Starting phenix.real_space_refine on Mon Feb 19 11:33:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ksm_23020/02_2024/7ksm_23020_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ksm_23020/02_2024/7ksm_23020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ksm_23020/02_2024/7ksm_23020.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ksm_23020/02_2024/7ksm_23020.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ksm_23020/02_2024/7ksm_23020_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ksm_23020/02_2024/7ksm_23020_updated.pdb" } resolution = 3.2 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.050 sd= 1.000 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 4 5.21 5 S 120 5.16 5 C 15541 2.51 5 N 4205 2.21 5 O 4661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 419": "OE1" <-> "OE2" Residue "A ARG 422": "NH1" <-> "NH2" Residue "A PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 476": "OE1" <-> "OE2" Residue "A ARG 482": "NH1" <-> "NH2" Residue "A GLU 489": "OE1" <-> "OE2" Residue "A ARG 511": "NH1" <-> "NH2" Residue "A ARG 534": "NH1" <-> "NH2" Residue "A ARG 538": "NH1" <-> "NH2" Residue "A PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 554": "OD1" <-> "OD2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A ASP 590": "OD1" <-> "OD2" Residue "A ASP 625": "OD1" <-> "OD2" Residue "A ASP 643": "OD1" <-> "OD2" Residue "A ARG 650": "NH1" <-> "NH2" Residue "A GLU 671": "OE1" <-> "OE2" Residue "A ARG 672": "NH1" <-> "NH2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A ASP 685": "OD1" <-> "OD2" Residue "A GLU 686": "OE1" <-> "OE2" Residue "A ASP 694": "OD1" <-> "OD2" Residue "A TYR 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 717": "OE1" <-> "OE2" Residue "A TYR 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 733": "OE1" <-> "OE2" Residue "A GLU 736": "OE1" <-> "OE2" Residue "A GLU 740": "OE1" <-> "OE2" Residue "A ARG 785": "NH1" <-> "NH2" Residue "A ARG 786": "NH1" <-> "NH2" Residue "A GLU 801": "OE1" <-> "OE2" Residue "A ASP 833": "OD1" <-> "OD2" Residue "A GLU 846": "OE1" <-> "OE2" Residue "A ARG 871": "NH1" <-> "NH2" Residue "A ARG 874": "NH1" <-> "NH2" Residue "A GLU 882": "OE1" <-> "OE2" Residue "A ASP 919": "OD1" <-> "OD2" Residue "A ASP 922": "OD1" <-> "OD2" Residue "A ARG 940": "NH1" <-> "NH2" Residue "B PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 422": "NH1" <-> "NH2" Residue "B ARG 424": "NH1" <-> "NH2" Residue "B ASP 436": "OD1" <-> "OD2" Residue "B PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 482": "NH1" <-> "NH2" Residue "B TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 496": "OD1" <-> "OD2" Residue "B PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 534": "NH1" <-> "NH2" Residue "B ARG 538": "NH1" <-> "NH2" Residue "B ARG 542": "NH1" <-> "NH2" Residue "B PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 597": "NH1" <-> "NH2" Residue "B TYR 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 647": "OE1" <-> "OE2" Residue "B ARG 650": "NH1" <-> "NH2" Residue "B GLU 671": "OE1" <-> "OE2" Residue "B ARG 672": "NH1" <-> "NH2" Residue "B ARG 679": "NH1" <-> "NH2" Residue "B ARG 705": "NH1" <-> "NH2" Residue "B GLU 717": "OE1" <-> "OE2" Residue "B GLU 731": "OE1" <-> "OE2" Residue "B GLU 733": "OE1" <-> "OE2" Residue "B GLU 754": "OE1" <-> "OE2" Residue "B ARG 755": "NH1" <-> "NH2" Residue "B GLU 781": "OE1" <-> "OE2" Residue "B ARG 785": "NH1" <-> "NH2" Residue "B ARG 786": "NH1" <-> "NH2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B ARG 822": "NH1" <-> "NH2" Residue "B PHE 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 852": "OD1" <-> "OD2" Residue "B ARG 871": "NH1" <-> "NH2" Residue "B PHE 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 922": "OD1" <-> "OD2" Residue "B GLU 937": "OE1" <-> "OE2" Residue "B ARG 940": "NH1" <-> "NH2" Residue "B PHE 943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 422": "NH1" <-> "NH2" Residue "C GLU 423": "OE1" <-> "OE2" Residue "C ARG 424": "NH1" <-> "NH2" Residue "C ASP 479": "OD1" <-> "OD2" Residue "C GLU 488": "OE1" <-> "OE2" Residue "C ARG 534": "NH1" <-> "NH2" Residue "C ARG 538": "NH1" <-> "NH2" Residue "C GLU 543": "OE1" <-> "OE2" Residue "C ARG 562": "NH1" <-> "NH2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C ARG 597": "NH1" <-> "NH2" Residue "C GLU 614": "OE1" <-> "OE2" Residue "C PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 643": "OD1" <-> "OD2" Residue "C GLU 647": "OE1" <-> "OE2" Residue "C ARG 650": "NH1" <-> "NH2" Residue "C ARG 672": "NH1" <-> "NH2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C GLU 686": "OE1" <-> "OE2" Residue "C GLU 706": "OE1" <-> "OE2" Residue "C ARG 721": "NH1" <-> "NH2" Residue "C GLU 731": "OE1" <-> "OE2" Residue "C GLU 733": "OE1" <-> "OE2" Residue "C ARG 755": "NH1" <-> "NH2" Residue "C ASP 758": "OD1" <-> "OD2" Residue "C ARG 786": "NH1" <-> "NH2" Residue "C ASP 791": "OD1" <-> "OD2" Residue "C GLU 808": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C ARG 871": "NH1" <-> "NH2" Residue "C ARG 874": "NH1" <-> "NH2" Residue "C GLU 882": "OE1" <-> "OE2" Residue "C GLU 897": "OE1" <-> "OE2" Residue "C GLU 915": "OE1" <-> "OE2" Residue "C ASP 919": "OD1" <-> "OD2" Residue "C GLU 929": "OE1" <-> "OE2" Residue "C PHE 943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 422": "NH1" <-> "NH2" Residue "D ARG 424": "NH1" <-> "NH2" Residue "D GLU 454": "OE1" <-> "OE2" Residue "D ASP 463": "OD1" <-> "OD2" Residue "D ASP 490": "OD1" <-> "OD2" Residue "D TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 534": "NH1" <-> "NH2" Residue "D ARG 538": "NH1" <-> "NH2" Residue "D TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 557": "OE1" <-> "OE2" Residue "D ARG 597": "NH1" <-> "NH2" Residue "D GLU 609": "OE1" <-> "OE2" Residue "D ASP 621": "OD1" <-> "OD2" Residue "D ASP 625": "OD1" <-> "OD2" Residue "D ARG 650": "NH1" <-> "NH2" Residue "D GLU 665": "OE1" <-> "OE2" Residue "D ARG 672": "NH1" <-> "NH2" Residue "D TYR 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 679": "NH1" <-> "NH2" Residue "D GLU 686": "OE1" <-> "OE2" Residue "D ARG 705": "NH1" <-> "NH2" Residue "D GLU 706": "OE1" <-> "OE2" Residue "D GLU 717": "OE1" <-> "OE2" Residue "D ARG 721": "NH1" <-> "NH2" Residue "D ARG 755": "NH1" <-> "NH2" Residue "D ASP 758": "OD1" <-> "OD2" Residue "D GLU 781": "OE1" <-> "OE2" Residue "D ARG 785": "NH1" <-> "NH2" Residue "D ARG 822": "NH1" <-> "NH2" Residue "D ASP 852": "OD1" <-> "OD2" Residue "D ARG 871": "NH1" <-> "NH2" Residue "D GLU 915": "OE1" <-> "OE2" Residue "D ARG 940": "NH1" <-> "NH2" Residue "D GLU 941": "OE1" <-> "OE2" Residue "D PHE 943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 419": "OE1" <-> "OE2" Residue "E GLU 440": "OE1" <-> "OE2" Residue "E GLU 454": "OE1" <-> "OE2" Residue "E ARG 459": "NH1" <-> "NH2" Residue "E ARG 482": "NH1" <-> "NH2" Residue "E GLU 488": "OE1" <-> "OE2" Residue "E ASP 490": "OD1" <-> "OD2" Residue "E ASP 496": "OD1" <-> "OD2" Residue "E ARG 511": "NH1" <-> "NH2" Residue "E ARG 534": "NH1" <-> "NH2" Residue "E ARG 538": "NH1" <-> "NH2" Residue "E ARG 597": "NH1" <-> "NH2" Residue "E GLU 609": "OE1" <-> "OE2" Residue "E GLU 614": "OE1" <-> "OE2" Residue "E TYR 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 650": "NH1" <-> "NH2" Residue "E ARG 672": "NH1" <-> "NH2" Residue "E ARG 679": "NH1" <-> "NH2" Residue "E ARG 705": "NH1" <-> "NH2" Residue "E GLU 706": "OE1" <-> "OE2" Residue "E GLU 731": "OE1" <-> "OE2" Residue "E ARG 755": "NH1" <-> "NH2" Residue "E ARG 785": "NH1" <-> "NH2" Residue "E ARG 786": "NH1" <-> "NH2" Residue "E GLU 801": "OE1" <-> "OE2" Residue "E GLU 808": "OE1" <-> "OE2" Residue "E ARG 871": "NH1" <-> "NH2" Residue "E GLU 915": "OE1" <-> "OE2" Residue "E PHE 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 922": "OD1" <-> "OD2" Residue "E GLU 929": "OE1" <-> "OE2" Residue "F ARG 422": "NH1" <-> "NH2" Residue "F GLU 427": "OE1" <-> "OE2" Residue "F ASP 436": "OD1" <-> "OD2" Residue "F ARG 482": "NH1" <-> "NH2" Residue "F GLU 495": "OE1" <-> "OE2" Residue "F GLU 503": "OE1" <-> "OE2" Residue "F ARG 511": "NH1" <-> "NH2" Residue "F ARG 534": "NH1" <-> "NH2" Residue "F ARG 538": "NH1" <-> "NH2" Residue "F GLU 557": "OE1" <-> "OE2" Residue "F ARG 562": "NH1" <-> "NH2" Residue "F TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 609": "OE1" <-> "OE2" Residue "F ASP 621": "OD1" <-> "OD2" Residue "F ASP 625": "OD1" <-> "OD2" Residue "F PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 643": "OD1" <-> "OD2" Residue "F ARG 650": "NH1" <-> "NH2" Residue "F ASP 651": "OD1" <-> "OD2" Residue "F ARG 652": "NH1" <-> "NH2" Residue "F ARG 672": "NH1" <-> "NH2" Residue "F ARG 679": "NH1" <-> "NH2" Residue "F ARG 710": "NH1" <-> "NH2" Residue "F GLU 736": "OE1" <-> "OE2" Residue "F PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 754": "OE1" <-> "OE2" Residue "F ASP 758": "OD1" <-> "OD2" Residue "F PHE 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 785": "NH1" <-> "NH2" Residue "F ARG 786": "NH1" <-> "NH2" Residue "F GLU 808": "OE1" <-> "OE2" Residue "F GLU 812": "OE1" <-> "OE2" Residue "F ARG 822": "NH1" <-> "NH2" Residue "F PHE 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 940": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24547 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4009 Classifications: {'peptide': 526} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 24, 'TRANS': 501} Chain breaks: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4041 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 24, 'TRANS': 495} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 4085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4085 Classifications: {'peptide': 526} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 23, 'TRANS': 502} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 4098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4098 Classifications: {'peptide': 525} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 500} Chain breaks: 1 Chain: "E" Number of atoms: 4073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4073 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 24, 'TRANS': 499} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "F" Number of atoms: 3999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 3999 Classifications: {'peptide': 516} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 491} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "G" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.03, per 1000 atoms: 0.53 Number of scatterers: 24547 At special positions: 0 Unit cell: (127.65, 138, 131.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 120 16.00 P 16 15.00 Mg 4 11.99 O 4661 8.00 N 4205 7.00 C 15541 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.09 Conformation dependent library (CDL) restraints added in 4.5 seconds 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5844 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 24 sheets defined 42.4% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.57 Creating SS restraints... Processing helix chain 'A' and resid 417 through 427 removed outlier: 3.641A pdb=" N PHE A 421 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.538A pdb=" N LEU A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 467 removed outlier: 3.643A pdb=" N THR A 458 " --> pdb=" O GLU A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 490 Processing helix chain 'A' and resid 495 through 511 Processing helix chain 'A' and resid 531 through 539 Processing helix chain 'A' and resid 555 through 557 No H-bonds generated for 'chain 'A' and resid 555 through 557' Processing helix chain 'A' and resid 572 through 578 removed outlier: 4.555A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 611 removed outlier: 4.174A pdb=" N GLU A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 647 through 650 No H-bonds generated for 'chain 'A' and resid 647 through 650' Processing helix chain 'A' and resid 663 through 672 Processing helix chain 'A' and resid 674 through 682 Processing helix chain 'A' and resid 693 through 702 Processing helix chain 'A' and resid 710 through 729 removed outlier: 3.614A pdb=" N LYS A 726 " --> pdb=" O LYS A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 746 removed outlier: 4.090A pdb=" N VAL A 746 " --> pdb=" O GLN A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 827 Processing helix chain 'A' and resid 853 through 869 removed outlier: 5.225A pdb=" N CYS A 858 " --> pdb=" O SER A 855 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET A 869 " --> pdb=" O SER A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 904 Processing helix chain 'A' and resid 914 through 921 removed outlier: 4.915A pdb=" N LYS A 918 " --> pdb=" O GLU A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 946 Processing helix chain 'B' and resid 423 through 426 No H-bonds generated for 'chain 'B' and resid 423 through 426' Processing helix chain 'B' and resid 432 through 446 Processing helix chain 'B' and resid 453 through 467 Processing helix chain 'B' and resid 480 through 490 removed outlier: 4.020A pdb=" N ASP B 490 " --> pdb=" O VAL B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 510 Processing helix chain 'B' and resid 532 through 540 Processing helix chain 'B' and resid 555 through 559 removed outlier: 3.525A pdb=" N LYS B 559 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 580 Processing helix chain 'B' and resid 603 through 610 Processing helix chain 'B' and resid 647 through 652 removed outlier: 3.853A pdb=" N ARG B 652 " --> pdb=" O PRO B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 672 Processing helix chain 'B' and resid 674 through 682 Processing helix chain 'B' and resid 693 through 702 Processing helix chain 'B' and resid 710 through 728 Processing helix chain 'B' and resid 743 through 746 No H-bonds generated for 'chain 'B' and resid 743 through 746' Processing helix chain 'B' and resid 808 through 828 removed outlier: 3.762A pdb=" N GLU B 812 " --> pdb=" O GLU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 837 No H-bonds generated for 'chain 'B' and resid 834 through 837' Processing helix chain 'B' and resid 850 through 869 Proline residue: B 854 - end of helix removed outlier: 5.796A pdb=" N GLY B 857 " --> pdb=" O GLY B 853 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N CYS B 858 " --> pdb=" O PRO B 854 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N THR B 859 " --> pdb=" O SER B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 904 Processing helix chain 'B' and resid 914 through 920 removed outlier: 4.815A pdb=" N LYS B 918 " --> pdb=" O GLU B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 945 Processing helix chain 'C' and resid 417 through 427 removed outlier: 4.485A pdb=" N GLU C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 447 removed outlier: 4.056A pdb=" N LEU C 447 " --> pdb=" O SER C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 467 Processing helix chain 'C' and resid 480 through 488 Processing helix chain 'C' and resid 495 through 510 Processing helix chain 'C' and resid 531 through 540 removed outlier: 4.023A pdb=" N SER C 535 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 559 removed outlier: 3.592A pdb=" N LYS C 559 " --> pdb=" O ALA C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 580 Processing helix chain 'C' and resid 603 through 610 Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 647 through 652 Processing helix chain 'C' and resid 663 through 672 Processing helix chain 'C' and resid 674 through 682 Processing helix chain 'C' and resid 693 through 703 Processing helix chain 'C' and resid 710 through 728 removed outlier: 3.551A pdb=" N LYS C 726 " --> pdb=" O LYS C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 746 Processing helix chain 'C' and resid 808 through 824 Processing helix chain 'C' and resid 853 through 869 removed outlier: 3.640A pdb=" N ALA C 856 " --> pdb=" O GLY C 853 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N CYS C 858 " --> pdb=" O SER C 855 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET C 869 " --> pdb=" O SER C 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 904 Processing helix chain 'C' and resid 914 through 921 removed outlier: 4.926A pdb=" N LYS C 918 " --> pdb=" O GLU C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 946 Processing helix chain 'D' and resid 418 through 426 Processing helix chain 'D' and resid 432 through 447 Processing helix chain 'D' and resid 453 through 466 removed outlier: 3.710A pdb=" N VAL D 457 " --> pdb=" O SER D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 488 Processing helix chain 'D' and resid 495 through 511 removed outlier: 3.803A pdb=" N ARG D 500 " --> pdb=" O ASP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 540 removed outlier: 3.528A pdb=" N LEU D 540 " --> pdb=" O ALA D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 559 removed outlier: 3.512A pdb=" N LYS D 559 " --> pdb=" O ALA D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 580 Processing helix chain 'D' and resid 592 through 594 No H-bonds generated for 'chain 'D' and resid 592 through 594' Processing helix chain 'D' and resid 603 through 610 Processing helix chain 'D' and resid 642 through 644 No H-bonds generated for 'chain 'D' and resid 642 through 644' Processing helix chain 'D' and resid 647 through 652 Processing helix chain 'D' and resid 663 through 672 Processing helix chain 'D' and resid 674 through 682 Processing helix chain 'D' and resid 693 through 703 Processing helix chain 'D' and resid 710 through 728 Processing helix chain 'D' and resid 741 through 744 Processing helix chain 'D' and resid 808 through 828 Processing helix chain 'D' and resid 834 through 837 No H-bonds generated for 'chain 'D' and resid 834 through 837' Processing helix chain 'D' and resid 854 through 869 removed outlier: 5.041A pdb=" N CYS D 858 " --> pdb=" O SER D 855 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET D 869 " --> pdb=" O SER D 866 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 904 Processing helix chain 'D' and resid 914 through 921 removed outlier: 3.870A pdb=" N LYS D 917 " --> pdb=" O ALA D 914 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LYS D 918 " --> pdb=" O GLU D 915 " (cutoff:3.500A) Processing helix chain 'D' and resid 939 through 946 Processing helix chain 'E' and resid 418 through 424 Processing helix chain 'E' and resid 432 through 447 Processing helix chain 'E' and resid 453 through 466 Processing helix chain 'E' and resid 480 through 490 removed outlier: 3.647A pdb=" N ASP E 490 " --> pdb=" O VAL E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 510 Processing helix chain 'E' and resid 529 through 540 Processing helix chain 'E' and resid 555 through 559 removed outlier: 3.557A pdb=" N LYS E 559 " --> pdb=" O ALA E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 580 Processing helix chain 'E' and resid 592 through 594 No H-bonds generated for 'chain 'E' and resid 592 through 594' Processing helix chain 'E' and resid 604 through 610 Processing helix chain 'E' and resid 647 through 652 Processing helix chain 'E' and resid 663 through 672 removed outlier: 3.547A pdb=" N ALA E 668 " --> pdb=" O GLN E 664 " (cutoff:3.500A) Processing helix chain 'E' and resid 674 through 682 Processing helix chain 'E' and resid 693 through 702 Processing helix chain 'E' and resid 710 through 729 removed outlier: 3.562A pdb=" N LYS E 714 " --> pdb=" O ARG E 710 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS E 726 " --> pdb=" O LYS E 722 " (cutoff:3.500A) Processing helix chain 'E' and resid 743 through 746 No H-bonds generated for 'chain 'E' and resid 743 through 746' Processing helix chain 'E' and resid 808 through 827 Processing helix chain 'E' and resid 854 through 869 removed outlier: 3.524A pdb=" N GLY E 857 " --> pdb=" O PRO E 854 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N CYS E 858 " --> pdb=" O SER E 855 " (cutoff:3.500A) Processing helix chain 'E' and resid 895 through 904 Processing helix chain 'E' and resid 914 through 922 removed outlier: 3.652A pdb=" N LYS E 917 " --> pdb=" O ALA E 914 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LYS E 918 " --> pdb=" O GLU E 915 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR E 921 " --> pdb=" O LYS E 918 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP E 922 " --> pdb=" O ASP E 919 " (cutoff:3.500A) Processing helix chain 'E' and resid 939 through 946 Processing helix chain 'F' and resid 420 through 427 Processing helix chain 'F' and resid 432 through 446 Processing helix chain 'F' and resid 453 through 467 removed outlier: 3.873A pdb=" N THR F 458 " --> pdb=" O GLU F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 490 Processing helix chain 'F' and resid 495 through 511 Processing helix chain 'F' and resid 531 through 540 Processing helix chain 'F' and resid 572 through 580 Processing helix chain 'F' and resid 592 through 594 No H-bonds generated for 'chain 'F' and resid 592 through 594' Processing helix chain 'F' and resid 604 through 611 Processing helix chain 'F' and resid 613 through 616 No H-bonds generated for 'chain 'F' and resid 613 through 616' Processing helix chain 'F' and resid 647 through 652 removed outlier: 3.633A pdb=" N ARG F 652 " --> pdb=" O PRO F 648 " (cutoff:3.500A) Processing helix chain 'F' and resid 663 through 672 removed outlier: 3.730A pdb=" N ALA F 668 " --> pdb=" O GLN F 664 " (cutoff:3.500A) Processing helix chain 'F' and resid 674 through 681 Processing helix chain 'F' and resid 693 through 702 Processing helix chain 'F' and resid 710 through 728 Processing helix chain 'F' and resid 808 through 828 Processing helix chain 'F' and resid 834 through 837 No H-bonds generated for 'chain 'F' and resid 834 through 837' Processing helix chain 'F' and resid 853 through 868 removed outlier: 3.501A pdb=" N GLY F 857 " --> pdb=" O PRO F 854 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N CYS F 858 " --> pdb=" O SER F 855 " (cutoff:3.500A) Processing helix chain 'F' and resid 895 through 904 Processing helix chain 'F' and resid 914 through 921 removed outlier: 3.740A pdb=" N LYS F 917 " --> pdb=" O ALA F 914 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LYS F 918 " --> pdb=" O GLU F 915 " (cutoff:3.500A) Processing helix chain 'F' and resid 939 through 946 Processing sheet with id= A, first strand: chain 'A' and resid 654 through 657 removed outlier: 6.267A pdb=" N ILE A 587 " --> pdb=" O ILE A 636 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N THR A 638 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE A 589 " --> pdb=" O THR A 638 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 764 through 771 Processing sheet with id= C, first strand: chain 'A' and resid 877 through 879 removed outlier: 6.505A pdb=" N CYS A 909 " --> pdb=" O ALA A 878 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLU A 932 " --> pdb=" O ILE A 910 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU A 912 " --> pdb=" O GLU A 932 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N HIS A 934 " --> pdb=" O LEU A 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 654 through 657 removed outlier: 6.368A pdb=" N PHE B 635 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N PHE B 521 " --> pdb=" O PHE B 635 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N CYS B 637 " --> pdb=" O PHE B 521 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 765 through 769 Processing sheet with id= F, first strand: chain 'B' and resid 781 through 784 Processing sheet with id= G, first strand: chain 'B' and resid 877 through 879 removed outlier: 6.503A pdb=" N CYS B 909 " --> pdb=" O ALA B 878 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU B 932 " --> pdb=" O ILE B 910 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU B 912 " --> pdb=" O GLU B 932 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N HIS B 934 " --> pdb=" O LEU B 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 654 through 657 removed outlier: 6.441A pdb=" N GLU C 543 " --> pdb=" O LEU C 586 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEU C 588 " --> pdb=" O GLU C 543 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE C 545 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ASP C 590 " --> pdb=" O PHE C 545 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N PHE C 547 " --> pdb=" O ASP C 590 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 765 through 767 Processing sheet with id= J, first strand: chain 'C' and resid 799 through 803 Processing sheet with id= K, first strand: chain 'C' and resid 877 through 879 removed outlier: 6.429A pdb=" N CYS C 909 " --> pdb=" O ALA C 878 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU C 932 " --> pdb=" O ILE C 910 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU C 912 " --> pdb=" O GLU C 932 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N HIS C 934 " --> pdb=" O LEU C 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'D' and resid 654 through 658 removed outlier: 6.117A pdb=" N PHE D 635 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N PHE D 521 " --> pdb=" O PHE D 635 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N CYS D 637 " --> pdb=" O PHE D 521 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N GLY D 523 " --> pdb=" O CYS D 637 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA D 639 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLU D 543 " --> pdb=" O LEU D 586 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU D 588 " --> pdb=" O GLU D 543 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE D 545 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ASP D 590 " --> pdb=" O PHE D 545 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N PHE D 547 " --> pdb=" O ASP D 590 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 765 through 770 Processing sheet with id= N, first strand: chain 'D' and resid 781 through 784 removed outlier: 6.491A pdb=" N SER D 799 " --> pdb=" O ILE D 840 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N LEU D 842 " --> pdb=" O SER D 799 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU D 801 " --> pdb=" O LEU D 842 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N VAL D 844 " --> pdb=" O GLU D 801 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR D 803 " --> pdb=" O VAL D 844 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 877 through 879 removed outlier: 6.833A pdb=" N CYS D 909 " --> pdb=" O ALA D 878 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLU D 932 " --> pdb=" O ILE D 910 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEU D 912 " --> pdb=" O GLU D 932 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N HIS D 934 " --> pdb=" O LEU D 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'E' and resid 635 through 639 removed outlier: 6.436A pdb=" N GLU E 654 " --> pdb=" O CYS E 520 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N TYR E 522 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE E 656 " --> pdb=" O TYR E 522 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 545 through 548 Processing sheet with id= R, first strand: chain 'E' and resid 689 through 691 removed outlier: 6.826A pdb=" N VAL E 735 " --> pdb=" O LYS E 690 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'E' and resid 764 through 771 removed outlier: 6.171A pdb=" N SER E 799 " --> pdb=" O ILE E 840 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LEU E 842 " --> pdb=" O SER E 799 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLU E 801 " --> pdb=" O LEU E 842 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 877 through 879 removed outlier: 6.474A pdb=" N CYS E 909 " --> pdb=" O ALA E 878 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLU E 932 " --> pdb=" O ILE E 910 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LEU E 912 " --> pdb=" O GLU E 932 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N HIS E 934 " --> pdb=" O LEU E 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'F' and resid 653 through 658 removed outlier: 6.428A pdb=" N ILE F 518 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE F 656 " --> pdb=" O ILE F 518 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N CYS F 520 " --> pdb=" O ILE F 656 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL F 658 " --> pdb=" O CYS F 520 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR F 522 " --> pdb=" O VAL F 658 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU F 519 " --> pdb=" O PHE F 635 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY F 523 " --> pdb=" O ALA F 639 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP F 590 " --> pdb=" O PHE F 547 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 689 through 691 removed outlier: 7.389A pdb=" N VAL F 735 " --> pdb=" O LYS F 690 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'F' and resid 764 through 770 removed outlier: 6.236A pdb=" N SER F 799 " --> pdb=" O ILE F 840 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LEU F 842 " --> pdb=" O SER F 799 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLU F 801 " --> pdb=" O LEU F 842 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 877 through 879 removed outlier: 6.568A pdb=" N CYS F 909 " --> pdb=" O ALA F 878 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLU F 932 " --> pdb=" O ILE F 910 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU F 912 " --> pdb=" O GLU F 932 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N HIS F 934 " --> pdb=" O LEU F 912 " (cutoff:3.500A) No H-bonds generated for sheet with id= X 906 hydrogen bonds defined for protein. 2409 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: 7.25 Time building geometry restraints manager: 10.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8093 1.34 - 1.46: 4056 1.46 - 1.58: 12615 1.58 - 1.69: 26 1.69 - 1.81: 198 Bond restraints: 24988 Sorted by residual: bond pdb=" C4 ATP A1000 " pdb=" C5 ATP A1000 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.74e+01 bond pdb=" C4 ATP D1001 " pdb=" C5 ATP D1001 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.52e+01 bond pdb=" C4 ATP D1002 " pdb=" C5 ATP D1002 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.32e+01 bond pdb=" C4 ATP B1000 " pdb=" C5 ATP B1000 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.24e+01 bond pdb=" C5 ATP A1000 " pdb=" C6 ATP A1000 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.34e+01 ... (remaining 24983 not shown) Histogram of bond angle deviations from ideal: 98.92 - 106.41: 737 106.41 - 113.90: 14594 113.90 - 121.40: 12707 121.40 - 128.89: 5688 128.89 - 136.38: 131 Bond angle restraints: 33857 Sorted by residual: angle pdb=" PB ATP D1002 " pdb=" O3B ATP D1002 " pdb=" PG ATP D1002 " ideal model delta sigma weight residual 139.87 119.95 19.92 1.00e+00 1.00e+00 3.97e+02 angle pdb=" PB ATP B1000 " pdb=" O3B ATP B1000 " pdb=" PG ATP B1000 " ideal model delta sigma weight residual 139.87 121.21 18.66 1.00e+00 1.00e+00 3.48e+02 angle pdb=" PA ATP B1000 " pdb=" O3A ATP B1000 " pdb=" PB ATP B1000 " ideal model delta sigma weight residual 136.83 118.72 18.11 1.00e+00 1.00e+00 3.28e+02 angle pdb=" PB ATP A1000 " pdb=" O3B ATP A1000 " pdb=" PG ATP A1000 " ideal model delta sigma weight residual 139.87 123.37 16.50 1.00e+00 1.00e+00 2.72e+02 angle pdb=" PB ATP D1001 " pdb=" O3B ATP D1001 " pdb=" PG ATP D1001 " ideal model delta sigma weight residual 139.87 123.51 16.36 1.00e+00 1.00e+00 2.68e+02 ... (remaining 33852 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 13688 17.99 - 35.98: 1291 35.98 - 53.97: 213 53.97 - 71.97: 67 71.97 - 89.96: 25 Dihedral angle restraints: 15284 sinusoidal: 6207 harmonic: 9077 Sorted by residual: dihedral pdb=" CA GLY A 571 " pdb=" C GLY A 571 " pdb=" N LYS A 572 " pdb=" CA LYS A 572 " ideal model delta harmonic sigma weight residual -180.00 -152.85 -27.15 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA ARG E 874 " pdb=" C ARG E 874 " pdb=" N GLN E 875 " pdb=" CA GLN E 875 " ideal model delta harmonic sigma weight residual -180.00 -154.47 -25.53 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA ARG F 874 " pdb=" C ARG F 874 " pdb=" N GLN F 875 " pdb=" CA GLN F 875 " ideal model delta harmonic sigma weight residual -180.00 -156.82 -23.18 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 15281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2356 0.037 - 0.073: 1102 0.073 - 0.110: 340 0.110 - 0.147: 89 0.147 - 0.183: 11 Chirality restraints: 3898 Sorted by residual: chirality pdb=" CB ILE A 573 " pdb=" CA ILE A 573 " pdb=" CG1 ILE A 573 " pdb=" CG2 ILE A 573 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CA PRO E 585 " pdb=" N PRO E 585 " pdb=" C PRO E 585 " pdb=" CB PRO E 585 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.37e-01 chirality pdb=" CA ASN B 584 " pdb=" N ASN B 584 " pdb=" C ASN B 584 " pdb=" CB ASN B 584 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.07e-01 ... (remaining 3895 not shown) Planarity restraints: 4327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 430 " -0.044 5.00e-02 4.00e+02 6.67e-02 7.12e+00 pdb=" N PRO B 431 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 431 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 431 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 844 " -0.041 5.00e-02 4.00e+02 6.11e-02 5.98e+00 pdb=" N PRO D 845 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO D 845 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 845 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 761 " -0.037 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO E 762 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO E 762 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 762 " -0.031 5.00e-02 4.00e+02 ... (remaining 4324 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 163 2.53 - 3.12: 18903 3.12 - 3.71: 37748 3.71 - 4.31: 54762 4.31 - 4.90: 90624 Nonbonded interactions: 202200 Sorted by model distance: nonbonded pdb=" OG1 THR D 530 " pdb="MG MG D1003 " model vdw 1.934 2.170 nonbonded pdb=" OG1 THR C 530 " pdb="MG MG C1001 " model vdw 1.937 2.170 nonbonded pdb=" O2B ATP A1000 " pdb="MG MG A1001 " model vdw 1.956 2.170 nonbonded pdb=" OG1 THR B 530 " pdb="MG MG B1001 " model vdw 1.980 2.170 nonbonded pdb="MG MG C1001 " pdb=" O2G ATP D1001 " model vdw 1.999 2.170 ... (remaining 202195 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 420 and (name N or name CA or name C or name O or name CB \ )) or resid 421 through 459 or (resid 460 and (name N or name CA or name C or n \ ame O or name CB )) or resid 461 through 497 or (resid 498 and (name N or name C \ A or name C or name O or name CB )) or resid 499 or (resid 500 and (name N or na \ me CA or name C or name O or name CB )) or resid 501 through 510 or (resid 511 a \ nd (name N or name CA or name C or name O or name CB )) or resid 512 through 514 \ or (resid 515 and (name N or name CA or name C or name O or name CB )) or resid \ 516 through 589 or (resid 590 and (name N or name CA or name C or name O or nam \ e CB )) or resid 591 through 595 or resid 603 through 720 or (resid 721 and (nam \ e N or name CA or name C or name O or name CB )) or resid 722 through 783 or res \ id 796 or (resid 797 and (name N or name CA or name C or name O or name CB )) or \ resid 798 through 811 or (resid 812 and (name N or name CA or name C or name O \ or name CB )) or resid 813 through 821 or (resid 822 through 823 and (name N or \ name CA or name C or name O or name CB )) or resid 824 through 827 or (resid 832 \ and (name N or name CA or name C or name O or name CB )) or resid 833 through 9 \ 28 or (resid 929 and (name N or name CA or name C or name O or name CB )) or res \ id 930 through 947)) selection = (chain 'B' and ((resid 420 and (name N or name CA or name C or name O or name CB \ )) or resid 421 through 433 or (resid 434 and (name N or name CA or name C or n \ ame O or name CB )) or resid 435 through 446 or (resid 447 through 448 and (name \ N or name CA or name C or name O or name CB )) or resid 449 or (resid 450 throu \ gh 452 and (name N or name CA or name C or name O or name CB )) or resid 453 thr \ ough 459 or (resid 460 and (name N or name CA or name C or name O or name CB )) \ or resid 461 through 463 or (resid 464 and (name N or name CA or name C or name \ O or name CB )) or resid 465 through 489 or (resid 490 and (name N or name CA or \ name C or name O or name CB )) or resid 491 through 497 or (resid 498 and (name \ N or name CA or name C or name O or name CB )) or resid 499 through 502 or (res \ id 503 and (name N or name CA or name C or name O or name CB )) or resid 504 thr \ ough 510 or (resid 511 and (name N or name CA or name C or name O or name CB )) \ or resid 512 through 514 or (resid 515 and (name N or name CA or name C or name \ O or name CB )) or resid 516 through 556 or (resid 557 and (name N or name CA or \ name C or name O or name CB )) or resid 558 through 562 or (resid 563 and (name \ N or name CA or name C or name O or name CB )) or resid 564 through 571 or (res \ id 572 and (name N or name CA or name C or name O or name CB )) or resid 573 thr \ ough 589 or (resid 590 and (name N or name CA or name C or name O or name CB )) \ or resid 591 through 595 or resid 603 or (resid 604 and (name N or name CA or na \ me C or name O or name CB )) or resid 605 through 611 or (resid 612 and (name N \ or name CA or name C or name O or name CB )) or resid 613 or (resid 614 and (nam \ e N or name CA or name C or name O or name CB )) or resid 615 through 619 or (re \ sid 620 and (name N or name CA or name C or name O or name CB )) or resid 621 th \ rough 720 or (resid 721 and (name N or name CA or name C or name O or name CB )) \ or resid 722 through 753 or (resid 754 and (name N or name CA or name C or name \ O or name CB )) or resid 755 through 783 or resid 796 or (resid 797 and (name N \ or name CA or name C or name O or name CB )) or resid 798 through 821 or (resid \ 822 through 823 and (name N or name CA or name C or name O or name CB )) or res \ id 824 through 827 or (resid 832 and (name N or name CA or name C or name O or n \ ame CB )) or resid 833 through 947)) selection = (chain 'C' and ((resid 420 and (name N or name CA or name C or name O or name CB \ )) or resid 421 through 433 or (resid 434 and (name N or name CA or name C or n \ ame O or name CB )) or resid 435 through 446 or (resid 447 through 448 and (name \ N or name CA or name C or name O or name CB )) or resid 449 or (resid 450 throu \ gh 452 and (name N or name CA or name C or name O or name CB )) or resid 453 thr \ ough 459 or (resid 460 and (name N or name CA or name C or name O or name CB )) \ or resid 461 through 463 or (resid 464 and (name N or name CA or name C or name \ O or name CB )) or resid 465 through 489 or (resid 490 and (name N or name CA or \ name C or name O or name CB )) or resid 491 through 497 or (resid 498 and (name \ N or name CA or name C or name O or name CB )) or resid 499 or (resid 500 and ( \ name N or name CA or name C or name O or name CB )) or resid 501 through 502 or \ (resid 503 and (name N or name CA or name C or name O or name CB )) or resid 504 \ through 514 or (resid 515 and (name N or name CA or name C or name O or name CB \ )) or resid 516 through 556 or (resid 557 and (name N or name CA or name C or n \ ame O or name CB )) or resid 558 through 562 or (resid 563 and (name N or name C \ A or name C or name O or name CB )) or resid 564 through 571 or (resid 572 and ( \ name N or name CA or name C or name O or name CB )) or resid 573 through 589 or \ (resid 590 and (name N or name CA or name C or name O or name CB )) or resid 591 \ through 595 or resid 603 or (resid 604 and (name N or name CA or name C or name \ O or name CB )) or resid 605 through 611 or (resid 612 and (name N or name CA o \ r name C or name O or name CB )) or resid 613 or (resid 614 and (name N or name \ CA or name C or name O or name CB )) or resid 615 through 619 or (resid 620 and \ (name N or name CA or name C or name O or name CB )) or resid 621 through 720 or \ (resid 721 and (name N or name CA or name C or name O or name CB )) or resid 72 \ 2 through 753 or (resid 754 and (name N or name CA or name C or name O or name C \ B )) or resid 755 through 783 or resid 796 or (resid 797 and (name N or name CA \ or name C or name O or name CB )) or resid 798 through 811 or (resid 812 and (na \ me N or name CA or name C or name O or name CB )) or resid 813 through 928 or (r \ esid 929 and (name N or name CA or name C or name O or name CB )) or resid 930 t \ hrough 947)) selection = (chain 'D' and ((resid 420 and (name N or name CA or name C or name O or name CB \ )) or resid 421 through 433 or (resid 434 and (name N or name CA or name C or n \ ame O or name CB )) or resid 435 through 446 or (resid 447 through 448 and (name \ N or name CA or name C or name O or name CB )) or resid 449 or (resid 450 throu \ gh 452 and (name N or name CA or name C or name O or name CB )) or resid 453 thr \ ough 459 or (resid 460 and (name N or name CA or name C or name O or name CB )) \ or resid 461 through 463 or (resid 464 and (name N or name CA or name C or name \ O or name CB )) or resid 465 through 489 or (resid 490 and (name N or name CA or \ name C or name O or name CB )) or resid 491 through 497 or (resid 498 and (name \ N or name CA or name C or name O or name CB )) or resid 499 or (resid 500 and ( \ name N or name CA or name C or name O or name CB )) or resid 501 through 502 or \ (resid 503 and (name N or name CA or name C or name O or name CB )) or resid 504 \ through 510 or (resid 511 and (name N or name CA or name C or name O or name CB \ )) or resid 512 through 514 or (resid 515 and (name N or name CA or name C or n \ ame O or name CB )) or resid 516 through 556 or (resid 557 and (name N or name C \ A or name C or name O or name CB )) or resid 558 through 562 or (resid 563 and ( \ name N or name CA or name C or name O or name CB )) or resid 564 through 571 or \ (resid 572 and (name N or name CA or name C or name O or name CB )) or resid 573 \ through 589 or (resid 590 and (name N or name CA or name C or name O or name CB \ )) or resid 591 through 595 or resid 603 or (resid 604 and (name N or name CA o \ r name C or name O or name CB )) or resid 605 through 611 or (resid 612 and (nam \ e N or name CA or name C or name O or name CB )) or resid 613 or (resid 614 and \ (name N or name CA or name C or name O or name CB )) or resid 615 through 619 or \ (resid 620 and (name N or name CA or name C or name O or name CB )) or resid 62 \ 1 through 720 or (resid 721 and (name N or name CA or name C or name O or name C \ B )) or resid 722 through 753 or (resid 754 and (name N or name CA or name C or \ name O or name CB )) or resid 755 through 783 or resid 796 or (resid 797 and (na \ me N or name CA or name C or name O or name CB )) or resid 798 through 811 or (r \ esid 812 and (name N or name CA or name C or name O or name CB )) or resid 813 t \ hrough 821 or (resid 822 through 823 and (name N or name CA or name C or name O \ or name CB )) or resid 824 through 827 or (resid 832 and (name N or name CA or n \ ame C or name O or name CB )) or resid 833 through 928 or (resid 929 and (name N \ or name CA or name C or name O or name CB )) or resid 930 through 947)) selection = (chain 'E' and ((resid 420 and (name N or name CA or name C or name O or name CB \ )) or resid 421 through 433 or (resid 434 and (name N or name CA or name C or n \ ame O or name CB )) or resid 435 through 446 or (resid 447 through 448 and (name \ N or name CA or name C or name O or name CB )) or resid 449 or (resid 450 throu \ gh 452 and (name N or name CA or name C or name O or name CB )) or resid 453 thr \ ough 459 or (resid 460 and (name N or name CA or name C or name O or name CB )) \ or resid 461 through 463 or (resid 464 and (name N or name CA or name C or name \ O or name CB )) or resid 465 through 489 or (resid 490 and (name N or name CA or \ name C or name O or name CB )) or resid 491 through 497 or (resid 498 and (name \ N or name CA or name C or name O or name CB )) or resid 499 or (resid 500 and ( \ name N or name CA or name C or name O or name CB )) or resid 501 through 502 or \ (resid 503 and (name N or name CA or name C or name O or name CB )) or resid 504 \ through 510 or (resid 511 and (name N or name CA or name C or name O or name CB \ )) or resid 512 through 514 or (resid 515 and (name N or name CA or name C or n \ ame O or name CB )) or resid 516 through 556 or (resid 557 and (name N or name C \ A or name C or name O or name CB )) or resid 558 through 562 or (resid 563 and ( \ name N or name CA or name C or name O or name CB )) or resid 564 through 571 or \ (resid 572 and (name N or name CA or name C or name O or name CB )) or resid 573 \ through 595 or resid 603 or (resid 604 and (name N or name CA or name C or name \ O or name CB )) or resid 605 through 611 or (resid 612 and (name N or name CA o \ r name C or name O or name CB )) or resid 613 or (resid 614 and (name N or name \ CA or name C or name O or name CB )) or resid 615 through 619 or (resid 620 and \ (name N or name CA or name C or name O or name CB )) or resid 621 through 720 or \ (resid 721 and (name N or name CA or name C or name O or name CB )) or resid 72 \ 2 through 753 or (resid 754 and (name N or name CA or name C or name O or name C \ B )) or resid 755 through 783 or resid 796 through 811 or (resid 812 and (name N \ or name CA or name C or name O or name CB )) or resid 813 through 821 or (resid \ 822 through 823 and (name N or name CA or name C or name O or name CB )) or res \ id 824 through 827 or (resid 832 and (name N or name CA or name C or name O or n \ ame CB )) or resid 833 through 928 or (resid 929 and (name N or name CA or name \ C or name O or name CB )) or resid 930 through 947)) selection = (chain 'F' and (resid 420 through 433 or (resid 434 and (name N or name CA or na \ me C or name O or name CB )) or resid 435 through 446 or (resid 447 through 448 \ and (name N or name CA or name C or name O or name CB )) or resid 449 or (resid \ 450 through 452 and (name N or name CA or name C or name O or name CB )) or resi \ d 453 through 463 or (resid 464 and (name N or name CA or name C or name O or na \ me CB )) or resid 465 through 489 or (resid 490 and (name N or name CA or name C \ or name O or name CB )) or resid 491 through 502 or (resid 503 and (name N or n \ ame CA or name C or name O or name CB )) or resid 504 through 510 or (resid 511 \ and (name N or name CA or name C or name O or name CB )) or resid 512 through 55 \ 6 or (resid 557 and (name N or name CA or name C or name O or name CB )) or resi \ d 558 through 562 or (resid 563 and (name N or name CA or name C or name O or na \ me CB )) or resid 564 through 571 or (resid 572 and (name N or name CA or name C \ or name O or name CB )) or resid 573 through 589 or (resid 590 and (name N or n \ ame CA or name C or name O or name CB )) or resid 591 through 603 or (resid 604 \ and (name N or name CA or name C or name O or name CB )) or resid 605 through 61 \ 1 or (resid 612 and (name N or name CA or name C or name O or name CB )) or resi \ d 613 or (resid 614 and (name N or name CA or name C or name O or name CB )) or \ resid 615 through 619 or (resid 620 and (name N or name CA or name C or name O o \ r name CB )) or resid 621 through 753 or (resid 754 and (name N or name CA or na \ me C or name O or name CB )) or resid 755 through 783 or resid 796 through 811 o \ r (resid 812 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 13 through 821 or (resid 822 through 823 and (name N or name CA or name C or nam \ e O or name CB )) or resid 824 through 827 or (resid 832 and (name N or name CA \ or name C or name O or name CB )) or resid 833 through 928 or (resid 929 and (na \ me N or name CA or name C or name O or name CB )) or resid 930 through 947)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.190 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: 2.390 Check model and map are aligned: 0.350 Set scattering table: 0.200 Process input model: 65.240 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 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 : 0.007 0.079 24988 Z= 0.450 Angle : 0.792 19.915 33857 Z= 0.499 Chirality : 0.046 0.183 3898 Planarity : 0.005 0.067 4327 Dihedral : 14.831 89.957 9440 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.08 % Allowed : 7.68 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.13), residues: 3109 helix: -0.76 (0.12), residues: 1389 sheet: -1.20 (0.24), residues: 403 loop : -2.66 (0.14), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 470 HIS 0.013 0.001 HIS D 841 PHE 0.020 0.002 PHE A 820 TYR 0.018 0.002 TYR E 939 ARG 0.008 0.001 ARG C 721 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 308 time to evaluate : 2.876 Fit side-chains revert: symmetry clash REVERT: B 552 MET cc_start: 0.9045 (ttm) cc_final: 0.8766 (ttp) REVERT: B 600 GLN cc_start: 0.6236 (mp10) cc_final: 0.6029 (mp10) REVERT: C 420 LYS cc_start: 0.8293 (ttpt) cc_final: 0.8085 (tttp) REVERT: E 681 LEU cc_start: 0.8848 (mm) cc_final: 0.8639 (mm) REVERT: E 810 MET cc_start: 0.8828 (tpt) cc_final: 0.8418 (tpt) REVERT: F 563 ARG cc_start: 0.7284 (mtp180) cc_final: 0.7014 (mtt90) outliers start: 2 outliers final: 1 residues processed: 309 average time/residue: 0.4393 time to fit residues: 200.1196 Evaluate side-chains 235 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 234 time to evaluate : 2.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 580 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 4.9990 chunk 236 optimal weight: 7.9990 chunk 131 optimal weight: 20.0000 chunk 80 optimal weight: 9.9990 chunk 159 optimal weight: 0.0870 chunk 126 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 94 optimal weight: 30.0000 chunk 148 optimal weight: 10.0000 chunk 182 optimal weight: 8.9990 chunk 283 optimal weight: 20.0000 overall best weight: 4.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 ASN A 491 HIS A 622 HIS B 433 HIS B 456 ASN ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 GLN B 839 HIS C 433 HIS ** C 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 711 ASN D 451 HIS D 456 ASN D 615 GLN D 841 HIS D 876 ASN D 934 HIS E 450 ASN E 456 ASN E 515 GLN E 575 GLN E 827 GLN E 839 HIS E 916 ASN ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 702 GLN F 743 GLN F 841 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24988 Z= 0.282 Angle : 0.581 8.044 33857 Z= 0.294 Chirality : 0.043 0.181 3898 Planarity : 0.005 0.061 4327 Dihedral : 8.042 82.191 3563 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.79 % Allowed : 11.75 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.14), residues: 3109 helix: 0.27 (0.13), residues: 1403 sheet: -0.68 (0.25), residues: 389 loop : -2.06 (0.15), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 470 HIS 0.009 0.001 HIS D 841 PHE 0.016 0.002 PHE A 820 TYR 0.017 0.001 TYR E 939 ARG 0.005 0.000 ARG B 482 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 252 time to evaluate : 2.886 Fit side-chains revert: symmetry clash REVERT: A 621 ASP cc_start: 0.7998 (t70) cc_final: 0.7744 (t0) REVERT: A 755 ARG cc_start: 0.6289 (mtm180) cc_final: 0.5774 (mtt180) REVERT: B 552 MET cc_start: 0.8997 (ttm) cc_final: 0.8705 (ttp) REVERT: B 600 GLN cc_start: 0.6417 (mp10) cc_final: 0.6184 (mp10) REVERT: B 756 MET cc_start: 0.8249 (ttm) cc_final: 0.8048 (ttm) REVERT: B 768 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8089 (pp) REVERT: C 420 LYS cc_start: 0.8303 (ttpt) cc_final: 0.8075 (tttp) REVERT: C 447 LEU cc_start: 0.8468 (pp) cc_final: 0.8205 (pp) REVERT: D 552 MET cc_start: 0.9268 (ttp) cc_final: 0.8953 (ttp) REVERT: F 562 ARG cc_start: 0.7648 (ttm110) cc_final: 0.7092 (mtm-85) REVERT: F 563 ARG cc_start: 0.7320 (mtp180) cc_final: 0.7094 (mtt90) REVERT: F 575 GLN cc_start: 0.8426 (mt0) cc_final: 0.7842 (mt0) REVERT: F 650 ARG cc_start: 0.7511 (mtp180) cc_final: 0.7106 (mtp180) outliers start: 47 outliers final: 31 residues processed: 283 average time/residue: 0.4009 time to fit residues: 173.3785 Evaluate side-chains 271 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 239 time to evaluate : 3.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 744 ASP Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 827 GLN Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 809 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 235 optimal weight: 8.9990 chunk 192 optimal weight: 20.0000 chunk 78 optimal weight: 2.9990 chunk 283 optimal weight: 5.9990 chunk 306 optimal weight: 3.9990 chunk 252 optimal weight: 6.9990 chunk 281 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN E 827 GLN ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24988 Z= 0.233 Angle : 0.544 8.071 33857 Z= 0.273 Chirality : 0.042 0.152 3898 Planarity : 0.005 0.062 4327 Dihedral : 7.797 84.594 3563 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.40 % Allowed : 13.31 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.15), residues: 3109 helix: 0.63 (0.14), residues: 1409 sheet: -0.36 (0.26), residues: 399 loop : -1.81 (0.16), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 470 HIS 0.004 0.001 HIS D 828 PHE 0.015 0.001 PHE A 820 TYR 0.015 0.001 TYR E 939 ARG 0.004 0.000 ARG F 511 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 258 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 554 ASP cc_start: 0.7533 (p0) cc_final: 0.7137 (t0) REVERT: A 766 MET cc_start: 0.8477 (ttp) cc_final: 0.8086 (ttp) REVERT: A 931 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8141 (pp) REVERT: B 552 MET cc_start: 0.8929 (ttm) cc_final: 0.8680 (ttp) REVERT: B 600 GLN cc_start: 0.6337 (mp10) cc_final: 0.6067 (mp10) REVERT: B 768 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8035 (pp) REVERT: C 420 LYS cc_start: 0.8274 (ttpt) cc_final: 0.8068 (tttp) REVERT: C 447 LEU cc_start: 0.8464 (pp) cc_final: 0.8166 (pp) REVERT: E 448 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8388 (mm) REVERT: E 655 MET cc_start: 0.8703 (mmm) cc_final: 0.8461 (mmm) REVERT: F 455 PHE cc_start: 0.6455 (t80) cc_final: 0.6169 (t80) REVERT: F 562 ARG cc_start: 0.7657 (ttm110) cc_final: 0.7111 (mtm-85) REVERT: F 575 GLN cc_start: 0.8483 (mt0) cc_final: 0.8038 (mt0) REVERT: F 650 ARG cc_start: 0.7397 (mtp180) cc_final: 0.7035 (mtp180) REVERT: F 705 ARG cc_start: 0.7927 (mmt90) cc_final: 0.7392 (mmt90) REVERT: F 852 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7323 (p0) outliers start: 63 outliers final: 40 residues processed: 300 average time/residue: 0.3973 time to fit residues: 182.3581 Evaluate side-chains 287 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 243 time to evaluate : 2.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 618 ASN Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 685 ASP Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 842 LEU Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 744 ASP Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 753 VAL Chi-restraints excluded: chain E residue 827 GLN Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 449 ASP Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 852 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 30.0000 chunk 213 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 190 optimal weight: 7.9990 chunk 284 optimal weight: 10.0000 chunk 301 optimal weight: 10.0000 chunk 148 optimal weight: 7.9990 chunk 269 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 HIS ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 827 GLN ** E 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 24988 Z= 0.442 Angle : 0.649 8.528 33857 Z= 0.326 Chirality : 0.046 0.185 3898 Planarity : 0.005 0.062 4327 Dihedral : 8.200 83.127 3563 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.46 % Allowed : 14.68 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.15), residues: 3109 helix: 0.49 (0.13), residues: 1407 sheet: -0.34 (0.26), residues: 405 loop : -1.76 (0.16), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 470 HIS 0.006 0.001 HIS D 828 PHE 0.024 0.002 PHE A 547 TYR 0.018 0.002 TYR E 939 ARG 0.005 0.001 ARG C 538 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 240 time to evaluate : 3.022 Fit side-chains revert: symmetry clash REVERT: A 554 ASP cc_start: 0.7589 (p0) cc_final: 0.7321 (t0) REVERT: A 778 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8650 (pp) REVERT: A 931 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8173 (pp) REVERT: B 552 MET cc_start: 0.8990 (ttm) cc_final: 0.8747 (ttp) REVERT: B 600 GLN cc_start: 0.6309 (mp10) cc_final: 0.6079 (mp10) REVERT: B 768 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8353 (pp) REVERT: B 778 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7235 (mt) REVERT: C 420 LYS cc_start: 0.8311 (ttpt) cc_final: 0.8088 (tttp) REVERT: C 447 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8135 (pp) REVERT: D 552 MET cc_start: 0.9268 (ttp) cc_final: 0.9015 (ttp) REVERT: E 448 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8628 (tp) REVERT: E 543 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7845 (mm-30) REVERT: E 781 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8456 (pt0) REVERT: E 810 MET cc_start: 0.8845 (tpt) cc_final: 0.8432 (tpt) REVERT: F 425 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8686 (mp) REVERT: F 562 ARG cc_start: 0.7653 (ttm110) cc_final: 0.7281 (mtm-85) REVERT: F 629 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7775 (t70) REVERT: F 650 ARG cc_start: 0.7407 (mtp180) cc_final: 0.7077 (mtp180) REVERT: F 852 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7443 (p0) REVERT: F 922 ASP cc_start: 0.8132 (p0) cc_final: 0.7912 (p0) outliers start: 91 outliers final: 58 residues processed: 305 average time/residue: 0.3750 time to fit residues: 175.7827 Evaluate side-chains 300 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 231 time to evaluate : 2.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 618 ASN Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 685 ASP Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 801 GLU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 882 GLU Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 753 VAL Chi-restraints excluded: chain E residue 781 GLU Chi-restraints excluded: chain E residue 827 GLN Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 449 ASP Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 531 SER Chi-restraints excluded: chain F residue 629 ASP Chi-restraints excluded: chain F residue 649 LEU Chi-restraints excluded: chain F residue 704 CYS Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 852 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 224 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 257 optimal weight: 0.9990 chunk 208 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 153 optimal weight: 2.9990 chunk 270 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 827 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24988 Z= 0.191 Angle : 0.530 8.100 33857 Z= 0.265 Chirality : 0.041 0.154 3898 Planarity : 0.004 0.061 4327 Dihedral : 7.705 85.693 3563 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.00 % Allowed : 15.63 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.15), residues: 3109 helix: 0.85 (0.14), residues: 1405 sheet: -0.10 (0.26), residues: 402 loop : -1.56 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 470 HIS 0.006 0.001 HIS E 828 PHE 0.019 0.001 PHE A 547 TYR 0.014 0.001 TYR E 939 ARG 0.004 0.000 ARG E 459 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 255 time to evaluate : 3.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 426 LYS cc_start: 0.7824 (pptt) cc_final: 0.7524 (pttp) REVERT: A 554 ASP cc_start: 0.7554 (p0) cc_final: 0.7163 (t0) REVERT: A 766 MET cc_start: 0.8455 (ttp) cc_final: 0.8011 (ttp) REVERT: A 778 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8524 (pp) REVERT: A 931 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8095 (pp) REVERT: B 552 MET cc_start: 0.8903 (ttm) cc_final: 0.8641 (ttp) REVERT: B 600 GLN cc_start: 0.6204 (mp10) cc_final: 0.5910 (mp10) REVERT: B 768 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8353 (pp) REVERT: C 447 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8153 (pp) REVERT: D 681 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7859 (mp) REVERT: E 448 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8596 (tp) REVERT: E 482 ARG cc_start: 0.7759 (tmt170) cc_final: 0.7288 (tmt170) REVERT: E 543 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7957 (mm-30) REVERT: E 781 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8423 (pt0) REVERT: F 562 ARG cc_start: 0.7580 (ttm110) cc_final: 0.7206 (mtm-85) REVERT: F 575 GLN cc_start: 0.8406 (mt0) cc_final: 0.7967 (mt0) REVERT: F 610 LEU cc_start: 0.8689 (tp) cc_final: 0.8476 (tp) REVERT: F 705 ARG cc_start: 0.7978 (mmt90) cc_final: 0.7415 (mmt90) REVERT: F 852 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7484 (p0) outliers start: 79 outliers final: 52 residues processed: 308 average time/residue: 0.4094 time to fit residues: 192.3449 Evaluate side-chains 301 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 240 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 909 CYS Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 618 ASN Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 685 ASP Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 801 GLU Chi-restraints excluded: chain D residue 842 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 882 GLU Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 744 ASP Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 753 VAL Chi-restraints excluded: chain E residue 781 GLU Chi-restraints excluded: chain E residue 827 GLN Chi-restraints excluded: chain E residue 928 THR Chi-restraints excluded: chain F residue 449 ASP Chi-restraints excluded: chain F residue 462 LEU Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 649 LEU Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 852 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 10.0000 chunk 271 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 177 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 301 optimal weight: 8.9990 chunk 250 optimal weight: 0.0980 chunk 139 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24988 Z= 0.215 Angle : 0.535 8.041 33857 Z= 0.267 Chirality : 0.041 0.149 3898 Planarity : 0.004 0.061 4327 Dihedral : 7.632 86.704 3563 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.08 % Allowed : 16.09 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.15), residues: 3109 helix: 0.99 (0.14), residues: 1400 sheet: -0.08 (0.26), residues: 407 loop : -1.42 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 470 HIS 0.004 0.001 HIS D 828 PHE 0.018 0.001 PHE A 547 TYR 0.014 0.001 TYR E 939 ARG 0.004 0.000 ARG E 459 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 247 time to evaluate : 2.828 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 426 LYS cc_start: 0.7927 (pptt) cc_final: 0.7604 (pttp) REVERT: A 554 ASP cc_start: 0.7508 (p0) cc_final: 0.7143 (t0) REVERT: A 755 ARG cc_start: 0.6193 (mtm180) cc_final: 0.5781 (mtt180) REVERT: A 766 MET cc_start: 0.8495 (ttp) cc_final: 0.8090 (ttp) REVERT: A 778 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8563 (pp) REVERT: A 931 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8114 (pp) REVERT: B 552 MET cc_start: 0.8888 (ttm) cc_final: 0.8629 (ttp) REVERT: B 600 GLN cc_start: 0.6191 (mp10) cc_final: 0.5894 (mp10) REVERT: B 768 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8365 (pp) REVERT: B 778 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7317 (mt) REVERT: C 447 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8152 (pp) REVERT: C 597 ARG cc_start: 0.6947 (ttp-110) cc_final: 0.6373 (ptp90) REVERT: D 419 GLU cc_start: 0.6091 (mp0) cc_final: 0.5803 (mp0) REVERT: D 681 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7835 (mp) REVERT: E 448 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8607 (tp) REVERT: E 543 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7931 (mm-30) REVERT: E 781 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8421 (pt0) REVERT: F 455 PHE cc_start: 0.6429 (t80) cc_final: 0.6148 (t80) REVERT: F 575 GLN cc_start: 0.8446 (mt0) cc_final: 0.7997 (mt0) REVERT: F 608 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8033 (mm) REVERT: F 705 ARG cc_start: 0.7985 (mmt90) cc_final: 0.7373 (mmt90) outliers start: 81 outliers final: 59 residues processed: 307 average time/residue: 0.3912 time to fit residues: 183.8854 Evaluate side-chains 305 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 236 time to evaluate : 2.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 909 CYS Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 618 ASN Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 685 ASP Chi-restraints excluded: chain C residue 744 ASP Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 801 GLU Chi-restraints excluded: chain D residue 842 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 744 ASP Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 753 VAL Chi-restraints excluded: chain E residue 781 GLU Chi-restraints excluded: chain E residue 806 LEU Chi-restraints excluded: chain E residue 928 THR Chi-restraints excluded: chain F residue 449 ASP Chi-restraints excluded: chain F residue 462 LEU Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain F residue 649 LEU Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 852 ASP Chi-restraints excluded: chain F residue 880 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 171 optimal weight: 0.0040 chunk 220 optimal weight: 9.9990 chunk 170 optimal weight: 3.9990 chunk 254 optimal weight: 7.9990 chunk 168 optimal weight: 10.0000 chunk 300 optimal weight: 0.4980 chunk 188 optimal weight: 0.9980 chunk 183 optimal weight: 30.0000 chunk 138 optimal weight: 4.9990 overall best weight: 2.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 805 GLN E 827 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24988 Z= 0.160 Angle : 0.505 7.645 33857 Z= 0.250 Chirality : 0.040 0.199 3898 Planarity : 0.004 0.059 4327 Dihedral : 7.288 88.118 3563 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.89 % Allowed : 16.39 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.15), residues: 3109 helix: 1.21 (0.14), residues: 1390 sheet: 0.10 (0.27), residues: 403 loop : -1.29 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 470 HIS 0.003 0.001 HIS D 828 PHE 0.023 0.001 PHE A 547 TYR 0.011 0.001 TYR E 939 ARG 0.006 0.000 ARG E 538 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 256 time to evaluate : 2.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 554 ASP cc_start: 0.7366 (p0) cc_final: 0.7128 (t0) REVERT: A 755 ARG cc_start: 0.6175 (mtm180) cc_final: 0.5757 (mtt180) REVERT: A 766 MET cc_start: 0.8405 (ttp) cc_final: 0.7990 (ttp) REVERT: A 778 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8582 (pp) REVERT: A 931 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8089 (pp) REVERT: B 552 MET cc_start: 0.8844 (ttm) cc_final: 0.8579 (ttp) REVERT: B 600 GLN cc_start: 0.6248 (mp10) cc_final: 0.5908 (mp10) REVERT: B 768 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8395 (pp) REVERT: B 778 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7239 (mt) REVERT: C 597 ARG cc_start: 0.7144 (ttp-110) cc_final: 0.6746 (ttp80) REVERT: D 419 GLU cc_start: 0.6157 (mp0) cc_final: 0.5914 (mp0) REVERT: D 620 LEU cc_start: 0.8699 (tt) cc_final: 0.8424 (tt) REVERT: E 448 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8596 (tp) REVERT: E 482 ARG cc_start: 0.7752 (tmt170) cc_final: 0.7307 (tmt170) REVERT: E 543 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7994 (mm-30) REVERT: F 439 ASP cc_start: 0.6748 (t0) cc_final: 0.5892 (p0) REVERT: F 562 ARG cc_start: 0.7443 (ttm110) cc_final: 0.6884 (mtm-85) REVERT: F 608 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7923 (mm) outliers start: 76 outliers final: 50 residues processed: 311 average time/residue: 0.3933 time to fit residues: 189.3331 Evaluate side-chains 296 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 239 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 909 CYS Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 685 ASP Chi-restraints excluded: chain C residue 744 ASP Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 744 ASP Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 753 VAL Chi-restraints excluded: chain E residue 806 LEU Chi-restraints excluded: chain E residue 827 GLN Chi-restraints excluded: chain E residue 928 THR Chi-restraints excluded: chain F residue 462 LEU Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain F residue 649 LEU Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 756 MET Chi-restraints excluded: chain F residue 771 THR Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 852 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 chunk 179 optimal weight: 8.9990 chunk 90 optimal weight: 20.0000 chunk 59 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 191 optimal weight: 6.9990 chunk 204 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 236 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 827 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 24988 Z= 0.340 Angle : 0.598 10.916 33857 Z= 0.298 Chirality : 0.044 0.207 3898 Planarity : 0.005 0.061 4327 Dihedral : 7.765 86.568 3563 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.20 % Allowed : 16.62 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.15), residues: 3109 helix: 1.04 (0.14), residues: 1390 sheet: 0.01 (0.27), residues: 389 loop : -1.36 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 464 HIS 0.005 0.001 HIS D 828 PHE 0.030 0.002 PHE A 547 TYR 0.017 0.002 TYR E 939 ARG 0.007 0.000 ARG B 459 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 240 time to evaluate : 3.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 MET cc_start: 0.7979 (tpp) cc_final: 0.7696 (tpp) REVERT: A 554 ASP cc_start: 0.7356 (p0) cc_final: 0.7141 (t0) REVERT: A 755 ARG cc_start: 0.6243 (mtm180) cc_final: 0.5822 (mtt180) REVERT: A 778 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8617 (pp) REVERT: A 931 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8123 (pp) REVERT: B 552 MET cc_start: 0.8923 (ttm) cc_final: 0.8655 (ttp) REVERT: B 600 GLN cc_start: 0.6295 (mp10) cc_final: 0.5997 (mp10) REVERT: B 768 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8382 (pp) REVERT: B 778 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7295 (mt) REVERT: C 597 ARG cc_start: 0.7108 (ttp-110) cc_final: 0.6671 (ttp80) REVERT: D 552 MET cc_start: 0.9259 (ttp) cc_final: 0.8930 (ttp) REVERT: D 681 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7839 (mp) REVERT: E 448 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8632 (tp) REVERT: E 543 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7903 (mm-30) REVERT: E 810 MET cc_start: 0.8841 (tpt) cc_final: 0.8420 (tpt) REVERT: F 435 MET cc_start: 0.6622 (tpt) cc_final: 0.6354 (tpt) REVERT: F 562 ARG cc_start: 0.7442 (ttm110) cc_final: 0.6883 (mtm-85) REVERT: F 608 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8109 (mm) outliers start: 84 outliers final: 67 residues processed: 299 average time/residue: 0.3743 time to fit residues: 174.5146 Evaluate side-chains 308 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 233 time to evaluate : 3.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 909 CYS Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 618 ASN Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 685 ASP Chi-restraints excluded: chain C residue 744 ASP Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 801 GLU Chi-restraints excluded: chain D residue 842 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 744 ASP Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 753 VAL Chi-restraints excluded: chain E residue 806 LEU Chi-restraints excluded: chain E residue 827 GLN Chi-restraints excluded: chain E residue 928 THR Chi-restraints excluded: chain F residue 449 ASP Chi-restraints excluded: chain F residue 462 LEU Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain F residue 649 LEU Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 756 MET Chi-restraints excluded: chain F residue 771 THR Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 852 ASP Chi-restraints excluded: chain F residue 880 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 40.0000 chunk 288 optimal weight: 0.0020 chunk 262 optimal weight: 20.0000 chunk 280 optimal weight: 5.9990 chunk 168 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 220 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 253 optimal weight: 7.9990 chunk 265 optimal weight: 30.0000 chunk 279 optimal weight: 9.9990 overall best weight: 5.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24988 Z= 0.312 Angle : 0.586 10.728 33857 Z= 0.292 Chirality : 0.043 0.234 3898 Planarity : 0.005 0.059 4327 Dihedral : 7.781 87.432 3563 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.08 % Allowed : 16.89 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 3109 helix: 1.00 (0.14), residues: 1390 sheet: 0.02 (0.27), residues: 389 loop : -1.34 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 470 HIS 0.005 0.001 HIS D 828 PHE 0.034 0.002 PHE A 547 TYR 0.016 0.001 TYR E 939 ARG 0.007 0.000 ARG B 459 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 232 time to evaluate : 2.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 MET cc_start: 0.7982 (tpp) cc_final: 0.7773 (tpp) REVERT: A 554 ASP cc_start: 0.7348 (p0) cc_final: 0.7143 (t0) REVERT: A 755 ARG cc_start: 0.6246 (mtm180) cc_final: 0.5827 (mtt180) REVERT: A 766 MET cc_start: 0.8642 (ttp) cc_final: 0.8269 (ttp) REVERT: A 778 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8568 (pp) REVERT: A 931 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8100 (pp) REVERT: B 552 MET cc_start: 0.8925 (ttm) cc_final: 0.8650 (ttp) REVERT: B 600 GLN cc_start: 0.6289 (mp10) cc_final: 0.5990 (mp10) REVERT: B 768 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8440 (pp) REVERT: B 778 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7302 (mt) REVERT: D 552 MET cc_start: 0.9250 (ttp) cc_final: 0.8915 (ttp) REVERT: D 681 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7819 (mp) REVERT: E 448 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8627 (tp) REVERT: F 435 MET cc_start: 0.6640 (tpt) cc_final: 0.6350 (tpt) REVERT: F 562 ARG cc_start: 0.7431 (ttm110) cc_final: 0.6902 (mtm-85) REVERT: F 608 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8032 (mm) outliers start: 81 outliers final: 65 residues processed: 288 average time/residue: 0.3780 time to fit residues: 169.0265 Evaluate side-chains 302 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 230 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain B residue 432 LYS Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 909 CYS Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 618 ASN Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 685 ASP Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 801 GLU Chi-restraints excluded: chain D residue 842 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 882 GLU Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 744 ASP Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 753 VAL Chi-restraints excluded: chain E residue 806 LEU Chi-restraints excluded: chain E residue 928 THR Chi-restraints excluded: chain F residue 449 ASP Chi-restraints excluded: chain F residue 462 LEU Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain F residue 649 LEU Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 756 MET Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 852 ASP Chi-restraints excluded: chain F residue 880 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 4.9990 chunk 296 optimal weight: 10.0000 chunk 180 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 205 optimal weight: 9.9990 chunk 310 optimal weight: 9.9990 chunk 286 optimal weight: 10.0000 chunk 247 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 191 optimal weight: 20.0000 chunk 151 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 827 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 24988 Z= 0.340 Angle : 0.604 9.879 33857 Z= 0.302 Chirality : 0.044 0.236 3898 Planarity : 0.005 0.061 4327 Dihedral : 7.884 85.120 3563 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.16 % Allowed : 16.89 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.15), residues: 3109 helix: 0.92 (0.14), residues: 1392 sheet: 0.03 (0.27), residues: 387 loop : -1.36 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 470 HIS 0.005 0.001 HIS D 828 PHE 0.036 0.002 PHE A 547 TYR 0.017 0.002 TYR E 939 ARG 0.007 0.000 ARG E 538 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 234 time to evaluate : 3.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 755 ARG cc_start: 0.6266 (mtm180) cc_final: 0.5847 (mtt180) REVERT: A 778 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8578 (pp) REVERT: A 931 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8077 (pp) REVERT: B 552 MET cc_start: 0.8928 (ttm) cc_final: 0.8650 (ttp) REVERT: B 600 GLN cc_start: 0.6315 (mp10) cc_final: 0.6020 (mp10) REVERT: B 609 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7180 (tm-30) REVERT: B 768 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8470 (pp) REVERT: B 778 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7322 (mt) REVERT: D 552 MET cc_start: 0.9247 (ttp) cc_final: 0.8931 (ttp) REVERT: D 681 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7849 (mp) REVERT: E 448 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8669 (tp) REVERT: E 810 MET cc_start: 0.8836 (tpt) cc_final: 0.8424 (tpt) REVERT: F 435 MET cc_start: 0.6548 (tpt) cc_final: 0.6240 (tpt) REVERT: F 562 ARG cc_start: 0.7490 (ttm110) cc_final: 0.6962 (mtm-85) REVERT: F 608 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8047 (mm) outliers start: 83 outliers final: 67 residues processed: 291 average time/residue: 0.3671 time to fit residues: 166.5423 Evaluate side-chains 305 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 231 time to evaluate : 2.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain B residue 432 LYS Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 909 CYS Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 618 ASN Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 685 ASP Chi-restraints excluded: chain C residue 744 ASP Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 801 GLU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 882 GLU Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 576 CYS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 744 ASP Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 753 VAL Chi-restraints excluded: chain E residue 806 LEU Chi-restraints excluded: chain E residue 827 GLN Chi-restraints excluded: chain E residue 928 THR Chi-restraints excluded: chain F residue 449 ASP Chi-restraints excluded: chain F residue 462 LEU Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 608 LEU Chi-restraints excluded: chain F residue 649 LEU Chi-restraints excluded: chain F residue 752 THR Chi-restraints excluded: chain F residue 756 MET Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 852 ASP Chi-restraints excluded: chain F residue 880 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 6.9990 chunk 263 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 228 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 247 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 254 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 827 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.102981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.083773 restraints weight = 42003.946| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.01 r_work: 0.2811 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24988 Z= 0.211 Angle : 0.551 11.978 33857 Z= 0.273 Chirality : 0.041 0.253 3898 Planarity : 0.004 0.059 4327 Dihedral : 7.602 88.510 3563 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.81 % Allowed : 17.19 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.15), residues: 3109 helix: 1.09 (0.14), residues: 1390 sheet: 0.07 (0.27), residues: 388 loop : -1.26 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 470 HIS 0.004 0.001 HIS E 828 PHE 0.037 0.001 PHE A 547 TYR 0.015 0.001 TYR E 939 ARG 0.006 0.000 ARG E 538 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4931.12 seconds wall clock time: 91 minutes 6.72 seconds (5466.72 seconds total)