Starting phenix.real_space_refine on Tue Feb 20 01:23:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x5f_6707/02_2024/5x5f_6707.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x5f_6707/02_2024/5x5f_6707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x5f_6707/02_2024/5x5f_6707.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x5f_6707/02_2024/5x5f_6707.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x5f_6707/02_2024/5x5f_6707.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x5f_6707/02_2024/5x5f_6707.pdb" } resolution = 4.2 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 ------------------------------------------------------------------------------- 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= 0.011 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: 4 Type Number sf(0) Gaussians S 153 5.16 5 C 16799 2.51 5 N 4372 2.21 5 O 5098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 34": "OD1" <-> "OD2" Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 306": "OD1" <-> "OD2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 444": "OD1" <-> "OD2" Residue "A TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "A GLU 565": "OE1" <-> "OE2" Residue "A TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 626": "NH1" <-> "NH2" Residue "A TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 887": "NH1" <-> "NH2" Residue "A TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 34": "OD1" <-> "OD2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "B TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 306": "OD1" <-> "OD2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 355": "OD1" <-> "OD2" Residue "B PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 444": "OD1" <-> "OD2" Residue "B TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 549": "OE1" <-> "OE2" Residue "B GLU 565": "OE1" <-> "OE2" Residue "B TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 626": "NH1" <-> "NH2" Residue "B TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 887": "NH1" <-> "NH2" Residue "B ASP 1059": "OD1" <-> "OD2" Residue "B TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 34": "OD1" <-> "OD2" Residue "C PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 252": "OE1" <-> "OE2" Residue "C TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 306": "OD1" <-> "OD2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 343": "OD1" <-> "OD2" Residue "C PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 444": "OD1" <-> "OD2" Residue "C TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 549": "OE1" <-> "OE2" Residue "C GLU 565": "OE1" <-> "OE2" Residue "C TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 580": "OD1" <-> "OD2" Residue "C TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 626": "NH1" <-> "NH2" Residue "C TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 887": "NH1" <-> "NH2" Residue "C ASP 1053": "OD1" <-> "OD2" Residue "C TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26422 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8806 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1141, 8800 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 42, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1048} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 1141, 8800 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 42, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1048} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 8993 Chain: "B" Number of atoms: 8806 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1141, 8800 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 42, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1048} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 1141, 8800 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 42, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1048} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 8993 Chain: "C" Number of atoms: 8810 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1141, 8804 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 39, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1051} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Conformer: "B" Number of residues, atoms: 1141, 8804 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 39, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1051} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 bond proxies already assigned to first conformer: 8997 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ASER A 51 " occ=0.46 ... (10 atoms not shown) pdb=" OG BSER A 51 " occ=0.54 residue: pdb=" N ASER B 51 " occ=0.46 ... (10 atoms not shown) pdb=" OG BSER B 51 " occ=0.54 residue: pdb=" N ASER C 51 " occ=0.46 ... (10 atoms not shown) pdb=" OG BSER C 51 " occ=0.54 Time building chain proxies: 25.78, per 1000 atoms: 0.98 Number of scatterers: 26422 At special positions: 0 Unit cell: (152.1, 159.9, 189.8, 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 153 16.00 O 5098 8.00 N 4372 7.00 C 16799 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.06 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.05 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.04 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 349 " distance=2.62 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.04 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.03 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 526 " distance=2.04 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.03 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.01 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.01 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.06 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.05 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.04 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.46 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.04 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.04 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.02 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.01 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.06 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.05 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.04 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.71 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.04 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.02 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.03 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.04 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.03 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.02 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.01 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " 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: 10.45 Conformation dependent library (CDL) restraints added in 9.6 seconds 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6384 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 48 sheets defined 23.8% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.69 Creating SS restraints... Processing helix chain 'A' and resid 37 through 40 Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.678A pdb=" N TYR A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 341 through 350 Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 410 through 418 removed outlier: 3.613A pdb=" N LEU A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 417 " --> pdb=" O LYS A 413 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 436 Processing helix chain 'A' and resid 449 through 456 removed outlier: 5.042A pdb=" N SER A 454 " --> pdb=" O SER A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 814 through 823 Processing helix chain 'A' and resid 824 through 852 removed outlier: 3.639A pdb=" N CYS A 828 " --> pdb=" O TYR A 824 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER A 829 " --> pdb=" O GLY A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 897 Processing helix chain 'A' and resid 907 through 914 Processing helix chain 'A' and resid 940 through 959 removed outlier: 4.471A pdb=" N ALA A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY A 957 " --> pdb=" O GLY A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 983 removed outlier: 3.972A pdb=" N VAL A 983 " --> pdb=" O ARG A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 993 removed outlier: 3.718A pdb=" N SER A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1011 Processing helix chain 'A' and resid 1018 through 1041 Processing helix chain 'A' and resid 1062 through 1107 Processing helix chain 'B' and resid 37 through 40 Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.678A pdb=" N TYR B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 342 through 350 Processing helix chain 'B' and resid 385 through 390 removed outlier: 4.195A pdb=" N LEU B 389 " --> pdb=" O PHE B 385 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER B 390 " --> pdb=" O SER B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 385 through 390' Processing helix chain 'B' and resid 395 through 399 Processing helix chain 'B' and resid 410 through 418 removed outlier: 3.612A pdb=" N LEU B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 417 " --> pdb=" O LYS B 413 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 436 removed outlier: 3.547A pdb=" N SER B 435 " --> pdb=" O ALA B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 456 removed outlier: 5.043A pdb=" N SER B 454 " --> pdb=" O SER B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 814 through 823 Processing helix chain 'B' and resid 824 through 852 removed outlier: 3.640A pdb=" N CYS B 828 " --> pdb=" O TYR B 824 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER B 829 " --> pdb=" O GLY B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 897 Processing helix chain 'B' and resid 907 through 914 Processing helix chain 'B' and resid 940 through 959 removed outlier: 4.470A pdb=" N ALA B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY B 957 " --> pdb=" O GLY B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 983 removed outlier: 3.974A pdb=" N VAL B 983 " --> pdb=" O ARG B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 993 removed outlier: 3.716A pdb=" N SER B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1011 Processing helix chain 'B' and resid 1018 through 1041 Processing helix chain 'B' and resid 1059 through 1107 removed outlier: 4.373A pdb=" N ASP B1064 " --> pdb=" O VAL B1060 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA B1065 " --> pdb=" O LEU B1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 40 Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.677A pdb=" N TYR C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 341 through 352 removed outlier: 3.607A pdb=" N SER C 345 " --> pdb=" O PHE C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 removed outlier: 4.196A pdb=" N LEU C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER C 390 " --> pdb=" O SER C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 385 through 390' Processing helix chain 'C' and resid 395 through 399 Processing helix chain 'C' and resid 410 through 418 removed outlier: 3.612A pdb=" N LEU C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU C 417 " --> pdb=" O LYS C 413 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 436 removed outlier: 3.547A pdb=" N SER C 435 " --> pdb=" O ALA C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 456 removed outlier: 5.042A pdb=" N SER C 454 " --> pdb=" O SER C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 814 through 823 Processing helix chain 'C' and resid 824 through 852 removed outlier: 3.639A pdb=" N CYS C 828 " --> pdb=" O TYR C 824 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER C 829 " --> pdb=" O GLY C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 897 Processing helix chain 'C' and resid 907 through 914 Processing helix chain 'C' and resid 940 through 959 removed outlier: 4.472A pdb=" N ALA C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY C 957 " --> pdb=" O GLY C 953 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 983 removed outlier: 3.971A pdb=" N VAL C 983 " --> pdb=" O ARG C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 993 removed outlier: 3.717A pdb=" N SER C 991 " --> pdb=" O GLN C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 997 through 1011 Processing helix chain 'C' and resid 1018 through 1041 Processing helix chain 'C' and resid 1059 through 1107 removed outlier: 4.061A pdb=" N ALA C1065 " --> pdb=" O LEU C1061 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 removed outlier: 6.251A pdb=" N ASP A 34 " --> pdb=" O VAL A 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 removed outlier: 4.072A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.547A pdb=" N ALA A 282 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 88 through 89 removed outlier: 7.159A pdb=" N SER A 88 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR A 206 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.509A pdb=" N LEU A 180 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR A 241 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA A 182 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE A 239 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TYR A 184 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N CYS A 237 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 127 through 129 removed outlier: 3.860A pdb=" N ALA A 309 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AA8, first strand: chain 'A' and resid 360 through 361 Processing sheet with id=AA9, first strand: chain 'A' and resid 374 through 375 removed outlier: 5.879A pdb=" N VAL A 374 " --> pdb=" O SER A 607 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 400 through 404 removed outlier: 3.599A pdb=" N LEU A 441 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A 440 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR A 483 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL A 420 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 407 through 409 Processing sheet with id=AB3, first strand: chain 'A' and resid 513 through 515 removed outlier: 6.070A pdb=" N SER A 557 " --> pdb=" O ASN A 501 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N CYS A 503 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL A 555 " --> pdb=" O CYS A 503 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ARG A 505 " --> pdb=" O TRP A 553 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TRP A 553 " --> pdb=" O ARG A 505 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 618 through 619 Processing sheet with id=AB5, first strand: chain 'A' and resid 779 through 782 removed outlier: 3.562A pdb=" N ILE A 782 " --> pdb=" O ILE A1147 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 803 through 804 Processing sheet with id=AB7, first strand: chain 'A' and resid 1122 through 1124 Processing sheet with id=AB8, first strand: chain 'B' and resid 33 through 35 removed outlier: 6.251A pdb=" N ASP B 34 " --> pdb=" O VAL B 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 68 through 75 removed outlier: 4.108A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.548A pdb=" N ALA B 282 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 88 through 89 removed outlier: 7.160A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.509A pdb=" N LEU B 180 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TYR B 241 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA B 182 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE B 239 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR B 184 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N CYS B 237 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 127 through 129 removed outlier: 3.858A pdb=" N ALA B 309 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AC6, first strand: chain 'B' and resid 360 through 361 Processing sheet with id=AC7, first strand: chain 'B' and resid 374 through 375 removed outlier: 5.879A pdb=" N VAL B 374 " --> pdb=" O SER B 607 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 400 through 404 removed outlier: 6.789A pdb=" N THR B 483 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL B 420 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 407 through 409 Processing sheet with id=AD1, first strand: chain 'B' and resid 513 through 515 removed outlier: 6.072A pdb=" N SER B 557 " --> pdb=" O ASN B 501 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N CYS B 503 " --> pdb=" O VAL B 555 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL B 555 " --> pdb=" O CYS B 503 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ARG B 505 " --> pdb=" O TRP B 553 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TRP B 553 " --> pdb=" O ARG B 505 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 618 through 619 Processing sheet with id=AD3, first strand: chain 'B' and resid 779 through 782 removed outlier: 3.563A pdb=" N ILE B 782 " --> pdb=" O ILE B1147 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 803 through 804 Processing sheet with id=AD5, first strand: chain 'B' and resid 1122 through 1124 Processing sheet with id=AD6, first strand: chain 'C' and resid 33 through 35 removed outlier: 6.250A pdb=" N ASP C 34 " --> pdb=" O VAL C 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 68 through 75 removed outlier: 4.069A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.547A pdb=" N ALA C 282 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 88 through 89 removed outlier: 7.159A pdb=" N SER C 88 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 110 through 111 removed outlier: 6.509A pdb=" N LEU C 180 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TYR C 241 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA C 182 " --> pdb=" O PHE C 239 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE C 239 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR C 184 " --> pdb=" O CYS C 237 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N CYS C 237 " --> pdb=" O TYR C 184 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 127 through 129 removed outlier: 3.856A pdb=" N ALA C 309 " --> pdb=" O THR C 139 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AE4, first strand: chain 'C' and resid 360 through 361 Processing sheet with id=AE5, first strand: chain 'C' and resid 374 through 375 removed outlier: 5.877A pdb=" N VAL C 374 " --> pdb=" O SER C 607 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 400 through 404 removed outlier: 6.787A pdb=" N THR C 483 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL C 420 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 407 through 409 Processing sheet with id=AE8, first strand: chain 'C' and resid 513 through 515 removed outlier: 6.071A pdb=" N SER C 557 " --> pdb=" O ASN C 501 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N CYS C 503 " --> pdb=" O VAL C 555 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL C 555 " --> pdb=" O CYS C 503 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG C 505 " --> pdb=" O TRP C 553 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TRP C 553 " --> pdb=" O ARG C 505 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 618 through 619 Processing sheet with id=AF1, first strand: chain 'C' and resid 779 through 782 removed outlier: 3.562A pdb=" N ILE C 782 " --> pdb=" O ILE C1147 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 803 through 804 Processing sheet with id=AF3, first strand: chain 'C' and resid 1122 through 1124 841 hydrogen bonds defined for protein. 2241 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: 10.07 Time building geometry restraints manager: 11.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4327 1.29 - 1.43: 7452 1.43 - 1.57: 15019 1.57 - 1.70: 28 1.70 - 1.84: 199 Bond restraints: 27025 Sorted by residual: bond pdb=" N CYS A 349 " pdb=" CA CYS A 349 " ideal model delta sigma weight residual 1.459 1.156 0.303 1.19e-02 7.06e+03 6.48e+02 bond pdb=" C CYS A 349 " pdb=" O CYS A 349 " ideal model delta sigma weight residual 1.236 1.411 -0.175 1.15e-02 7.56e+03 2.31e+02 bond pdb=" N MET A 696 " pdb=" CA MET A 696 " ideal model delta sigma weight residual 1.456 1.592 -0.136 1.50e-02 4.44e+03 8.26e+01 bond pdb=" CA CYS A 349 " pdb=" CB CYS A 349 " ideal model delta sigma weight residual 1.529 1.638 -0.109 1.55e-02 4.16e+03 4.92e+01 bond pdb=" N ARG B 822 " pdb=" CA ARG B 822 " ideal model delta sigma weight residual 1.458 1.548 -0.090 1.30e-02 5.92e+03 4.84e+01 ... (remaining 27020 not shown) Histogram of bond angle deviations from ideal: 94.92 - 104.34: 503 104.34 - 113.75: 14689 113.75 - 123.17: 19579 123.17 - 132.59: 1920 132.59 - 142.00: 58 Bond angle restraints: 36749 Sorted by residual: angle pdb=" O CYS A 349 " pdb=" C CYS A 349 " pdb=" N SER A 350 " ideal model delta sigma weight residual 122.07 104.98 17.09 1.03e+00 9.43e-01 2.75e+02 angle pdb=" N CYS A 349 " pdb=" CA CYS A 349 " pdb=" C CYS A 349 " ideal model delta sigma weight residual 111.07 94.92 16.15 1.07e+00 8.73e-01 2.28e+02 angle pdb=" N ASN A 406 " pdb=" CA ASN A 406 " pdb=" C ASN A 406 " ideal model delta sigma weight residual 113.72 96.18 17.54 1.52e+00 4.33e-01 1.33e+02 angle pdb=" CA CYS A 349 " pdb=" C CYS A 349 " pdb=" N SER A 350 " ideal model delta sigma weight residual 117.07 129.37 -12.30 1.14e+00 7.69e-01 1.16e+02 angle pdb=" C CYS A 349 " pdb=" N SER A 350 " pdb=" CA SER A 350 " ideal model delta sigma weight residual 121.50 136.82 -15.32 1.43e+00 4.89e-01 1.15e+02 ... (remaining 36744 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.90: 15398 26.90 - 53.79: 593 53.79 - 80.69: 67 80.69 - 107.58: 10 107.58 - 134.48: 9 Dihedral angle restraints: 16077 sinusoidal: 6087 harmonic: 9990 Sorted by residual: dihedral pdb=" CA SER B 856 " pdb=" C SER B 856 " pdb=" N GLN B 857 " pdb=" CA GLN B 857 " ideal model delta harmonic sigma weight residual -180.00 -45.52 -134.48 0 5.00e+00 4.00e-02 7.23e+02 dihedral pdb=" CA SER C 856 " pdb=" C SER C 856 " pdb=" N GLN C 857 " pdb=" CA GLN C 857 " ideal model delta harmonic sigma weight residual -180.00 -45.64 -134.36 0 5.00e+00 4.00e-02 7.22e+02 dihedral pdb=" CA SER A 856 " pdb=" C SER A 856 " pdb=" N GLN A 857 " pdb=" CA GLN A 857 " ideal model delta harmonic sigma weight residual -180.00 -45.65 -134.35 0 5.00e+00 4.00e-02 7.22e+02 ... (remaining 16074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.192: 3998 0.192 - 0.384: 120 0.384 - 0.576: 10 0.576 - 0.767: 1 0.767 - 0.959: 2 Chirality restraints: 4131 Sorted by residual: chirality pdb=" CA ASN A 582 " pdb=" N ASN A 582 " pdb=" C ASN A 582 " pdb=" CB ASN A 582 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.30e+01 chirality pdb=" CA GLN B 627 " pdb=" N GLN B 627 " pdb=" C GLN B 627 " pdb=" CB GLN B 627 " both_signs ideal model delta sigma weight residual False 2.51 1.68 0.83 2.00e-01 2.50e+01 1.72e+01 chirality pdb=" CA ARG C1057 " pdb=" N ARG C1057 " pdb=" C ARG C1057 " pdb=" CB ARG C1057 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.99e+00 ... (remaining 4128 not shown) Planarity restraints: 4750 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 520 " -0.038 2.00e-02 2.50e+03 8.03e-02 6.44e+01 pdb=" C ALA A 520 " 0.139 2.00e-02 2.50e+03 pdb=" O ALA A 520 " -0.055 2.00e-02 2.50e+03 pdb=" N ASN A 521 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 280 " -0.025 2.00e-02 2.50e+03 5.24e-02 2.74e+01 pdb=" CD GLN C 280 " 0.091 2.00e-02 2.50e+03 pdb=" OE1 GLN C 280 " -0.033 2.00e-02 2.50e+03 pdb=" NE2 GLN C 280 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 280 " -0.025 2.00e-02 2.50e+03 5.22e-02 2.73e+01 pdb=" CD GLN B 280 " 0.090 2.00e-02 2.50e+03 pdb=" OE1 GLN B 280 " -0.033 2.00e-02 2.50e+03 pdb=" NE2 GLN B 280 " -0.032 2.00e-02 2.50e+03 ... (remaining 4747 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.13: 80 2.13 - 2.82: 8588 2.82 - 3.51: 36007 3.51 - 4.21: 66498 4.21 - 4.90: 109792 Nonbonded interactions: 220965 Sorted by model distance: nonbonded pdb=" O GLN B 427 " pdb=" O ARG C1057 " model vdw 1.433 3.040 nonbonded pdb=" O ASP B 510 " pdb=" ND2 ASN C 436 " model vdw 1.454 2.520 nonbonded pdb=" OH TYR B 58 " pdb=" O GLY B 331 " model vdw 1.465 2.440 nonbonded pdb=" OH TYR C 58 " pdb=" O GLY C 331 " model vdw 1.465 2.440 nonbonded pdb=" OH TYR A 58 " pdb=" O GLY A 331 " model vdw 1.466 2.440 ... (remaining 220960 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 18 through 50 or resid 52 through 1206)) selection = (chain 'B' and (resid 18 through 50 or resid 52 through 1206)) selection = (chain 'C' and (resid 18 through 50 or resid 52 through 59 or (resid 60 and (nam \ e N or name CA or name C or name O or name CB )) or resid 61 through 1206)) } 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=0.46 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: 0.500 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: 0.020 Extract box with map and model: 3.350 Check model and map are aligned: 0.360 Set scattering table: 0.230 Process input model: 88.890 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.180 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:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5786 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 : 0.011 0.303 27025 Z= 0.701 Angle : 1.702 25.705 36749 Z= 0.982 Chirality : 0.085 0.959 4131 Planarity : 0.009 0.114 4750 Dihedral : 14.738 134.478 9585 Min Nonbonded Distance : 1.433 Molprobity Statistics. All-atom Clashscore : 32.76 Ramachandran Plot: Outliers : 1.42 % Allowed : 13.04 % Favored : 85.54 % Rotamer: Outliers : 5.99 % Allowed : 7.29 % Favored : 86.71 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.28 % Twisted Proline : 0.00 % Twisted General : 1.78 % 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: -3.79 (0.12), residues: 3390 helix: -2.88 (0.14), residues: 682 sheet: -1.15 (0.21), residues: 572 loop : -2.96 (0.11), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.005 TRP A 960 HIS 0.017 0.004 HIS C1138 PHE 0.038 0.004 PHE A1172 TYR 0.046 0.004 TYR B1171 ARG 0.012 0.002 ARG C 119 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 672 time to evaluate : 2.957 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: A 78 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.6852 (tm-30) REVERT: A 127 THR cc_start: 0.6987 (m) cc_final: 0.6311 (p) REVERT: A 346 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8315 (tp-100) REVERT: A 361 TYR cc_start: 0.8238 (m-80) cc_final: 0.7946 (m-80) REVERT: A 487 ASN cc_start: 0.1989 (OUTLIER) cc_final: 0.0891 (t0) REVERT: A 493 LYS cc_start: -0.5398 (OUTLIER) cc_final: -0.6200 (mmtm) REVERT: A 581 THR cc_start: 0.6070 (OUTLIER) cc_final: 0.5782 (m) REVERT: A 786 PHE cc_start: 0.8146 (m-80) cc_final: 0.7923 (m-10) REVERT: A 819 GLN cc_start: 0.8843 (mt0) cc_final: 0.8394 (tp40) REVERT: A 891 GLU cc_start: 0.8901 (tt0) cc_final: 0.8651 (tt0) REVERT: A 1015 THR cc_start: 0.8231 (p) cc_final: 0.7982 (t) REVERT: A 1061 LEU cc_start: 0.7076 (mt) cc_final: 0.6705 (mm) REVERT: A 1086 LEU cc_start: 0.9212 (mt) cc_final: 0.8841 (mp) REVERT: B 438 TYR cc_start: 0.1159 (OUTLIER) cc_final: 0.0240 (m-80) REVERT: B 511 ARG cc_start: 0.0163 (OUTLIER) cc_final: -0.0234 (mpt-90) REVERT: B 609 TYR cc_start: 0.3474 (OUTLIER) cc_final: 0.3147 (p90) REVERT: B 724 VAL cc_start: 0.5399 (OUTLIER) cc_final: 0.5193 (p) REVERT: B 830 LYS cc_start: 0.9214 (mttt) cc_final: 0.8989 (ptpt) REVERT: B 928 TYR cc_start: 0.7184 (m-80) cc_final: 0.6878 (m-10) REVERT: B 993 ASN cc_start: 0.8544 (m-40) cc_final: 0.7786 (p0) REVERT: B 1017 GLU cc_start: 0.8449 (pm20) cc_final: 0.8232 (pp20) REVERT: B 1036 LEU cc_start: 0.8856 (mt) cc_final: 0.8656 (mm) REVERT: B 1082 VAL cc_start: 0.9532 (t) cc_final: 0.9179 (p) REVERT: B 1086 LEU cc_start: 0.9272 (mt) cc_final: 0.9020 (mp) REVERT: B 1172 PHE cc_start: 0.8312 (m-80) cc_final: 0.7809 (m-80) REVERT: C 58 TYR cc_start: 0.6282 (OUTLIER) cc_final: 0.6046 (t80) REVERT: C 367 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6834 (pp20) REVERT: C 564 THR cc_start: 0.0440 (OUTLIER) cc_final: 0.0143 (m) REVERT: C 655 VAL cc_start: 0.7770 (t) cc_final: 0.7419 (m) REVERT: C 659 VAL cc_start: 0.7715 (p) cc_final: 0.7167 (p) REVERT: C 697 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.5971 (tp) REVERT: C 843 ASP cc_start: 0.8164 (m-30) cc_final: 0.7882 (m-30) REVERT: C 892 ASP cc_start: 0.9010 (m-30) cc_final: 0.8729 (m-30) REVERT: C 1042 ASN cc_start: 0.7622 (p0) cc_final: 0.7357 (p0) REVERT: C 1053 ASP cc_start: 0.5741 (m-30) cc_final: 0.4702 (m-30) REVERT: C 1064 ASP cc_start: 0.8434 (m-30) cc_final: 0.8152 (m-30) REVERT: C 1097 GLN cc_start: 0.8730 (tp40) cc_final: 0.8437 (tm-30) outliers start: 175 outliers final: 38 residues processed: 813 average time/residue: 0.3802 time to fit residues: 480.8633 Evaluate side-chains 394 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 344 time to evaluate : 2.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 288 optimal weight: 6.9990 chunk 259 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 268 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 162 optimal weight: 50.0000 chunk 199 optimal weight: 3.9990 chunk 310 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN ** A 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 GLN A 792 GLN A 812 ASN A 839 ASN ** A1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 GLN A1097 GLN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1176 ASN A1201 ASN ** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 GLN B 599 GLN B 792 GLN B 836 HIS B 839 ASN ** B1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 GLN ** B1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1084 GLN C 111 GLN C 599 GLN C 812 ASN C 839 ASN ** C1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1028 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1201 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5986 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 27025 Z= 0.300 Angle : 1.052 15.771 36749 Z= 0.544 Chirality : 0.059 0.387 4131 Planarity : 0.007 0.115 4750 Dihedral : 8.546 55.003 3711 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 23.39 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.95 % Favored : 87.61 % Rotamer: Outliers : 0.27 % Allowed : 2.81 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.74 % Twisted Proline : 0.00 % Twisted General : 1.10 % 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: -3.07 (0.13), residues: 3390 helix: -1.47 (0.16), residues: 693 sheet: -0.52 (0.22), residues: 564 loop : -2.85 (0.12), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 310 HIS 0.006 0.001 HIS B 670 PHE 0.041 0.002 PHE A 341 TYR 0.039 0.003 TYR B 577 ARG 0.014 0.001 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 478 time to evaluate : 2.956 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: A 127 THR cc_start: 0.7412 (m) cc_final: 0.6736 (p) REVERT: A 384 ASP cc_start: 0.5781 (p0) cc_final: 0.5515 (p0) REVERT: A 625 VAL cc_start: 0.8605 (t) cc_final: 0.8389 (p) REVERT: A 786 PHE cc_start: 0.8434 (m-80) cc_final: 0.8119 (m-10) REVERT: A 819 GLN cc_start: 0.8788 (mt0) cc_final: 0.8278 (tp40) REVERT: A 943 MET cc_start: 0.8210 (ttp) cc_final: 0.7366 (tpp) REVERT: A 1015 THR cc_start: 0.8278 (p) cc_final: 0.8058 (t) REVERT: B 49 ASP cc_start: 0.7721 (t0) cc_final: 0.7371 (m-30) REVERT: B 84 MET cc_start: 0.8238 (ttp) cc_final: 0.7956 (ttm) REVERT: B 790 VAL cc_start: 0.6603 (m) cc_final: 0.6316 (m) REVERT: B 815 GLN cc_start: 0.8286 (mp10) cc_final: 0.8040 (mm110) REVERT: B 823 GLU cc_start: 0.8428 (tt0) cc_final: 0.8167 (tt0) REVERT: B 827 PHE cc_start: 0.7837 (m-80) cc_final: 0.7208 (m-80) REVERT: B 830 LYS cc_start: 0.9153 (mttt) cc_final: 0.8320 (ptpt) REVERT: B 848 ASN cc_start: 0.8817 (t0) cc_final: 0.8534 (t0) REVERT: B 939 MET cc_start: 0.7976 (mtp) cc_final: 0.7663 (tpp) REVERT: B 993 ASN cc_start: 0.8555 (m-40) cc_final: 0.7931 (p0) REVERT: B 1116 PHE cc_start: 0.7088 (m-10) cc_final: 0.6550 (m-10) REVERT: B 1172 PHE cc_start: 0.8096 (m-80) cc_final: 0.7706 (m-80) REVERT: C 367 GLU cc_start: 0.7535 (mt-10) cc_final: 0.6961 (pp20) REVERT: C 655 VAL cc_start: 0.7834 (t) cc_final: 0.7278 (m) REVERT: C 938 LEU cc_start: 0.8886 (tt) cc_final: 0.8643 (tt) REVERT: C 1042 ASN cc_start: 0.7527 (p0) cc_final: 0.7298 (p0) REVERT: C 1044 PHE cc_start: 0.7920 (t80) cc_final: 0.7622 (t80) REVERT: C 1064 ASP cc_start: 0.8594 (m-30) cc_final: 0.8264 (m-30) REVERT: C 1097 GLN cc_start: 0.8964 (tp40) cc_final: 0.8719 (tp40) REVERT: C 1179 ARG cc_start: 0.7928 (mtm180) cc_final: 0.7449 (tpm170) outliers start: 8 outliers final: 2 residues processed: 483 average time/residue: 0.3833 time to fit residues: 294.2472 Evaluate side-chains 309 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 307 time to evaluate : 3.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 172 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 258 optimal weight: 4.9990 chunk 211 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 311 optimal weight: 3.9990 chunk 336 optimal weight: 6.9990 chunk 277 optimal weight: 7.9990 chunk 308 optimal weight: 8.9990 chunk 106 optimal weight: 0.9980 chunk 249 optimal weight: 8.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 HIS A 377 GLN ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 GLN A1009 GLN A1085 GLN A1132 ASN ** A1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN ** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 766 HIS ** B1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1084 GLN B1132 ASN ** B1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN ** C 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1028 ASN C1129 ASN ** C1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1201 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6109 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 27025 Z= 0.289 Angle : 1.001 14.380 36749 Z= 0.512 Chirality : 0.055 0.316 4131 Planarity : 0.007 0.107 4750 Dihedral : 7.948 56.790 3711 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 22.21 Ramachandran Plot: Outliers : 0.44 % Allowed : 13.31 % Favored : 86.25 % Rotamer: Outliers : 0.03 % Allowed : 2.67 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.77 % Twisted Proline : 0.00 % Twisted General : 0.64 % 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: -2.72 (0.13), residues: 3390 helix: -0.55 (0.18), residues: 686 sheet: -0.72 (0.21), residues: 614 loop : -2.76 (0.12), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 960 HIS 0.006 0.001 HIS B1122 PHE 0.037 0.002 PHE A 418 TYR 0.037 0.002 TYR B1171 ARG 0.010 0.001 ARG C1179 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 415 time to evaluate : 2.884 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: A 127 THR cc_start: 0.7974 (m) cc_final: 0.7316 (p) REVERT: A 786 PHE cc_start: 0.8749 (m-80) cc_final: 0.8523 (m-80) REVERT: A 819 GLN cc_start: 0.8723 (mt0) cc_final: 0.8294 (tp40) REVERT: A 894 LEU cc_start: 0.8941 (pp) cc_final: 0.8705 (pp) REVERT: A 943 MET cc_start: 0.8000 (ttp) cc_final: 0.7522 (ttp) REVERT: A 1121 THR cc_start: 0.7892 (t) cc_final: 0.7320 (m) REVERT: B 49 ASP cc_start: 0.7665 (t0) cc_final: 0.7358 (m-30) REVERT: B 452 MET cc_start: 0.0734 (mtp) cc_final: 0.0514 (mtm) REVERT: B 815 GLN cc_start: 0.8569 (mp10) cc_final: 0.8330 (mm110) REVERT: B 823 GLU cc_start: 0.8371 (tt0) cc_final: 0.8136 (tt0) REVERT: B 938 LEU cc_start: 0.9003 (tp) cc_final: 0.8729 (tp) REVERT: B 939 MET cc_start: 0.8138 (mtp) cc_final: 0.7903 (tpp) REVERT: B 993 ASN cc_start: 0.8568 (m-40) cc_final: 0.7736 (p0) REVERT: B 1172 PHE cc_start: 0.8171 (m-80) cc_final: 0.7922 (m-80) REVERT: C 367 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7092 (pp20) REVERT: C 892 ASP cc_start: 0.8973 (m-30) cc_final: 0.8628 (m-30) outliers start: 1 outliers final: 1 residues processed: 415 average time/residue: 0.3481 time to fit residues: 235.1784 Evaluate side-chains 279 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 278 time to evaluate : 2.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 307 optimal weight: 10.0000 chunk 233 optimal weight: 0.0020 chunk 161 optimal weight: 50.0000 chunk 34 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 208 optimal weight: 0.9990 chunk 312 optimal weight: 20.0000 chunk 330 optimal weight: 5.9990 chunk 163 optimal weight: 30.0000 chunk 295 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 overall best weight: 2.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 ASN A 785 ASN ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1145 ASN ** A1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 GLN ** B1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1084 GLN ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1129 ASN ** B1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN C 769 GLN ** C 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6127 moved from start: 0.5411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 27025 Z= 0.250 Angle : 0.951 14.615 36749 Z= 0.485 Chirality : 0.054 0.306 4131 Planarity : 0.006 0.105 4750 Dihedral : 7.491 52.307 3711 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.33 % Allowed : 13.01 % Favored : 86.66 % Rotamer: Outliers : 0.07 % Allowed : 2.40 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.77 % Twisted Proline : 0.68 % Twisted General : 0.58 % 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: -2.60 (0.13), residues: 3390 helix: -0.31 (0.19), residues: 690 sheet: -0.84 (0.21), residues: 588 loop : -2.64 (0.12), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 960 HIS 0.005 0.001 HIS B1122 PHE 0.040 0.002 PHE A 341 TYR 0.038 0.002 TYR A1186 ARG 0.010 0.001 ARG C 841 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 401 time to evaluate : 3.082 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: A 127 THR cc_start: 0.8123 (m) cc_final: 0.7461 (p) REVERT: A 161 MET cc_start: 0.6623 (tpp) cc_final: 0.6316 (tpt) REVERT: A 792 GLN cc_start: 0.8451 (mp10) cc_final: 0.8234 (mm110) REVERT: A 927 GLN cc_start: 0.7803 (pt0) cc_final: 0.7326 (pt0) REVERT: A 943 MET cc_start: 0.7859 (ttp) cc_final: 0.7259 (ttp) REVERT: A 960 TRP cc_start: 0.5293 (t-100) cc_final: 0.4393 (t-100) REVERT: A 1001 PHE cc_start: 0.7654 (t80) cc_final: 0.7425 (t80) REVERT: B 49 ASP cc_start: 0.7747 (t0) cc_final: 0.7379 (m-30) REVERT: B 366 PHE cc_start: 0.7709 (m-10) cc_final: 0.7455 (m-10) REVERT: B 452 MET cc_start: 0.0576 (mtp) cc_final: 0.0363 (mtm) REVERT: B 569 MET cc_start: 0.3086 (pmm) cc_final: 0.2508 (pmm) REVERT: B 815 GLN cc_start: 0.8604 (mp10) cc_final: 0.8362 (mm110) REVERT: B 833 GLN cc_start: 0.9338 (mt0) cc_final: 0.9132 (mt0) REVERT: B 906 MET cc_start: 0.6952 (ppp) cc_final: 0.6648 (ppp) REVERT: B 938 LEU cc_start: 0.9074 (tp) cc_final: 0.8827 (tp) REVERT: B 939 MET cc_start: 0.8244 (mtp) cc_final: 0.7825 (tpp) REVERT: B 993 ASN cc_start: 0.7943 (m-40) cc_final: 0.7635 (p0) REVERT: B 1039 GLU cc_start: 0.9223 (pp20) cc_final: 0.9011 (pp20) REVERT: B 1163 ASN cc_start: 0.8340 (p0) cc_final: 0.7801 (m-40) REVERT: B 1172 PHE cc_start: 0.8064 (m-80) cc_final: 0.7799 (m-80) REVERT: C 367 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7114 (pp20) REVERT: C 892 ASP cc_start: 0.8894 (m-30) cc_final: 0.8542 (m-30) REVERT: C 992 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7843 (mt-10) outliers start: 2 outliers final: 0 residues processed: 403 average time/residue: 0.3502 time to fit residues: 229.8053 Evaluate side-chains 279 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 2.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 275 optimal weight: 0.6980 chunk 187 optimal weight: 3.9990 chunk 4 optimal weight: 0.0170 chunk 246 optimal weight: 50.0000 chunk 136 optimal weight: 0.4980 chunk 282 optimal weight: 8.9990 chunk 228 optimal weight: 50.0000 chunk 0 optimal weight: 40.0000 chunk 168 optimal weight: 20.0000 chunk 296 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 overall best weight: 2.0422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 HIS A 576 GLN ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 280 GLN ** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN B1009 GLN ** B1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6111 moved from start: 0.5826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27025 Z= 0.227 Angle : 0.925 13.134 36749 Z= 0.470 Chirality : 0.053 0.295 4131 Planarity : 0.006 0.101 4750 Dihedral : 7.209 47.500 3711 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 21.29 Ramachandran Plot: Outliers : 0.33 % Allowed : 13.34 % Favored : 86.34 % Rotamer: Outliers : 0.07 % Allowed : 1.85 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.77 % Twisted Proline : 1.36 % Twisted General : 0.49 % 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: -2.44 (0.13), residues: 3390 helix: -0.18 (0.19), residues: 702 sheet: -0.76 (0.21), residues: 609 loop : -2.55 (0.12), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 960 HIS 0.015 0.001 HIS A 486 PHE 0.040 0.002 PHE B 354 TYR 0.047 0.002 TYR B 648 ARG 0.006 0.001 ARG C 841 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 377 time to evaluate : 2.769 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: A 127 THR cc_start: 0.8092 (m) cc_final: 0.7477 (p) REVERT: A 161 MET cc_start: 0.6443 (tpp) cc_final: 0.6158 (tpt) REVERT: A 569 MET cc_start: -0.2434 (ptt) cc_final: -0.3433 (ttt) REVERT: A 841 ARG cc_start: 0.9168 (ptp90) cc_final: 0.8887 (ptp90) REVERT: A 848 ASN cc_start: 0.9020 (p0) cc_final: 0.8806 (p0) REVERT: A 927 GLN cc_start: 0.8053 (pt0) cc_final: 0.7452 (pt0) REVERT: A 943 MET cc_start: 0.7834 (ttp) cc_final: 0.7233 (ttp) REVERT: B 49 ASP cc_start: 0.7552 (t0) cc_final: 0.7305 (m-30) REVERT: B 569 MET cc_start: 0.2967 (pmm) cc_final: 0.2546 (pmm) REVERT: B 815 GLN cc_start: 0.8606 (mp10) cc_final: 0.8360 (mm110) REVERT: B 833 GLN cc_start: 0.9305 (mt0) cc_final: 0.9103 (mt0) REVERT: B 906 MET cc_start: 0.6753 (ppp) cc_final: 0.6368 (ppp) REVERT: B 939 MET cc_start: 0.8075 (mtp) cc_final: 0.7809 (tpp) REVERT: B 993 ASN cc_start: 0.7820 (m-40) cc_final: 0.7585 (p0) REVERT: B 1076 THR cc_start: 0.8719 (m) cc_final: 0.8510 (m) REVERT: B 1086 LEU cc_start: 0.8948 (mt) cc_final: 0.8454 (mt) REVERT: B 1090 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8090 (mp0) REVERT: B 1163 ASN cc_start: 0.7974 (p0) cc_final: 0.7389 (m-40) REVERT: B 1185 SER cc_start: 0.8951 (m) cc_final: 0.8370 (p) REVERT: C 843 ASP cc_start: 0.7976 (m-30) cc_final: 0.7481 (m-30) REVERT: C 892 ASP cc_start: 0.8959 (m-30) cc_final: 0.8715 (m-30) REVERT: C 992 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7810 (mt-10) REVERT: C 1064 ASP cc_start: 0.8658 (m-30) cc_final: 0.8347 (m-30) outliers start: 2 outliers final: 0 residues processed: 379 average time/residue: 0.3627 time to fit residues: 224.8613 Evaluate side-chains 269 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 111 optimal weight: 3.9990 chunk 297 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 194 optimal weight: 5.9990 chunk 81 optimal weight: 0.0370 chunk 330 optimal weight: 9.9990 chunk 274 optimal weight: 10.0000 chunk 153 optimal weight: 30.0000 chunk 27 optimal weight: 30.0000 chunk 109 optimal weight: 7.9990 chunk 173 optimal weight: 20.0000 overall best weight: 5.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 ASN A 766 HIS ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1016 ASN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 ASN B 114 ASN ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1016 ASN B1056 GLN ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1201 ASN ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1104 ASN ** C1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6282 moved from start: 0.6391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 27025 Z= 0.318 Angle : 0.972 14.605 36749 Z= 0.494 Chirality : 0.054 0.294 4131 Planarity : 0.006 0.100 4750 Dihedral : 7.313 47.578 3711 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 24.60 Ramachandran Plot: Outliers : 0.33 % Allowed : 13.93 % Favored : 85.74 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.77 % Twisted Proline : 0.00 % Twisted General : 0.43 % 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: -2.58 (0.13), residues: 3390 helix: -0.19 (0.19), residues: 695 sheet: -0.88 (0.21), residues: 569 loop : -2.66 (0.12), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 960 HIS 0.006 0.001 HIS B 766 PHE 0.041 0.002 PHE A 341 TYR 0.043 0.002 TYR A1186 ARG 0.007 0.001 ARG B1179 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 3.157 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: A 161 MET cc_start: 0.6993 (tpp) cc_final: 0.6736 (tpt) REVERT: A 343 ASP cc_start: 0.6948 (m-30) cc_final: 0.6507 (m-30) REVERT: A 786 PHE cc_start: 0.8728 (m-80) cc_final: 0.8522 (m-10) REVERT: A 849 LEU cc_start: 0.8863 (tp) cc_final: 0.8629 (tt) REVERT: A 927 GLN cc_start: 0.7842 (pt0) cc_final: 0.7422 (pt0) REVERT: A 943 MET cc_start: 0.7719 (ttp) cc_final: 0.7324 (ttp) REVERT: A 952 LEU cc_start: 0.8771 (mp) cc_final: 0.8501 (tt) REVERT: A 987 GLN cc_start: 0.8328 (mm-40) cc_final: 0.7953 (mm-40) REVERT: A 1076 THR cc_start: 0.9160 (m) cc_final: 0.8913 (p) REVERT: A 1100 LYS cc_start: 0.9090 (mtmm) cc_final: 0.8432 (ptpp) REVERT: A 1164 CYS cc_start: 0.6548 (t) cc_final: 0.6197 (t) REVERT: B 569 MET cc_start: 0.3148 (pmm) cc_final: 0.2769 (pmm) REVERT: B 815 GLN cc_start: 0.8384 (mp10) cc_final: 0.8173 (mm110) REVERT: B 906 MET cc_start: 0.6618 (ppp) cc_final: 0.6195 (ppp) REVERT: B 939 MET cc_start: 0.8287 (mtp) cc_final: 0.7785 (tpp) REVERT: B 993 ASN cc_start: 0.8007 (m-40) cc_final: 0.7758 (p0) REVERT: B 1039 GLU cc_start: 0.9250 (pp20) cc_final: 0.9050 (pp20) REVERT: B 1086 LEU cc_start: 0.9021 (mt) cc_final: 0.8494 (mt) REVERT: B 1090 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8206 (mp0) REVERT: B 1163 ASN cc_start: 0.7820 (p0) cc_final: 0.7402 (p0) REVERT: B 1185 SER cc_start: 0.9035 (m) cc_final: 0.8641 (p) REVERT: C 563 MET cc_start: 0.0763 (mmp) cc_final: 0.0556 (mmm) REVERT: C 892 ASP cc_start: 0.8891 (m-30) cc_final: 0.8584 (m-30) REVERT: C 1064 ASP cc_start: 0.8731 (m-30) cc_final: 0.8388 (m-30) outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 0.3746 time to fit residues: 216.5436 Evaluate side-chains 254 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 2.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 319 optimal weight: 10.0000 chunk 37 optimal weight: 40.0000 chunk 188 optimal weight: 4.9990 chunk 241 optimal weight: 20.0000 chunk 187 optimal weight: 5.9990 chunk 278 optimal weight: 1.9990 chunk 184 optimal weight: 0.0040 chunk 329 optimal weight: 3.9990 chunk 206 optimal weight: 8.9990 chunk 200 optimal weight: 1.9990 chunk 152 optimal weight: 20.0000 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 GLN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 ASN B 218 ASN ** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1079 ASN B1084 GLN ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1201 ASN C 486 HIS ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6214 moved from start: 0.6646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 27025 Z= 0.232 Angle : 0.922 13.422 36749 Z= 0.467 Chirality : 0.053 0.303 4131 Planarity : 0.006 0.099 4750 Dihedral : 7.020 44.111 3711 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 21.75 Ramachandran Plot: Outliers : 0.33 % Allowed : 13.13 % Favored : 86.54 % Rotamer: Outliers : 0.03 % Allowed : 1.27 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.77 % Twisted Proline : 1.36 % Twisted General : 0.37 % 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: -2.47 (0.14), residues: 3390 helix: -0.08 (0.19), residues: 692 sheet: -0.75 (0.22), residues: 577 loop : -2.61 (0.12), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 253 HIS 0.010 0.001 HIS C 486 PHE 0.032 0.002 PHE B 354 TYR 0.045 0.002 TYR A1186 ARG 0.007 0.001 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 360 time to evaluate : 2.762 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: A 127 THR cc_start: 0.7789 (m) cc_final: 0.7294 (p) REVERT: A 251 LEU cc_start: 0.5530 (tp) cc_final: 0.4582 (pt) REVERT: A 343 ASP cc_start: 0.6953 (m-30) cc_final: 0.6475 (m-30) REVERT: A 696 MET cc_start: 0.8040 (mmp) cc_final: 0.7742 (mmp) REVERT: A 841 ARG cc_start: 0.9206 (ptp90) cc_final: 0.8938 (ptp90) REVERT: A 849 LEU cc_start: 0.8868 (tp) cc_final: 0.8590 (tt) REVERT: A 927 GLN cc_start: 0.7964 (pt0) cc_final: 0.7448 (pt0) REVERT: A 987 GLN cc_start: 0.8304 (mm-40) cc_final: 0.7942 (mm-40) REVERT: A 1076 THR cc_start: 0.9114 (m) cc_final: 0.8862 (p) REVERT: A 1100 LYS cc_start: 0.9063 (mtmm) cc_final: 0.8433 (ptpp) REVERT: A 1164 CYS cc_start: 0.6196 (t) cc_final: 0.5951 (t) REVERT: B 815 GLN cc_start: 0.8431 (mp10) cc_final: 0.8182 (mm110) REVERT: B 906 MET cc_start: 0.6535 (ppp) cc_final: 0.6142 (ppp) REVERT: B 939 MET cc_start: 0.8323 (mtp) cc_final: 0.7755 (tpp) REVERT: B 993 ASN cc_start: 0.7917 (m-40) cc_final: 0.7661 (p0) REVERT: B 1039 GLU cc_start: 0.9231 (pp20) cc_final: 0.9019 (pp20) REVERT: B 1086 LEU cc_start: 0.9008 (mt) cc_final: 0.8433 (mt) REVERT: B 1163 ASN cc_start: 0.7762 (p0) cc_final: 0.7159 (m-40) REVERT: B 1185 SER cc_start: 0.9002 (m) cc_final: 0.8609 (p) REVERT: C 563 MET cc_start: 0.0587 (mmp) cc_final: 0.0305 (mmm) REVERT: C 892 ASP cc_start: 0.8856 (m-30) cc_final: 0.8455 (m-30) REVERT: C 938 LEU cc_start: 0.9162 (tt) cc_final: 0.8883 (tt) REVERT: C 1064 ASP cc_start: 0.8710 (m-30) cc_final: 0.8380 (m-30) outliers start: 1 outliers final: 0 residues processed: 361 average time/residue: 0.3511 time to fit residues: 206.3428 Evaluate side-chains 260 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 203 optimal weight: 0.8980 chunk 131 optimal weight: 8.9990 chunk 196 optimal weight: 0.1980 chunk 99 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 209 optimal weight: 9.9990 chunk 224 optimal weight: 0.7980 chunk 162 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 259 optimal weight: 6.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 GLN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 GLN B1079 ASN ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1201 ASN ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 769 GLN ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1009 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6180 moved from start: 0.6901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27025 Z= 0.216 Angle : 0.908 12.279 36749 Z= 0.459 Chirality : 0.053 0.300 4131 Planarity : 0.006 0.102 4750 Dihedral : 6.853 41.840 3711 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.30 % Allowed : 13.16 % Favored : 86.54 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.77 % Twisted Proline : 1.36 % Twisted General : 0.28 % 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: -2.42 (0.14), residues: 3390 helix: 0.03 (0.19), residues: 690 sheet: -0.92 (0.22), residues: 574 loop : -2.52 (0.12), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 253 HIS 0.005 0.001 HIS B1122 PHE 0.043 0.002 PHE C 778 TYR 0.046 0.002 TYR A1186 ARG 0.007 0.000 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 364 time to evaluate : 3.151 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: A 127 THR cc_start: 0.7781 (m) cc_final: 0.7318 (p) REVERT: A 251 LEU cc_start: 0.5630 (tp) cc_final: 0.4627 (pt) REVERT: A 563 MET cc_start: 0.5394 (mmm) cc_final: 0.2418 (ptt) REVERT: A 696 MET cc_start: 0.8173 (mmp) cc_final: 0.7969 (mmp) REVERT: A 848 ASN cc_start: 0.9062 (p0) cc_final: 0.8821 (p0) REVERT: A 849 LEU cc_start: 0.8787 (tp) cc_final: 0.8574 (tt) REVERT: A 987 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7819 (mm-40) REVERT: A 1076 THR cc_start: 0.9088 (m) cc_final: 0.8830 (p) REVERT: A 1100 LYS cc_start: 0.9035 (mtmm) cc_final: 0.8401 (ptpp) REVERT: B 906 MET cc_start: 0.6525 (ppp) cc_final: 0.6124 (ppp) REVERT: B 961 THR cc_start: 0.7849 (m) cc_final: 0.7558 (m) REVERT: B 964 LEU cc_start: 0.8696 (pt) cc_final: 0.8363 (tp) REVERT: B 993 ASN cc_start: 0.7883 (m-40) cc_final: 0.7642 (p0) REVERT: B 1039 GLU cc_start: 0.9213 (pp20) cc_final: 0.8970 (pp20) REVERT: B 1163 ASN cc_start: 0.7821 (p0) cc_final: 0.7186 (m-40) REVERT: B 1185 SER cc_start: 0.8981 (m) cc_final: 0.8568 (p) REVERT: C 827 PHE cc_start: 0.8946 (m-80) cc_final: 0.8722 (m-10) REVERT: C 938 LEU cc_start: 0.9050 (tt) cc_final: 0.8827 (tt) REVERT: C 987 GLN cc_start: 0.8328 (tm-30) cc_final: 0.8123 (tm-30) REVERT: C 1064 ASP cc_start: 0.8715 (m-30) cc_final: 0.8380 (m-30) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.3586 time to fit residues: 212.9249 Evaluate side-chains 252 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 2.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 299 optimal weight: 6.9990 chunk 315 optimal weight: 0.1980 chunk 288 optimal weight: 0.0070 chunk 307 optimal weight: 0.7980 chunk 184 optimal weight: 0.6980 chunk 133 optimal weight: 30.0000 chunk 241 optimal weight: 20.0000 chunk 94 optimal weight: 9.9990 chunk 277 optimal weight: 5.9990 chunk 290 optimal weight: 0.9990 chunk 306 optimal weight: 5.9990 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 ASN ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 GLN A1097 GLN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 GLN B1079 ASN B1084 GLN ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1201 ASN ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6109 moved from start: 0.7090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27025 Z= 0.200 Angle : 0.894 13.701 36749 Z= 0.450 Chirality : 0.052 0.300 4131 Planarity : 0.006 0.106 4750 Dihedral : 6.615 41.017 3711 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.87 % Favored : 86.87 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.77 % Twisted Proline : 1.36 % Twisted General : 0.25 % 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: -2.34 (0.14), residues: 3390 helix: 0.07 (0.19), residues: 691 sheet: -0.77 (0.22), residues: 582 loop : -2.50 (0.12), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 253 HIS 0.005 0.001 HIS B1122 PHE 0.029 0.002 PHE A1001 TYR 0.047 0.002 TYR A 642 ARG 0.005 0.000 ARG C 841 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 364 time to evaluate : 3.093 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: A 127 THR cc_start: 0.7766 (m) cc_final: 0.7281 (p) REVERT: A 251 LEU cc_start: 0.5471 (tp) cc_final: 0.4816 (pt) REVERT: A 563 MET cc_start: 0.5011 (mmm) cc_final: 0.2203 (ptt) REVERT: A 696 MET cc_start: 0.8137 (mmp) cc_final: 0.7933 (mmp) REVERT: A 849 LEU cc_start: 0.8765 (tp) cc_final: 0.8560 (tt) REVERT: A 987 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7795 (mm-40) REVERT: A 1039 GLU cc_start: 0.8267 (pp20) cc_final: 0.8027 (pp20) REVERT: A 1076 THR cc_start: 0.8988 (m) cc_final: 0.8748 (p) REVERT: A 1100 LYS cc_start: 0.9005 (mtmm) cc_final: 0.8512 (ptpp) REVERT: B 833 GLN cc_start: 0.9346 (mt0) cc_final: 0.9141 (mt0) REVERT: B 906 MET cc_start: 0.6497 (ppp) cc_final: 0.6115 (ppp) REVERT: B 961 THR cc_start: 0.7335 (m) cc_final: 0.6902 (m) REVERT: B 993 ASN cc_start: 0.7791 (m-40) cc_final: 0.7574 (p0) REVERT: B 1039 GLU cc_start: 0.9283 (pp20) cc_final: 0.9076 (pp20) REVERT: B 1163 ASN cc_start: 0.7672 (p0) cc_final: 0.7185 (m-40) REVERT: B 1185 SER cc_start: 0.8891 (m) cc_final: 0.8565 (p) REVERT: C 271 VAL cc_start: 0.6518 (t) cc_final: 0.6316 (t) REVERT: C 906 MET cc_start: 0.6768 (mmm) cc_final: 0.6531 (mmt) REVERT: C 987 GLN cc_start: 0.8324 (tm-30) cc_final: 0.7778 (tm-30) REVERT: C 1064 ASP cc_start: 0.8671 (m-30) cc_final: 0.8337 (m-30) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.3586 time to fit residues: 215.3207 Evaluate side-chains 274 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 201 optimal weight: 0.7980 chunk 324 optimal weight: 8.9990 chunk 198 optimal weight: 0.0870 chunk 154 optimal weight: 6.9990 chunk 225 optimal weight: 5.9990 chunk 340 optimal weight: 10.0000 chunk 313 optimal weight: 10.0000 chunk 271 optimal weight: 6.9990 chunk 28 optimal weight: 0.0030 chunk 209 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 overall best weight: 0.5770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 GLN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1056 GLN B1066 GLN B1084 GLN ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1201 ASN ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1177 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6081 moved from start: 0.7280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27025 Z= 0.199 Angle : 0.889 12.971 36749 Z= 0.447 Chirality : 0.052 0.303 4131 Planarity : 0.006 0.106 4750 Dihedral : 6.454 38.999 3711 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.66 % Favored : 87.07 % Rotamer: Outliers : 0.03 % Allowed : 0.21 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.77 % Twisted Proline : 2.04 % Twisted General : 0.25 % 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: -2.24 (0.14), residues: 3390 helix: 0.15 (0.19), residues: 695 sheet: -0.63 (0.21), residues: 618 loop : -2.49 (0.13), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 253 HIS 0.006 0.001 HIS B1122 PHE 0.034 0.002 PHE A1001 TYR 0.043 0.002 TYR A 642 ARG 0.008 0.000 ARG C1179 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 368 time to evaluate : 2.987 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: A 127 THR cc_start: 0.7740 (m) cc_final: 0.7270 (p) REVERT: A 251 LEU cc_start: 0.5420 (tp) cc_final: 0.4818 (pt) REVERT: A 563 MET cc_start: 0.4953 (mmm) cc_final: 0.2224 (ptt) REVERT: A 849 LEU cc_start: 0.8862 (tp) cc_final: 0.8598 (tt) REVERT: A 938 LEU cc_start: 0.9310 (tt) cc_final: 0.9095 (tt) REVERT: A 987 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7655 (mm-40) REVERT: A 1090 GLU cc_start: 0.9303 (mp0) cc_final: 0.8864 (mp0) REVERT: A 1100 LYS cc_start: 0.8992 (mtmm) cc_final: 0.8422 (ptpp) REVERT: B 833 GLN cc_start: 0.9364 (mt0) cc_final: 0.9154 (mt0) REVERT: B 896 ASP cc_start: 0.8792 (m-30) cc_final: 0.8471 (t70) REVERT: B 906 MET cc_start: 0.6475 (ppp) cc_final: 0.6072 (ppp) REVERT: B 941 VAL cc_start: 0.8535 (m) cc_final: 0.8195 (m) REVERT: B 961 THR cc_start: 0.7358 (m) cc_final: 0.6980 (m) REVERT: B 1039 GLU cc_start: 0.9254 (pp20) cc_final: 0.9040 (pp20) REVERT: B 1075 LEU cc_start: 0.9045 (mm) cc_final: 0.8665 (mm) REVERT: B 1163 ASN cc_start: 0.7609 (p0) cc_final: 0.7223 (m-40) REVERT: B 1185 SER cc_start: 0.8903 (m) cc_final: 0.8552 (p) REVERT: C 569 MET cc_start: 0.2868 (ptp) cc_final: 0.2537 (ptp) REVERT: C 849 LEU cc_start: 0.9443 (tp) cc_final: 0.9233 (tt) REVERT: C 906 MET cc_start: 0.6689 (mmm) cc_final: 0.6480 (mmt) REVERT: C 1017 GLU cc_start: 0.8086 (pp20) cc_final: 0.7737 (pp20) REVERT: C 1064 ASP cc_start: 0.8644 (m-30) cc_final: 0.8310 (m-30) outliers start: 1 outliers final: 0 residues processed: 368 average time/residue: 0.3498 time to fit residues: 210.3805 Evaluate side-chains 268 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 2.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 215 optimal weight: 6.9990 chunk 289 optimal weight: 0.0070 chunk 83 optimal weight: 10.0000 chunk 250 optimal weight: 7.9990 chunk 40 optimal weight: 30.0000 chunk 75 optimal weight: 4.9990 chunk 271 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 279 optimal weight: 30.0000 chunk 34 optimal weight: 8.9990 chunk 50 optimal weight: 0.5980 overall best weight: 2.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 ASN A1084 GLN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 HIS ** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 839 ASN B1084 GLN ** B1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1201 ASN ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.113163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.091594 restraints weight = 221647.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.092625 restraints weight = 137795.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.093696 restraints weight = 93964.340| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3785 r_free = 0.3785 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3785 r_free = 0.3785 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.7484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27025 Z= 0.231 Angle : 0.895 13.086 36749 Z= 0.452 Chirality : 0.052 0.297 4131 Planarity : 0.006 0.107 4750 Dihedral : 6.479 39.907 3711 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 20.81 Ramachandran Plot: Outliers : 0.27 % Allowed : 13.16 % Favored : 86.57 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.77 % Twisted Proline : 1.36 % Twisted General : 0.25 % 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: -2.21 (0.14), residues: 3390 helix: 0.17 (0.19), residues: 700 sheet: -0.45 (0.22), residues: 576 loop : -2.50 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 960 HIS 0.004 0.001 HIS B1122 PHE 0.040 0.002 PHE C 764 TYR 0.043 0.002 TYR A1186 ARG 0.008 0.001 ARG A 887 =============================================================================== Job complete usr+sys time: 5619.78 seconds wall clock time: 103 minutes 59.00 seconds (6239.00 seconds total)