Starting phenix.real_space_refine on Sat Mar 16 12:39:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc5_25022/03_2024/7sc5_25022.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc5_25022/03_2024/7sc5_25022.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc5_25022/03_2024/7sc5_25022.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc5_25022/03_2024/7sc5_25022.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc5_25022/03_2024/7sc5_25022.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc5_25022/03_2024/7sc5_25022.pdb" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 9192 2.51 5 N 2511 2.21 5 O 2901 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 158": "NH1" <-> "NH2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B GLU 632": "OE1" <-> "OE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C GLU 275": "OE1" <-> "OE2" Residue "D ARG 557": "NH1" <-> "NH2" Residue "D GLU 632": "OE1" <-> "OE2" Residue "E ARG 158": "NH1" <-> "NH2" Residue "E GLU 275": "OE1" <-> "OE2" Residue "F ARG 557": "NH1" <-> "NH2" Residue "F GLU 632": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14703 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3464 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 4 Chain: "B" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1163 Classifications: {'peptide': 150} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 147} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3464 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 4 Chain: "D" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1163 Classifications: {'peptide': 150} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 147} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "E" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3464 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 4 Chain: "F" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1163 Classifications: {'peptide': 150} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 147} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.30, per 1000 atoms: 0.50 Number of scatterers: 14703 At special positions: 0 Unit cell: (122.57, 130.81, 129.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 99 16.00 O 2901 8.00 N 2511 7.00 C 9192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 149 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 330 " distance=2.02 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 443 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 416 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 149 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 330 " distance=2.02 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 443 " distance=2.03 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 416 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 149 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 330 " distance=2.02 Simple disulfide: pdb=" SG CYS E 377 " - pdb=" SG CYS E 443 " distance=2.03 Simple disulfide: pdb=" SG CYS E 384 " - pdb=" SG CYS E 416 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 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=3, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 601 " - " ASN A 152 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 331 " " NAG A 605 " - " ASN A 446 " " NAG A 606 " - " ASN A 391 " " NAG A 607 " - " ASN A 385 " " NAG A 608 " - " ASN A 88 " " NAG A 609 " - " ASN A 148 " " NAG B 801 " - " ASN B 625 " " NAG B 802 " - " ASN B 618 " " NAG B 803 " - " ASN B 637 " " NAG C 601 " - " ASN C 152 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 301 " " NAG C 604 " - " ASN C 331 " " NAG C 605 " - " ASN C 446 " " NAG C 606 " - " ASN C 391 " " NAG C 607 " - " ASN C 385 " " NAG C 608 " - " ASN C 88 " " NAG C 609 " - " ASN C 148 " " NAG D 801 " - " ASN D 625 " " NAG D 802 " - " ASN D 618 " " NAG D 803 " - " ASN D 637 " " NAG E 601 " - " ASN E 152 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 301 " " NAG E 604 " - " ASN E 331 " " NAG E 605 " - " ASN E 446 " " NAG E 606 " - " ASN E 391 " " NAG E 607 " - " ASN E 385 " " NAG E 608 " - " ASN E 88 " " NAG E 609 " - " ASN E 148 " " NAG F 801 " - " ASN F 625 " " NAG F 802 " - " ASN F 618 " " NAG F 803 " - " ASN F 637 " " NAG H 1 " - " ASN A 234 " " NAG I 1 " - " ASN A 354 " " NAG K 1 " - " ASN C 234 " " NAG L 1 " - " ASN C 354 " " NAG N 1 " - " ASN E 234 " " NAG O 1 " - " ASN E 354 " NAG-SER " NAG G 1 " - " SER A 445 " " NAG J 1 " - " SER C 445 " " NAG M 1 " - " SER E 445 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.09 Conformation dependent library (CDL) restraints added in 2.6 seconds 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3324 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 27 sheets defined 24.4% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 333 through 352 removed outlier: 3.972A pdb=" N LYS A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N HIS A 351 " --> pdb=" O GLN A 347 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 479 removed outlier: 3.936A pdb=" N TRP A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 539 Processing helix chain 'B' and resid 540 through 542 No H-bonds generated for 'chain 'B' and resid 540 through 542' Processing helix chain 'B' and resid 543 through 551 removed outlier: 3.694A pdb=" N GLN B 551 " --> pdb=" O GLY B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 558 Processing helix chain 'B' and resid 570 through 596 removed outlier: 4.085A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLN B 590 " --> pdb=" O TYR B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 652 removed outlier: 4.087A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER B 649 " --> pdb=" O LEU B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 660 Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 333 through 352 removed outlier: 3.972A pdb=" N LYS C 350 " --> pdb=" O LYS C 346 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N HIS C 351 " --> pdb=" O GLN C 347 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE C 352 " --> pdb=" O LEU C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 473 through 479 removed outlier: 3.937A pdb=" N TRP C 477 " --> pdb=" O MET C 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 539 Processing helix chain 'D' and resid 540 through 542 No H-bonds generated for 'chain 'D' and resid 540 through 542' Processing helix chain 'D' and resid 543 through 551 removed outlier: 3.693A pdb=" N GLN D 551 " --> pdb=" O GLY D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 558 Processing helix chain 'D' and resid 570 through 596 removed outlier: 4.086A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLN D 590 " --> pdb=" O TYR D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 652 removed outlier: 4.087A pdb=" N GLU D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU D 648 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER D 649 " --> pdb=" O LEU D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 660 Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 333 through 352 removed outlier: 3.971A pdb=" N LYS E 350 " --> pdb=" O LYS E 346 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N HIS E 351 " --> pdb=" O GLN E 347 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE E 352 " --> pdb=" O LEU E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 372 removed outlier: 3.558A pdb=" N THR E 371 " --> pdb=" O ASP E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 479 removed outlier: 3.937A pdb=" N TRP E 477 " --> pdb=" O MET E 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 539 Processing helix chain 'F' and resid 540 through 542 No H-bonds generated for 'chain 'F' and resid 540 through 542' Processing helix chain 'F' and resid 543 through 551 removed outlier: 3.693A pdb=" N GLN F 551 " --> pdb=" O GLY F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 552 through 558 Processing helix chain 'F' and resid 570 through 596 removed outlier: 4.085A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLN F 590 " --> pdb=" O TYR F 586 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 652 removed outlier: 4.085A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER F 649 " --> pdb=" O LEU F 645 " (cutoff:3.500A) Processing helix chain 'F' and resid 653 through 660 Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 497 removed outlier: 6.264A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYS B 604 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 133 removed outlier: 3.701A pdb=" N PHE A 151 " --> pdb=" O VAL A 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 173 through 174 Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.823A pdb=" N LEU A 260 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 272 through 273 removed outlier: 3.542A pdb=" N LEU A 450 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 441 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER A 445 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA A 328 " --> pdb=" O CYS A 416 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AA9, first strand: chain 'A' and resid 421 through 423 Processing sheet with id=AB1, first strand: chain 'C' and resid 492 through 497 removed outlier: 6.107A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS D 604 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB3, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AB4, first strand: chain 'C' and resid 130 through 133 removed outlier: 3.701A pdb=" N PHE C 151 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 173 through 174 Processing sheet with id=AB6, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.824A pdb=" N LEU C 260 " --> pdb=" O THR C 448 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 272 through 273 removed outlier: 3.542A pdb=" N LEU C 450 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE C 441 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER C 445 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA C 328 " --> pdb=" O CYS C 416 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AB9, first strand: chain 'C' and resid 421 through 423 Processing sheet with id=AC1, first strand: chain 'E' and resid 492 through 497 removed outlier: 6.204A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS F 604 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC3, first strand: chain 'E' and resid 91 through 93 Processing sheet with id=AC4, first strand: chain 'E' and resid 130 through 133 removed outlier: 3.701A pdb=" N PHE E 151 " --> pdb=" O VAL E 164 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 173 through 174 Processing sheet with id=AC6, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.823A pdb=" N LEU E 260 " --> pdb=" O THR E 448 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 272 through 273 removed outlier: 3.542A pdb=" N LEU E 450 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE E 441 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER E 445 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA E 328 " --> pdb=" O CYS E 416 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 304 through 308 Processing sheet with id=AC9, first strand: chain 'E' and resid 421 through 423 441 hydrogen bonds defined for protein. 1245 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: 4.18 Time building geometry restraints manager: 6.46 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: 4603 1.34 - 1.46: 3045 1.46 - 1.57: 7190 1.57 - 1.69: 3 1.69 - 1.81: 132 Bond restraints: 14973 Sorted by residual: bond pdb=" C THR E 123 " pdb=" N PRO E 124 " ideal model delta sigma weight residual 1.335 1.376 -0.041 9.40e-03 1.13e+04 1.88e+01 bond pdb=" C THR C 123 " pdb=" N PRO C 124 " ideal model delta sigma weight residual 1.335 1.375 -0.040 9.40e-03 1.13e+04 1.83e+01 bond pdb=" C THR A 123 " pdb=" N PRO A 124 " ideal model delta sigma weight residual 1.335 1.375 -0.040 9.40e-03 1.13e+04 1.80e+01 bond pdb=" C1 BMA M 3 " pdb=" C2 BMA M 3 " ideal model delta sigma weight residual 1.519 1.594 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.593 -0.074 2.00e-02 2.50e+03 1.38e+01 ... (remaining 14968 not shown) Histogram of bond angle deviations from ideal: 98.96 - 105.99: 277 105.99 - 113.02: 8657 113.02 - 120.04: 4990 120.04 - 127.07: 6176 127.07 - 134.10: 231 Bond angle restraints: 20331 Sorted by residual: angle pdb=" C MET E 153 " pdb=" N THR E 154 " pdb=" CA THR E 154 " ideal model delta sigma weight residual 121.54 133.28 -11.74 1.91e+00 2.74e-01 3.78e+01 angle pdb=" C MET C 153 " pdb=" N THR C 154 " pdb=" CA THR C 154 " ideal model delta sigma weight residual 121.54 133.26 -11.72 1.91e+00 2.74e-01 3.77e+01 angle pdb=" C MET A 153 " pdb=" N THR A 154 " pdb=" CA THR A 154 " ideal model delta sigma weight residual 121.54 133.23 -11.69 1.91e+00 2.74e-01 3.75e+01 angle pdb=" CA SER F 612 " pdb=" C SER F 612 " pdb=" O SER F 612 " ideal model delta sigma weight residual 118.91 109.69 9.22 1.60e+00 3.91e-01 3.32e+01 angle pdb=" CA SER D 612 " pdb=" C SER D 612 " pdb=" O SER D 612 " ideal model delta sigma weight residual 118.91 109.73 9.18 1.60e+00 3.91e-01 3.29e+01 ... (remaining 20326 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.33: 9048 22.33 - 44.66: 582 44.66 - 66.99: 117 66.99 - 89.32: 63 89.32 - 111.65: 24 Dihedral angle restraints: 9834 sinusoidal: 4719 harmonic: 5115 Sorted by residual: dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual 93.00 172.34 -79.34 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual 93.00 172.32 -79.32 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " pdb=" SG CYS E 74 " pdb=" CB CYS E 74 " ideal model delta sinusoidal sigma weight residual 93.00 172.31 -79.31 1 1.00e+01 1.00e-02 7.82e+01 ... (remaining 9831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 2344 0.114 - 0.227: 119 0.227 - 0.341: 9 0.341 - 0.455: 15 0.455 - 0.568: 3 Chirality restraints: 2490 Sorted by residual: chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.07e+00 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN E 234 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.07e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 7.98e+00 ... (remaining 2487 not shown) Planarity restraints: 2562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 609 " -0.265 2.00e-02 2.50e+03 2.22e-01 6.13e+02 pdb=" C7 NAG E 609 " 0.071 2.00e-02 2.50e+03 pdb=" C8 NAG E 609 " -0.179 2.00e-02 2.50e+03 pdb=" N2 NAG E 609 " 0.371 2.00e-02 2.50e+03 pdb=" O7 NAG E 609 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 609 " -0.256 2.00e-02 2.50e+03 2.14e-01 5.71e+02 pdb=" C7 NAG C 609 " 0.069 2.00e-02 2.50e+03 pdb=" C8 NAG C 609 " -0.176 2.00e-02 2.50e+03 pdb=" N2 NAG C 609 " 0.357 2.00e-02 2.50e+03 pdb=" O7 NAG C 609 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 609 " -0.242 2.00e-02 2.50e+03 2.01e-01 5.07e+02 pdb=" C7 NAG A 609 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG A 609 " -0.169 2.00e-02 2.50e+03 pdb=" N2 NAG A 609 " 0.334 2.00e-02 2.50e+03 pdb=" O7 NAG A 609 " 0.012 2.00e-02 2.50e+03 ... (remaining 2559 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 230 2.55 - 3.14: 11369 3.14 - 3.72: 23109 3.72 - 4.31: 30743 4.31 - 4.90: 48887 Nonbonded interactions: 114338 Sorted by model distance: nonbonded pdb=" O ASP C 367 " pdb=" N GLU C 369 " model vdw 1.959 2.520 nonbonded pdb=" O3 NAG A 609 " pdb=" O7 NAG A 609 " model vdw 2.053 2.440 nonbonded pdb=" O3 NAG C 609 " pdb=" O7 NAG C 609 " model vdw 2.060 2.440 nonbonded pdb=" O3 NAG E 609 " pdb=" O7 NAG E 609 " model vdw 2.070 2.440 nonbonded pdb=" ND2 ASN E 362 " pdb=" O THR E 371 " model vdw 2.196 2.520 ... (remaining 114333 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 12.640 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 37.910 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 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 : 0.008 0.075 14973 Z= 0.503 Angle : 1.108 11.737 20331 Z= 0.592 Chirality : 0.070 0.568 2490 Planarity : 0.009 0.222 2520 Dihedral : 17.367 111.646 6420 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.30 % Favored : 88.47 % Rotamer: Outliers : 0.97 % Allowed : 7.52 % Favored : 91.50 % 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: -5.17 (0.16), residues: 1734 helix: -3.87 (0.12), residues: 405 sheet: -2.56 (0.22), residues: 474 loop : -3.75 (0.17), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 394 HIS 0.010 0.002 HIS C 373 PHE 0.013 0.002 PHE A 93 TYR 0.015 0.002 TYR C 165 ARG 0.007 0.001 ARG C 158 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 179 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 MET cc_start: 0.5687 (ttt) cc_final: 0.4003 (ttm) REVERT: B 567 LYS cc_start: 0.8217 (mmtm) cc_final: 0.7901 (mmtm) REVERT: B 601 LYS cc_start: 0.9086 (mtmm) cc_final: 0.8587 (mtmm) REVERT: B 632 GLU cc_start: 0.9367 (tp30) cc_final: 0.9082 (tp30) REVERT: B 651 ASN cc_start: 0.9048 (t0) cc_final: 0.8822 (t0) REVERT: B 657 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8777 (mt-10) REVERT: C 69 TRP cc_start: 0.9256 (m-90) cc_final: 0.8715 (m-90) REVERT: C 424 MET cc_start: 0.5931 (ttt) cc_final: 0.4315 (ttm) REVERT: C 447 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9249 (mp) REVERT: D 601 LYS cc_start: 0.8840 (mtmm) cc_final: 0.8465 (mtmm) REVERT: D 632 GLU cc_start: 0.9328 (tp30) cc_final: 0.8966 (tp30) REVERT: D 657 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8691 (mt-10) REVERT: E 69 TRP cc_start: 0.9174 (m-90) cc_final: 0.8696 (m-90) REVERT: E 264 SER cc_start: 0.9099 (t) cc_final: 0.8761 (m) REVERT: F 601 LYS cc_start: 0.8805 (mtmm) cc_final: 0.8271 (mtmm) REVERT: F 632 GLU cc_start: 0.9287 (tp30) cc_final: 0.8964 (tp30) REVERT: F 633 LYS cc_start: 0.9730 (mttt) cc_final: 0.9481 (mttp) REVERT: F 651 ASN cc_start: 0.9097 (t0) cc_final: 0.8681 (t0) REVERT: F 657 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8728 (mt-10) outliers start: 15 outliers final: 9 residues processed: 194 average time/residue: 0.2968 time to fit residues: 81.6186 Evaluate side-chains 120 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain F residue 636 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 160 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN A 276 ASN A 295 ASN A 300 ASN A 373 HIS A 423 ASN B 550 GLN B 564 HIS ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 ASN C 262 ASN C 276 ASN C 295 ASN C 300 ASN C 373 HIS C 423 ASN D 550 GLN D 551 GLN D 564 HIS D 656 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 ASN E 276 ASN E 295 ASN E 300 ASN E 373 HIS E 423 ASN F 550 GLN F 551 GLN F 564 HIS F 575 GLN ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14973 Z= 0.293 Angle : 0.800 9.837 20331 Z= 0.398 Chirality : 0.051 0.258 2490 Planarity : 0.004 0.045 2520 Dihedral : 13.447 76.950 3132 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.15 % Favored : 86.68 % Rotamer: Outliers : 3.18 % Allowed : 11.87 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.18), residues: 1734 helix: -1.38 (0.23), residues: 405 sheet: -2.02 (0.23), residues: 444 loop : -3.43 (0.17), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 394 HIS 0.004 0.001 HIS B 564 PHE 0.013 0.001 PHE C 93 TYR 0.015 0.002 TYR C 383 ARG 0.009 0.001 ARG D 588 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 130 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8884 (pp) REVERT: B 632 GLU cc_start: 0.9309 (tp30) cc_final: 0.8985 (tp30) REVERT: B 651 ASN cc_start: 0.9093 (t0) cc_final: 0.8780 (t0) REVERT: B 657 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8729 (mt-10) REVERT: C 69 TRP cc_start: 0.9249 (m-90) cc_final: 0.8678 (m-90) REVERT: C 271 MET cc_start: 0.8698 (mmm) cc_final: 0.8324 (mmm) REVERT: D 574 LYS cc_start: 0.9161 (mmmt) cc_final: 0.8953 (pttm) REVERT: D 601 LYS cc_start: 0.8827 (mtmm) cc_final: 0.8422 (mtmm) REVERT: D 632 GLU cc_start: 0.9294 (tp30) cc_final: 0.8917 (tp30) REVERT: D 657 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8634 (mt-10) REVERT: E 69 TRP cc_start: 0.9191 (m-90) cc_final: 0.8608 (m-90) REVERT: E 264 SER cc_start: 0.9173 (t) cc_final: 0.8754 (m) REVERT: F 601 LYS cc_start: 0.8729 (mtmm) cc_final: 0.8138 (mtmm) REVERT: F 632 GLU cc_start: 0.9184 (tp30) cc_final: 0.8854 (tp30) REVERT: F 633 LYS cc_start: 0.9716 (mttt) cc_final: 0.9512 (mttp) REVERT: F 651 ASN cc_start: 0.9286 (t0) cc_final: 0.9000 (t0) REVERT: F 654 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8127 (tm-30) REVERT: F 657 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8710 (mt-10) outliers start: 49 outliers final: 25 residues processed: 167 average time/residue: 0.2724 time to fit residues: 66.5690 Evaluate side-chains 139 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 113 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain D residue 589 ASP Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain F residue 589 ASP Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 161 optimal weight: 6.9990 chunk 173 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 159 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 GLN B 564 HIS B 575 GLN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 564 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14973 Z= 0.263 Angle : 0.746 9.508 20331 Z= 0.371 Chirality : 0.050 0.246 2490 Planarity : 0.004 0.054 2520 Dihedral : 11.246 57.826 3130 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.65 % Favored : 88.00 % Rotamer: Outliers : 3.18 % Allowed : 15.11 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.19), residues: 1734 helix: -0.46 (0.25), residues: 405 sheet: -1.77 (0.24), residues: 426 loop : -3.18 (0.18), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 571 HIS 0.005 0.001 HIS F 564 PHE 0.027 0.001 PHE E 360 TYR 0.010 0.001 TYR E 484 ARG 0.006 0.000 ARG E 467 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 121 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8835 (pp) REVERT: A 424 MET cc_start: 0.6719 (ttt) cc_final: 0.5814 (ttm) REVERT: B 574 LYS cc_start: 0.9170 (mmmt) cc_final: 0.8960 (ptmt) REVERT: B 601 LYS cc_start: 0.9176 (mtpp) cc_final: 0.8968 (mtpp) REVERT: B 632 GLU cc_start: 0.9294 (tp30) cc_final: 0.9018 (tp30) REVERT: B 651 ASN cc_start: 0.9216 (t0) cc_final: 0.8974 (t0) REVERT: B 657 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8714 (mt-10) REVERT: C 69 TRP cc_start: 0.9246 (m-90) cc_final: 0.8712 (m-90) REVERT: C 424 MET cc_start: 0.6566 (ttt) cc_final: 0.6000 (ttm) REVERT: D 601 LYS cc_start: 0.8866 (mtmm) cc_final: 0.8490 (mtmm) REVERT: D 632 GLU cc_start: 0.9299 (tp30) cc_final: 0.8937 (tp30) REVERT: D 657 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8651 (mt-10) REVERT: E 69 TRP cc_start: 0.9184 (m-90) cc_final: 0.8625 (m-90) REVERT: F 632 GLU cc_start: 0.9199 (tp30) cc_final: 0.8895 (tp30) REVERT: F 633 LYS cc_start: 0.9704 (mttt) cc_final: 0.9498 (mttp) REVERT: F 651 ASN cc_start: 0.9060 (t0) cc_final: 0.8601 (t0) REVERT: F 654 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8302 (tm-30) REVERT: F 657 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8850 (mt-10) outliers start: 49 outliers final: 26 residues processed: 162 average time/residue: 0.2779 time to fit residues: 65.5326 Evaluate side-chains 136 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 109 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 589 ASP Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 4.9990 chunk 121 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 108 optimal weight: 6.9990 chunk 161 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 HIS ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 ASN ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 ASN ** E 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14973 Z= 0.287 Angle : 0.749 9.487 20331 Z= 0.368 Chirality : 0.050 0.243 2490 Planarity : 0.004 0.035 2520 Dihedral : 9.988 57.309 3121 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.23 % Allowed : 13.44 % Favored : 86.33 % Rotamer: Outliers : 3.50 % Allowed : 17.12 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.96 (0.19), residues: 1734 helix: -0.06 (0.27), residues: 405 sheet: -1.79 (0.24), residues: 426 loop : -3.07 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 571 HIS 0.005 0.001 HIS B 564 PHE 0.024 0.001 PHE A 360 TYR 0.009 0.001 TYR C 484 ARG 0.003 0.000 ARG D 588 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 116 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8807 (pp) REVERT: A 424 MET cc_start: 0.6711 (ttt) cc_final: 0.5903 (ttm) REVERT: B 632 GLU cc_start: 0.9270 (tp30) cc_final: 0.9022 (tp30) REVERT: B 651 ASN cc_start: 0.9253 (t0) cc_final: 0.9028 (t0) REVERT: B 657 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8753 (mt-10) REVERT: C 69 TRP cc_start: 0.9268 (m-90) cc_final: 0.8723 (m-90) REVERT: C 424 MET cc_start: 0.6598 (ttt) cc_final: 0.6298 (ttm) REVERT: D 601 LYS cc_start: 0.8812 (mtmm) cc_final: 0.8580 (mtpp) REVERT: D 632 GLU cc_start: 0.9294 (tp30) cc_final: 0.8988 (tp30) REVERT: D 657 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8636 (mt-10) REVERT: E 69 TRP cc_start: 0.9172 (m-90) cc_final: 0.8617 (m-90) REVERT: F 601 LYS cc_start: 0.8997 (mtpp) cc_final: 0.8529 (ptpp) REVERT: F 626 MET cc_start: 0.8690 (ttm) cc_final: 0.8453 (ttm) REVERT: F 632 GLU cc_start: 0.9194 (tp30) cc_final: 0.8925 (tp30) REVERT: F 633 LYS cc_start: 0.9686 (mttt) cc_final: 0.9479 (mttp) REVERT: F 651 ASN cc_start: 0.9235 (t0) cc_final: 0.8922 (t0) REVERT: F 654 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8505 (tm-30) REVERT: F 657 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8869 (mt-10) outliers start: 54 outliers final: 45 residues processed: 157 average time/residue: 0.2538 time to fit residues: 59.4726 Evaluate side-chains 153 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 107 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 589 ASP Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 85 HIS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 455 ASP Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 589 ASP Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 2 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 153 optimal weight: 0.1980 chunk 43 optimal weight: 0.8980 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 HIS ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14973 Z= 0.275 Angle : 0.721 9.412 20331 Z= 0.355 Chirality : 0.049 0.248 2490 Planarity : 0.003 0.035 2520 Dihedral : 9.385 57.369 3121 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.34 % Favored : 87.31 % Rotamer: Outliers : 4.15 % Allowed : 18.35 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.84 (0.19), residues: 1734 helix: 0.10 (0.27), residues: 405 sheet: -1.77 (0.24), residues: 426 loop : -2.98 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 571 HIS 0.005 0.001 HIS B 564 PHE 0.014 0.001 PHE E 360 TYR 0.010 0.001 TYR E 484 ARG 0.004 0.000 ARG D 588 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 116 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8745 (pp) REVERT: B 632 GLU cc_start: 0.9276 (tp30) cc_final: 0.9042 (tp30) REVERT: B 657 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8763 (mt-10) REVERT: C 69 TRP cc_start: 0.9240 (m-90) cc_final: 0.8745 (m-90) REVERT: C 271 MET cc_start: 0.8455 (tpt) cc_final: 0.8214 (tmm) REVERT: C 447 ILE cc_start: 0.9406 (OUTLIER) cc_final: 0.9172 (mp) REVERT: D 601 LYS cc_start: 0.8832 (mtmm) cc_final: 0.8620 (mtpp) REVERT: D 632 GLU cc_start: 0.9290 (tp30) cc_final: 0.9006 (tp30) REVERT: D 657 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8637 (mt-10) REVERT: E 69 TRP cc_start: 0.9160 (m-90) cc_final: 0.8603 (m-90) REVERT: F 601 LYS cc_start: 0.8978 (mtpp) cc_final: 0.8526 (ptpp) REVERT: F 632 GLU cc_start: 0.9186 (tp30) cc_final: 0.8938 (tp30) REVERT: F 633 LYS cc_start: 0.9681 (mttt) cc_final: 0.9474 (mttp) REVERT: F 651 ASN cc_start: 0.9196 (t0) cc_final: 0.8894 (t0) REVERT: F 654 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8445 (tm-30) REVERT: F 657 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8871 (mt-10) outliers start: 64 outliers final: 52 residues processed: 167 average time/residue: 0.2604 time to fit residues: 64.6773 Evaluate side-chains 158 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 104 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 85 HIS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 85 HIS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 427 ARG Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 589 ASP Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 85 HIS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 589 ASP Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 4.9990 chunk 154 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 171 optimal weight: 10.0000 chunk 142 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 HIS ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14973 Z= 0.223 Angle : 0.700 9.463 20331 Z= 0.345 Chirality : 0.049 0.259 2490 Planarity : 0.003 0.035 2520 Dihedral : 9.057 57.611 3121 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.29 % Allowed : 12.69 % Favored : 87.02 % Rotamer: Outliers : 3.70 % Allowed : 20.04 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.66 (0.20), residues: 1734 helix: 0.20 (0.28), residues: 399 sheet: -1.51 (0.26), residues: 375 loop : -2.87 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 571 HIS 0.006 0.001 HIS B 564 PHE 0.014 0.001 PHE A 360 TYR 0.007 0.001 TYR A 316 ARG 0.007 0.000 ARG F 557 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 115 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8689 (pp) REVERT: B 632 GLU cc_start: 0.9290 (tp30) cc_final: 0.9046 (tp30) REVERT: B 657 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8723 (mt-10) REVERT: C 69 TRP cc_start: 0.9254 (m-90) cc_final: 0.8742 (m-90) REVERT: D 601 LYS cc_start: 0.8830 (mtmm) cc_final: 0.8571 (mtpp) REVERT: D 632 GLU cc_start: 0.9287 (tp30) cc_final: 0.9005 (tp30) REVERT: D 657 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8656 (mt-10) REVERT: E 69 TRP cc_start: 0.9148 (m-90) cc_final: 0.8643 (m-90) REVERT: E 153 MET cc_start: 0.7346 (tpt) cc_final: 0.7106 (tpt) REVERT: F 601 LYS cc_start: 0.8941 (mtpp) cc_final: 0.8518 (ptpp) REVERT: F 632 GLU cc_start: 0.9175 (tp30) cc_final: 0.8933 (tp30) REVERT: F 633 LYS cc_start: 0.9668 (mttt) cc_final: 0.9462 (mttp) REVERT: F 651 ASN cc_start: 0.9103 (t0) cc_final: 0.8787 (t0) REVERT: F 654 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8439 (tm-30) REVERT: F 657 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8887 (mt-10) outliers start: 57 outliers final: 49 residues processed: 160 average time/residue: 0.2570 time to fit residues: 61.2297 Evaluate side-chains 159 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 109 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 85 HIS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 589 ASP Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 85 HIS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain F residue 589 ASP Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 3.9990 chunk 19 optimal weight: 0.0020 chunk 97 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 170 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 HIS ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14973 Z= 0.160 Angle : 0.685 9.653 20331 Z= 0.336 Chirality : 0.048 0.264 2490 Planarity : 0.003 0.032 2520 Dihedral : 8.553 58.748 3121 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.25 % Favored : 88.58 % Rotamer: Outliers : 3.24 % Allowed : 21.27 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.20), residues: 1734 helix: 0.17 (0.28), residues: 405 sheet: -1.33 (0.26), residues: 381 loop : -2.88 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 571 HIS 0.007 0.001 HIS B 564 PHE 0.011 0.001 PHE E 360 TYR 0.007 0.001 TYR A 217 ARG 0.005 0.000 ARG F 557 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 124 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASP cc_start: 0.9049 (m-30) cc_final: 0.8842 (m-30) REVERT: A 260 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8684 (pp) REVERT: B 632 GLU cc_start: 0.9281 (tp30) cc_final: 0.9030 (tp30) REVERT: B 654 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7570 (tm-30) REVERT: B 657 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8786 (mt-10) REVERT: C 69 TRP cc_start: 0.9291 (m-90) cc_final: 0.8826 (m-90) REVERT: D 601 LYS cc_start: 0.8786 (mtmm) cc_final: 0.8389 (mtmm) REVERT: D 632 GLU cc_start: 0.9279 (tp30) cc_final: 0.8984 (tp30) REVERT: D 657 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8600 (mt-10) REVERT: E 69 TRP cc_start: 0.9182 (m-90) cc_final: 0.8773 (m-90) REVERT: E 153 MET cc_start: 0.7284 (tpt) cc_final: 0.7045 (tpt) REVERT: E 424 MET cc_start: 0.6596 (ttt) cc_final: 0.6101 (ttm) REVERT: F 601 LYS cc_start: 0.8927 (mtpp) cc_final: 0.8555 (ptpp) REVERT: F 632 GLU cc_start: 0.9156 (tp30) cc_final: 0.8921 (tp30) REVERT: F 633 LYS cc_start: 0.9661 (mttt) cc_final: 0.9455 (mttp) REVERT: F 651 ASN cc_start: 0.9036 (t0) cc_final: 0.8716 (t0) REVERT: F 654 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8394 (tm-30) REVERT: F 657 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8815 (mt-10) outliers start: 50 outliers final: 36 residues processed: 162 average time/residue: 0.2752 time to fit residues: 67.1118 Evaluate side-chains 156 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 119 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 51 optimal weight: 0.0770 chunk 33 optimal weight: 7.9990 chunk 108 optimal weight: 0.7980 chunk 116 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 15 optimal weight: 0.0170 chunk 134 optimal weight: 4.9990 chunk 155 optimal weight: 0.0040 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 HIS ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14973 Z= 0.149 Angle : 0.676 9.634 20331 Z= 0.331 Chirality : 0.049 0.332 2490 Planarity : 0.003 0.031 2520 Dihedral : 8.294 58.121 3121 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer: Outliers : 3.24 % Allowed : 21.85 % Favored : 74.90 % 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: -2.52 (0.20), residues: 1734 helix: 0.07 (0.27), residues: 420 sheet: -1.14 (0.28), residues: 339 loop : -2.81 (0.18), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 571 HIS 0.008 0.001 HIS B 564 PHE 0.031 0.001 PHE C 360 TYR 0.016 0.001 TYR F 643 ARG 0.004 0.000 ARG C 467 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 124 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8653 (pp) REVERT: B 632 GLU cc_start: 0.9283 (tp30) cc_final: 0.9033 (tp30) REVERT: B 657 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8746 (mt-10) REVERT: C 69 TRP cc_start: 0.9278 (m-90) cc_final: 0.9008 (m-90) REVERT: D 601 LYS cc_start: 0.8796 (mtmm) cc_final: 0.8543 (mtpp) REVERT: D 632 GLU cc_start: 0.9238 (tp30) cc_final: 0.8883 (tp30) REVERT: D 633 LYS cc_start: 0.9658 (mttm) cc_final: 0.9308 (mttp) REVERT: D 654 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7647 (tm-30) REVERT: D 657 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8680 (mt-10) REVERT: E 69 TRP cc_start: 0.9157 (m-90) cc_final: 0.8782 (m-90) REVERT: E 424 MET cc_start: 0.6452 (ttt) cc_final: 0.6024 (ttm) REVERT: F 601 LYS cc_start: 0.8977 (mtpp) cc_final: 0.8623 (ptpp) REVERT: F 632 GLU cc_start: 0.9119 (tp30) cc_final: 0.8797 (tp30) REVERT: F 633 LYS cc_start: 0.9701 (mttt) cc_final: 0.9456 (mttp) REVERT: F 651 ASN cc_start: 0.9034 (t0) cc_final: 0.8744 (t0) REVERT: F 654 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8414 (tm-30) REVERT: F 657 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8862 (mt-10) outliers start: 50 outliers final: 35 residues processed: 162 average time/residue: 0.2567 time to fit residues: 62.1355 Evaluate side-chains 152 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 116 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 446 ASN Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 446 ASN Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 8.9990 chunk 149 optimal weight: 10.0000 chunk 158 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14973 Z= 0.256 Angle : 0.708 9.488 20331 Z= 0.348 Chirality : 0.048 0.255 2490 Planarity : 0.003 0.068 2520 Dihedral : 8.414 57.252 3120 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.69 % Favored : 86.97 % Rotamer: Outliers : 3.57 % Allowed : 21.47 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.45 (0.20), residues: 1734 helix: 0.29 (0.28), residues: 402 sheet: -1.10 (0.27), residues: 363 loop : -2.82 (0.18), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 571 HIS 0.002 0.001 HIS E 351 PHE 0.027 0.001 PHE C 360 TYR 0.011 0.001 TYR F 643 ARG 0.003 0.000 ARG C 359 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 115 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8632 (pp) REVERT: B 530 MET cc_start: 0.7886 (mtm) cc_final: 0.7644 (pmm) REVERT: B 632 GLU cc_start: 0.9269 (tp30) cc_final: 0.9064 (tp30) REVERT: B 657 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8798 (mt-10) REVERT: C 69 TRP cc_start: 0.9290 (m-90) cc_final: 0.8793 (m-90) REVERT: D 601 LYS cc_start: 0.8830 (mtmm) cc_final: 0.8608 (mtpp) REVERT: D 632 GLU cc_start: 0.9281 (tp30) cc_final: 0.8994 (tp30) REVERT: D 633 LYS cc_start: 0.9659 (mttm) cc_final: 0.9343 (mttp) REVERT: D 654 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7935 (tm-30) REVERT: D 657 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8741 (mt-10) REVERT: E 69 TRP cc_start: 0.9190 (m-90) cc_final: 0.8712 (m-90) REVERT: E 424 MET cc_start: 0.6552 (ttt) cc_final: 0.6023 (ttm) REVERT: F 601 LYS cc_start: 0.8983 (mtpp) cc_final: 0.8589 (ptpp) REVERT: F 632 GLU cc_start: 0.9188 (tp30) cc_final: 0.8965 (tp30) REVERT: F 633 LYS cc_start: 0.9697 (mttt) cc_final: 0.9486 (mttp) REVERT: F 651 ASN cc_start: 0.9122 (t0) cc_final: 0.8863 (t0) REVERT: F 654 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8481 (tm-30) REVERT: F 657 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8840 (mt-10) outliers start: 55 outliers final: 45 residues processed: 156 average time/residue: 0.3026 time to fit residues: 72.6103 Evaluate side-chains 156 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 110 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 352 PHE Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 589 ASP Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 2.9990 chunk 79 optimal weight: 0.0570 chunk 116 optimal weight: 2.9990 chunk 176 optimal weight: 40.0000 chunk 162 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 chunk 111 optimal weight: 9.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14973 Z= 0.211 Angle : 0.698 9.448 20331 Z= 0.345 Chirality : 0.048 0.269 2490 Planarity : 0.003 0.047 2520 Dihedral : 8.381 57.141 3120 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.76 % Favored : 87.95 % Rotamer: Outliers : 3.11 % Allowed : 22.24 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 (0.20), residues: 1734 helix: 0.27 (0.28), residues: 402 sheet: -1.04 (0.27), residues: 363 loop : -2.80 (0.18), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 571 HIS 0.002 0.000 HIS E 105 PHE 0.024 0.001 PHE C 360 TYR 0.012 0.001 TYR F 643 ARG 0.005 0.000 ARG C 359 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 114 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8640 (pp) REVERT: B 632 GLU cc_start: 0.9270 (tp30) cc_final: 0.9048 (tp30) REVERT: B 657 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8804 (mt-10) REVERT: C 69 TRP cc_start: 0.9272 (m-90) cc_final: 0.8772 (m-90) REVERT: C 107 ASP cc_start: 0.8651 (m-30) cc_final: 0.8410 (m-30) REVERT: D 601 LYS cc_start: 0.8845 (mtmm) cc_final: 0.8621 (mtpp) REVERT: D 632 GLU cc_start: 0.9276 (tp30) cc_final: 0.9011 (tp30) REVERT: D 633 LYS cc_start: 0.9653 (mttm) cc_final: 0.9326 (mttp) REVERT: D 657 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8745 (mt-10) REVERT: E 69 TRP cc_start: 0.9171 (m-90) cc_final: 0.8695 (m-90) REVERT: E 424 MET cc_start: 0.6563 (ttt) cc_final: 0.5771 (ttm) REVERT: F 601 LYS cc_start: 0.8969 (mtpp) cc_final: 0.8580 (ptpp) REVERT: F 632 GLU cc_start: 0.9242 (tp30) cc_final: 0.9015 (tp30) REVERT: F 633 LYS cc_start: 0.9717 (mttt) cc_final: 0.9486 (mttp) REVERT: F 651 ASN cc_start: 0.9127 (t0) cc_final: 0.8865 (t0) REVERT: F 654 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8469 (tm-30) REVERT: F 657 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8797 (mt-10) outliers start: 48 outliers final: 44 residues processed: 153 average time/residue: 0.2713 time to fit residues: 63.2649 Evaluate side-chains 157 residues out of total 1569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 112 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 446 ASN Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 352 PHE Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 446 ASN Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 589 ASP Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 0.0470 chunk 129 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 140 optimal weight: 4.9990 chunk 58 optimal weight: 0.0670 chunk 144 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.0770 chunk 123 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.5976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.051778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.041825 restraints weight = 96311.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.042961 restraints weight = 58739.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.043794 restraints weight = 43090.124| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14973 Z= 0.158 Angle : 0.686 9.511 20331 Z= 0.337 Chirality : 0.048 0.281 2490 Planarity : 0.003 0.032 2520 Dihedral : 8.134 58.422 3120 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.65 % Favored : 88.35 % Rotamer: Outliers : 2.79 % Allowed : 22.57 % Favored : 74.64 % 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: -2.38 (0.20), residues: 1734 helix: 0.24 (0.28), residues: 402 sheet: -0.92 (0.27), residues: 363 loop : -2.79 (0.18), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 571 HIS 0.002 0.000 HIS A 373 PHE 0.024 0.001 PHE C 360 TYR 0.008 0.001 TYR F 643 ARG 0.005 0.000 ARG C 359 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2574.38 seconds wall clock time: 48 minutes 26.25 seconds (2906.25 seconds total)