid 8 through 19 Processing helix chain 'H' and resid 8 through 19 Processing helix chain 'I' and resid 8 through 19 Processing helix chain 'J' and resid 8 through 19 Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 14 through 20 Processing helix chain 'D' and resid 2 through 7 Processing helix chain 'D' and resid 12 through 18 removed outlier: 3.688A pdb=" N GLU D 17 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN D 18 " --> pdb=" O TYR D 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 7 Processing helix chain 'E' and resid 13 through 18 removed outlier: 3.533A pdb=" N GLU E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASN E 18 " --> pdb=" O TYR E 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 13 through 18' Processing helix chain 'F' and resid 2 through 7 Processing helix chain 'F' and resid 13 through 20 removed outlier: 3.758A pdb=" N GLU F 17 " --> pdb=" O TYR F 14 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ASN F 18 " --> pdb=" O GLN F 15 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 14 removed outlier: 3.508A pdb=" N GLN A 34 " --> pdb=" O MET A 11 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 36 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU A 93 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N GLU A 120 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE A 95 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASN A 122 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS A 121 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASN A 148 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 Processing sheet with id=AA4, first strand: chain 'A' and resid 212 through 216 removed outlier: 5.549A pdb=" N LEU A 213 " --> pdb=" O CYS A 228 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N CYS A 228 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 7.002A 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 Processing sheet with id=AA6, first strand: chain 'A' and resid 245 through 248 Processing sheet with id=AA7, first strand: chain 'A' and resid 278 through 279 Processing sheet with id=AA8, first strand: chain 'A' and resid 292 through 294 removed outlier: 3.625A pdb=" N THR A 302 " --> pdb=" O THR A 293 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 312 Processing sheet with id=AB1, first strand: chain 'A' and resid 319 through 321 removed outlier: 7.687A pdb=" N PHE A 427 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N TYR A 401 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N HIS A 429 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU A 403 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 472 through 473 Processing sheet with id=AB3, first strand: chain 'A' and resid 479 through 480 Processing sheet with id=AB4, first strand: chain 'A' and resid 530 through 534 removed outlier: 3.628A pdb=" N GLY A 502 " --> pdb=" O LEU A 571 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 601 through 606 removed outlier: 5.447A pdb=" N ASP A 602 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS A 618 " --> pdb=" O ASP A 602 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 613 " --> pdb=" O ILE A 772 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 761 through 765 removed outlier: 3.759A pdb=" N VAL A 632 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 821 through 824 Processing sheet with id=AB8, first strand: chain 'A' and resid 859 through 864 removed outlier: 4.107A pdb=" N GLY A 882 " --> pdb=" O VAL A 907 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 907 " --> pdb=" O GLY A 882 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 11 through 14 removed outlier: 3.509A pdb=" N GLN B 34 " --> pdb=" O MET B 11 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 36 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL B 66 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU B 93 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N GLU B 120 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE B 95 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ASN B 122 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS B 121 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASN B 148 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AC2, first strand: chain 'B' and resid 171 through 173 Processing sheet with id=AC3, first strand: chain 'B' and resid 212 through 216 removed outlier: 5.566A pdb=" N LEU B 213 " --> pdb=" O CYS B 228 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N CYS B 228 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASN B 215 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 231 through 233 Processing sheet with id=AC5, first strand: chain 'B' and resid 245 through 248 Processing sheet with id=AC6, first strand: chain 'B' and resid 292 through 293 removed outlier: 3.570A pdb=" N THR B 302 " --> pdb=" O THR B 293 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 312 Processing sheet with id=AC8, first strand: chain 'B' and resid 318 through 321 removed outlier: 7.679A pdb=" N PHE B 427 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TYR B 401 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N HIS B 429 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU B 403 " --> pdb=" O HIS B 429 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 472 through 473 Processing sheet with id=AD1, first strand: chain 'B' and resid 479 through 480 Processing sheet with id=AD2, first strand: chain 'B' and resid 530 through 534 removed outlier: 3.643A pdb=" N GLY B 502 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 601 through 606 removed outlier: 5.392A pdb=" N ASP B 602 " --> pdb=" O LYS B 618 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS B 618 " --> pdb=" O ASP B 602 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 613 " --> pdb=" O ILE B 772 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 761 through 765 removed outlier: 3.808A pdb=" N VAL B 632 " --> pdb=" O GLU B 762 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 821 through 824 Processing sheet with id=AD6, first strand: chain 'B' and resid 859 through 864 removed outlier: 3.511A pdb=" N LEU B 846 " --> pdb=" O THR B 891 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY B 882 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 907 " --> pdb=" O GLY B 882 " (cutoff:3.500A) 375 hydrogen bonds defined for protein. 966 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: 5.15 Time building geometry restraints manager: 5.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4822 1.34 - 1.46: 3506 1.46 - 1.58: 6609 1.58 - 1.70: 1 1.70 - 1.82: 148 Bond restraints: 15086 Sorted by residual: bond pdb=" CB PRO B 720 " pdb=" CG PRO B 720 " ideal model delta sigma weight residual 1.492 1.591 -0.099 5.00e-02 4.00e+02 3.96e+00 bond pdb=" CA LEU B 305 " pdb=" C LEU B 305 " ideal model delta sigma weight residual 1.526 1.510 0.016 1.36e-02 5.41e+03 1.35e+00 bond pdb=" CA LEU A 305 " pdb=" C LEU A 305 " ideal model delta sigma weight residual 1.526 1.511 0.014 1.36e-02 5.41e+03 1.13e+00 bond pdb=" CB GLU B 6 " pdb=" CG GLU B 6 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.32e-01 bond pdb=" C GLN E 5 " pdb=" N CYS E 6 " ideal model delta sigma weight residual 1.332 1.345 -0.013 1.42e-02 4.96e+03 8.68e-01 ... (remaining 15081 not shown) Histogram of bond angle deviations from ideal: 99.17 - 106.13: 410 106.13 - 113.09: 7925 113.09 - 120.05: 5184 120.05 - 127.01: 6721 127.01 - 133.97: 200 Bond angle restraints: 20440 Sorted by residual: angle pdb=" C THR A 580 " pdb=" N TYR A 581 " pdb=" CA TYR A 581 " ideal model delta sigma weight residual 121.54 132.03 -10.49 1.91e+00 2.74e-01 3.02e+01 angle pdb=" C THR B 580 " pdb=" N TYR B 581 " pdb=" CA TYR B 581 " ideal model delta sigma weight residual 121.54 131.92 -10.38 1.91e+00 2.74e-01 2.95e+01 angle pdb=" C GLU A 469 " pdb=" N ASN A 470 " pdb=" CA ASN A 470 " ideal model delta sigma weight residual 121.54 128.38 -6.84 1.91e+00 2.74e-01 1.28e+01 angle pdb=" C GLU B 469 " pdb=" N ASN B 470 " pdb=" CA ASN B 470 " ideal model delta sigma weight residual 121.54 128.26 -6.72 1.91e+00 2.74e-01 1.24e+01 angle pdb=" N GLY I 8 " pdb=" CA GLY I 8 " pdb=" C GLY I 8 " ideal model delta sigma weight residual 111.35 115.50 -4.15 1.20e+00 6.94e-01 1.20e+01 ... (remaining 20435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 8212 16.10 - 32.21: 692 32.21 - 48.31: 174 48.31 - 64.41: 42 64.41 - 80.51: 26 Dihedral angle restraints: 9146 sinusoidal: 3816 harmonic: 5330 Sorted by residual: dihedral pdb=" CB CYS B 288 " pdb=" SG CYS B 288 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 170.92 -77.92 1 1.00e+01 1.00e-02 7.59e+01 dihedral pdb=" CB CYS A 288 " pdb=" SG CYS A 288 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 165.21 -72.21 1 1.00e+01 1.00e-02 6.67e+01 dihedral pdb=" CB CYS E 6 " pdb=" SG CYS E 6 " pdb=" SG CYS E 11 " pdb=" CB CYS E 11 " ideal model delta sinusoidal sigma weight residual 93.00 39.14 53.86 1 1.00e+01 1.00e-02 3.94e+01 ... (remaining 9143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1464 0.036 - 0.072: 518 0.072 - 0.108: 153 0.108 - 0.144: 75 0.144 - 0.180: 6 Chirality restraints: 2216 Sorted by residual: chirality pdb=" CB ILE A 174 " pdb=" CA ILE A 174 " pdb=" CG1 ILE A 174 " pdb=" CG2 ILE A 174 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.06e-01 chirality pdb=" CB ILE B 174 " pdb=" CA ILE B 174 " pdb=" CG1 ILE B 174 " pdb=" CG2 ILE B 174 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.99e-01 chirality pdb=" CB THR B 690 " pdb=" CA THR B 690 " pdb=" OG1 THR B 690 " pdb=" CG2 THR B 690 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.88e-01 ... (remaining 2213 not shown) Planarity restraints: 2642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 580 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C THR B 580 " -0.042 2.00e-02 2.50e+03 pdb=" O THR B 580 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR B 581 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 580 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.77e+00 pdb=" C THR A 580 " -0.042 2.00e-02 2.50e+03 pdb=" O THR A 580 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR A 581 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 836 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO B 837 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 837 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 837 " 0.024 5.00e-02 4.00e+02 ... (remaining 2639 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 358 2.70 - 3.25: 14045 3.25 - 3.80: 22611 3.80 - 4.35: 30781 4.35 - 4.90: 50028 Nonbonded interactions: 117823 Sorted by model distance: nonbonded pdb=" O ASP A 535 " pdb=" OH TYR E 14 " model vdw 2.149 2.440 nonbonded pdb=" O ASP B 535 " pdb=" OH TYR F 14 " model vdw 2.199 2.440 nonbonded pdb=" NH2 ARG A 889 " pdb=" OG1 THR A 891 " model vdw 2.241 2.520 nonbonded pdb=" NH2 ARG B 889 " pdb=" OG1 THR B 891 " model vdw 2.243 2.520 nonbonded pdb=" OG1 THR A 41 " pdb=" O TYR A 67 " model vdw 2.266 2.440 ... (remaining 117818 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' selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 1 through 2 or resid 4 through 12 or resid 14 through 21)) \ selection = (chain 'D' and (resid 1 through 2 or resid 4 through 12 or resid 14 through 21)) \ selection = (chain 'E' and (resid 1 through 2 or resid 4 through 12 or resid 14 through 21)) \ selection = (chain 'F' and (resid 1 through 2 or resid 4 through 12 or resid 14 through 21)) \ } ncs_group { reference = (chain 'G' and resid 2 through 26) selection = (chain 'H' and resid 2 through 26) selection = chain 'I' selection = chain 'J' } 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 individual isotropic 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: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.020 Extract box with map and model: 10.970 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 38.940 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.090 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 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 : 0.002 0.099 15086 Z= 0.150 Angle : 0.565 10.495 20440 Z= 0.303 Chirality : 0.044 0.180 2216 Planarity : 0.003 0.044 2642 Dihedral : 13.076 80.513 5568 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.50 % Favored : 94.22 % Rotamer: Outliers : 0.24 % Allowed : 0.54 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.86 (0.21), residues: 1782 helix: -0.31 (0.34), residues: 242 sheet: 0.45 (0.31), residues: 368 loop : -0.99 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 414 HIS 0.003 0.000 HIS I 5 PHE 0.021 0.001 PHE A 574 TYR 0.012 0.001 TYR A 507 ARG 0.007 0.000 ARG B 759 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 143 time to evaluate : 1.588 Fit side-chains revert: symmetry clash REVERT: A 867 HIS cc_start: 0.7477 (m90) cc_final: 0.7177 (m90) outliers start: 4 outliers final: 1 residues processed: 146 average time/residue: 0.2266 time to fit residues: 52.5211 Evaluate side-chains 102 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 3 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 161 optimal weight: 20.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 HIS J 3 ASN E 15 GLN F 15 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 15086 Z= 0.392 Angle : 0.635 6.538 20440 Z= 0.331 Chirality : 0.047 0.173 2216 Planarity : 0.004 0.044 2642 Dihedral : 4.916 26.932 1994 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.90 % Favored : 92.99 % Rotamer: Outliers : 1.08 % Allowed : 7.52 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.87 (0.21), residues: 1782 helix: 0.11 (0.34), residues: 236 sheet: 0.38 (0.30), residues: 366 loop : -1.08 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 412 HIS 0.015 0.001 HIS J 5 PHE 0.014 0.002 PHE A 703 TYR 0.023 0.002 TYR A 507 ARG 0.004 0.001 ARG A 759 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 1.756 Fit side-chains REVERT: A 763 LYS cc_start: 0.8035 (tmtt) cc_final: 0.7726 (ttmt) REVERT: A 867 HIS cc_start: 0.7538 (m90) cc_final: 0.7196 (m90) outliers start: 18 outliers final: 10 residues processed: 107 average time/residue: 0.2432 time to fit residues: 42.5865 Evaluate side-chains 101 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 MET Chi-restraints excluded: chain A residue 781 TYR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain E residue 16 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 chunk 174 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 160 optimal weight: 20.0000 chunk 55 optimal weight: 8.9990 chunk 129 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 GLN B 34 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 15086 Z= 0.408 Angle : 0.633 5.724 20440 Z= 0.331 Chirality : 0.046 0.172 2216 Planarity : 0.004 0.047 2642 Dihedral : 5.166 28.800 1992 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.35 % Favored : 92.54 % Rotamer: Outliers : 1.32 % Allowed : 10.65 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.14 (0.20), residues: 1782 helix: -0.43 (0.32), residues: 270 sheet: 0.23 (0.29), residues: 366 loop : -1.21 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 899 HIS 0.007 0.001 HIS B 440 PHE 0.020 0.002 PHE A 574 TYR 0.024 0.002 TYR B 507 ARG 0.013 0.001 ARG A 889 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 99 time to evaluate : 1.692 Fit side-chains REVERT: A 792 SER cc_start: 0.3227 (OUTLIER) cc_final: 0.2901 (t) REVERT: A 867 HIS cc_start: 0.7601 (m90) cc_final: 0.7242 (m90) REVERT: B 42 ARG cc_start: 0.7933 (mmm-85) cc_final: 0.7509 (mmm160) REVERT: B 300 MET cc_start: 0.7231 (tpt) cc_final: 0.7018 (tpt) REVERT: B 792 SER cc_start: 0.3411 (OUTLIER) cc_final: 0.3133 (m) outliers start: 22 outliers final: 12 residues processed: 117 average time/residue: 0.2360 time to fit residues: 43.3086 Evaluate side-chains 100 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 513 GLN Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 701 SER Chi-restraints excluded: chain B residue 792 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain J residue 2 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 162 optimal weight: 9.9990 chunk 172 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 143 optimal weight: 9.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15086 Z= 0.311 Angle : 0.604 9.163 20440 Z= 0.314 Chirality : 0.046 0.268 2216 Planarity : 0.004 0.047 2642 Dihedral : 5.068 28.201 1992 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.90 % Favored : 92.99 % Rotamer: Outliers : 1.62 % Allowed : 13.06 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.12 (0.20), residues: 1782 helix: -0.35 (0.32), residues: 270 sheet: 0.28 (0.29), residues: 354 loop : -1.22 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 899 HIS 0.005 0.001 HIS B 440 PHE 0.016 0.002 PHE A 574 TYR 0.020 0.002 TYR B 581 ARG 0.003 0.000 ARG A 759 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 94 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 792 SER cc_start: 0.3320 (OUTLIER) cc_final: 0.3042 (t) REVERT: B 42 ARG cc_start: 0.7911 (mmm-85) cc_final: 0.7581 (mmm160) REVERT: B 300 MET cc_start: 0.7281 (tpt) cc_final: 0.7053 (tpt) REVERT: B 792 SER cc_start: 0.3491 (OUTLIER) cc_final: 0.3150 (t) REVERT: I 13 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8541 (mm-30) outliers start: 27 outliers final: 16 residues processed: 113 average time/residue: 0.2719 time to fit residues: 48.0295 Evaluate side-chains 107 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 701 SER Chi-restraints excluded: chain B residue 792 SER Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain F residue 16 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 128 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 HIS B 34 GLN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 712 HIS J 3 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15086 Z= 0.232 Angle : 0.564 7.041 20440 Z= 0.294 Chirality : 0.044 0.207 2216 Planarity : 0.003 0.046 2642 Dihedral : 4.929 28.581 1992 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.23 % Favored : 93.66 % Rotamer: Outliers : 1.74 % Allowed : 14.20 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.02 (0.20), residues: 1782 helix: -0.25 (0.32), residues: 270 sheet: 0.27 (0.29), residues: 348 loop : -1.12 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 412 HIS 0.004 0.001 HIS B 440 PHE 0.019 0.001 PHE A 574 TYR 0.019 0.001 TYR A 581 ARG 0.005 0.000 ARG A 658 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 92 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7902 (mmm-85) cc_final: 0.7579 (mmm160) REVERT: A 792 SER cc_start: 0.3455 (OUTLIER) cc_final: 0.3107 (t) REVERT: B 42 ARG cc_start: 0.7894 (mmm-85) cc_final: 0.7565 (mmm160) REVERT: B 300 MET cc_start: 0.7231 (tpt) cc_final: 0.6991 (tpt) REVERT: B 581 TYR cc_start: 0.7455 (OUTLIER) cc_final: 0.6292 (t80) REVERT: B 792 SER cc_start: 0.3519 (OUTLIER) cc_final: 0.3169 (t) REVERT: I 13 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8596 (mm-30) outliers start: 29 outliers final: 17 residues processed: 115 average time/residue: 0.2252 time to fit residues: 42.6403 Evaluate side-chains 111 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 91 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 581 TYR Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 701 SER Chi-restraints excluded: chain B residue 792 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 17 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 101 optimal weight: 9.9990 chunk 42 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 chunk 14 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15086 Z= 0.212 Angle : 0.552 8.892 20440 Z= 0.288 Chirality : 0.044 0.182 2216 Planarity : 0.003 0.046 2642 Dihedral : 4.784 28.121 1992 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.29 % Favored : 93.60 % Rotamer: Outliers : 1.56 % Allowed : 14.80 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.98 (0.20), residues: 1782 helix: -0.29 (0.32), residues: 272 sheet: 0.27 (0.29), residues: 350 loop : -1.07 (0.19), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 412 HIS 0.006 0.001 HIS A 712 PHE 0.017 0.001 PHE B 574 TYR 0.019 0.001 TYR A 581 ARG 0.006 0.000 ARG B 658 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 91 time to evaluate : 1.579 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7896 (mmm-85) cc_final: 0.7577 (mmm160) REVERT: A 581 TYR cc_start: 0.7589 (OUTLIER) cc_final: 0.6073 (t80) REVERT: A 792 SER cc_start: 0.3491 (OUTLIER) cc_final: 0.3130 (t) REVERT: B 42 ARG cc_start: 0.7885 (mmm-85) cc_final: 0.7568 (mmm160) REVERT: B 581 TYR cc_start: 0.7537 (OUTLIER) cc_final: 0.6288 (t80) REVERT: B 792 SER cc_start: 0.3616 (OUTLIER) cc_final: 0.3400 (m) REVERT: I 13 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8582 (mm-30) outliers start: 26 outliers final: 17 residues processed: 111 average time/residue: 0.2099 time to fit residues: 38.0698 Evaluate side-chains 109 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 581 TYR Chi-restraints excluded: chain B residue 596 ASN Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 701 SER Chi-restraints excluded: chain B residue 792 SER Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 17 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 4.9990 chunk 98 optimal weight: 0.4980 chunk 125 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 144 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 171 optimal weight: 0.0370 chunk 107 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 overall best weight: 2.4862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 612 GLN J 3 ASN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15086 Z= 0.329 Angle : 0.603 7.085 20440 Z= 0.314 Chirality : 0.045 0.189 2216 Planarity : 0.004 0.044 2642 Dihedral : 5.094 30.089 1992 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.81 % Allowed : 14.80 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.06 (0.20), residues: 1782 helix: -0.24 (0.32), residues: 272 sheet: 0.25 (0.29), residues: 362 loop : -1.19 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 899 HIS 0.007 0.001 HIS A 712 PHE 0.019 0.002 PHE B 574 TYR 0.024 0.002 TYR A 581 ARG 0.004 0.000 ARG A 658 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 93 time to evaluate : 1.825 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7926 (mmm-85) cc_final: 0.7632 (mmm160) REVERT: A 581 TYR cc_start: 0.7660 (OUTLIER) cc_final: 0.6106 (t80) REVERT: A 792 SER cc_start: 0.3547 (OUTLIER) cc_final: 0.3320 (m) REVERT: B 42 ARG cc_start: 0.7912 (mmm-85) cc_final: 0.7613 (mmm160) REVERT: B 581 TYR cc_start: 0.7633 (OUTLIER) cc_final: 0.6063 (t80) REVERT: B 792 SER cc_start: 0.3677 (OUTLIER) cc_final: 0.3253 (t) outliers start: 30 outliers final: 19 residues processed: 119 average time/residue: 0.2244 time to fit residues: 43.0229 Evaluate side-chains 110 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 87 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 513 GLN Chi-restraints excluded: chain B residue 581 TYR Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 596 ASN Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 701 SER Chi-restraints excluded: chain B residue 792 SER Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain F residue 16 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 51 optimal weight: 0.0970 chunk 33 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 164 optimal weight: 0.7980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15086 Z= 0.216 Angle : 0.562 9.733 20440 Z= 0.293 Chirality : 0.044 0.179 2216 Planarity : 0.003 0.046 2642 Dihedral : 4.880 28.324 1992 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.74 % Allowed : 15.76 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.96 (0.20), residues: 1782 helix: -0.22 (0.32), residues: 272 sheet: 0.32 (0.29), residues: 348 loop : -1.08 (0.19), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 899 HIS 0.005 0.001 HIS A 712 PHE 0.020 0.001 PHE A 574 TYR 0.021 0.001 TYR A 581 ARG 0.004 0.000 ARG B 658 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 94 time to evaluate : 1.644 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7900 (mmm-85) cc_final: 0.7613 (mmm160) REVERT: A 581 TYR cc_start: 0.7636 (OUTLIER) cc_final: 0.6065 (t80) REVERT: A 792 SER cc_start: 0.3562 (OUTLIER) cc_final: 0.3322 (m) REVERT: B 42 ARG cc_start: 0.7892 (mmm-85) cc_final: 0.7597 (mmm160) REVERT: B 581 TYR cc_start: 0.7434 (OUTLIER) cc_final: 0.5934 (t80) outliers start: 29 outliers final: 19 residues processed: 117 average time/residue: 0.2277 time to fit residues: 42.8838 Evaluate side-chains 114 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 92 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 581 TYR Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 596 ASN Chi-restraints excluded: chain B residue 701 SER Chi-restraints excluded: chain B residue 792 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 17 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 2.9990 chunk 159 optimal weight: 30.0000 chunk 164 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 144 optimal weight: 10.0000 chunk 151 optimal weight: 0.1980 chunk 104 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 GLN J 3 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15086 Z= 0.201 Angle : 0.556 7.423 20440 Z= 0.290 Chirality : 0.044 0.212 2216 Planarity : 0.003 0.044 2642 Dihedral : 4.827 27.640 1992 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.26 % Allowed : 16.19 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.84 (0.21), residues: 1782 helix: -0.11 (0.33), residues: 260 sheet: 0.38 (0.30), residues: 348 loop : -0.99 (0.19), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 899 HIS 0.005 0.001 HIS A 712 PHE 0.017 0.001 PHE A 574 TYR 0.020 0.001 TYR A 581 ARG 0.004 0.000 ARG A 658 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 97 time to evaluate : 1.550 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7925 (mmm-85) cc_final: 0.7640 (mmm160) REVERT: A 581 TYR cc_start: 0.7641 (OUTLIER) cc_final: 0.5978 (t80) REVERT: A 867 HIS cc_start: 0.7662 (m90) cc_final: 0.7240 (m-70) REVERT: B 42 ARG cc_start: 0.7920 (mmm-85) cc_final: 0.7633 (mmm160) REVERT: B 581 TYR cc_start: 0.7414 (OUTLIER) cc_final: 0.5896 (t80) outliers start: 21 outliers final: 17 residues processed: 112 average time/residue: 0.2194 time to fit residues: 39.5121 Evaluate side-chains 113 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 94 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 513 GLN Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 581 TYR Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 596 ASN Chi-restraints excluded: chain B residue 701 SER Chi-restraints excluded: chain B residue 792 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 17 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 177 optimal weight: 0.0470 chunk 163 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 86 optimal weight: 0.0980 chunk 112 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 overall best weight: 1.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15086 Z= 0.218 Angle : 0.565 8.226 20440 Z= 0.294 Chirality : 0.044 0.219 2216 Planarity : 0.003 0.046 2642 Dihedral : 4.844 30.470 1992 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.50 % Allowed : 16.00 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.87 (0.21), residues: 1782 helix: -0.29 (0.32), residues: 272 sheet: 0.42 (0.30), residues: 348 loop : -0.99 (0.19), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 899 HIS 0.005 0.001 HIS A 712 PHE 0.018 0.001 PHE A 574 TYR 0.021 0.001 TYR A 581 ARG 0.004 0.000 ARG A 658 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 95 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7928 (mmm-85) cc_final: 0.7644 (mmm160) REVERT: A 581 TYR cc_start: 0.7675 (OUTLIER) cc_final: 0.5992 (t80) REVERT: B 581 TYR cc_start: 0.7368 (OUTLIER) cc_final: 0.5849 (t80) outliers start: 25 outliers final: 21 residues processed: 113 average time/residue: 0.2198 time to fit residues: 39.8029 Evaluate side-chains 117 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 94 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 513 GLN Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 581 TYR Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 596 ASN Chi-restraints excluded: chain B residue 701 SER Chi-restraints excluded: chain B residue 792 SER Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 17 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 59 optimal weight: 0.0770 chunk 145 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.1140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.116393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.079808 restraints weight = 35492.442| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.17 r_work: 0.3242 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15086 Z= 0.196 Angle : 0.553 8.510 20440 Z= 0.288 Chirality : 0.044 0.216 2216 Planarity : 0.003 0.044 2642 Dihedral : 4.731 27.245 1992 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.62 % Allowed : 15.94 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.80 (0.21), residues: 1782 helix: -0.15 (0.33), residues: 260 sheet: 0.34 (0.30), residues: 352 loop : -0.92 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 899 HIS 0.004 0.001 HIS A 712 PHE 0.017 0.001 PHE A 574 TYR 0.020 0.001 TYR B 581 ARG 0.004 0.000 ARG B 658 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3030.19 seconds wall clock time: 55 minutes 29.23 seconds (3329.23 seconds total)