Starting phenix.real_space_refine on Wed Nov 20 06:58:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f9m_28945/11_2024/8f9m_28945.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f9m_28945/11_2024/8f9m_28945.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f9m_28945/11_2024/8f9m_28945.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f9m_28945/11_2024/8f9m_28945.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f9m_28945/11_2024/8f9m_28945.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f9m_28945/11_2024/8f9m_28945.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 884 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 12727 2.51 5 N 3456 2.21 5 O 4001 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 20313 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3434 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 23, 'TRANS': 409} Chain breaks: 4 Chain: "C" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "D" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 789 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "B" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "E" Number of atoms: 3442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3442 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 23, 'TRANS': 410} Chain breaks: 4 Chain: "J" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "M" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 789 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "G" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "F" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3434 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 23, 'TRANS': 409} Chain breaks: 4 Chain: "K" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "N" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 789 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "I" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "H" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 565 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'TRANS': 112} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 113 Planarities with less than four sites: {'UNK:plan-1': 113} Unresolved non-hydrogen planarities: 113 Chain: "L" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 550 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'TRANS': 109} Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 330 Unresolved non-hydrogen dihedrals: 110 Planarities with less than four sites: {'UNK:plan-1': 110} Unresolved non-hydrogen planarities: 110 Chain: "O" 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: "P" 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: "Q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "R" 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: "S" 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: "T" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "U" 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: "V" 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: "W" 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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: "E" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "G" 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: "F" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "I" 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: 13.67, per 1000 atoms: 0.67 Number of scatterers: 20313 At special positions: 0 Unit cell: (123.393, 136.987, 171.495, 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 129 16.00 O 4001 8.00 N 3456 7.00 C 12727 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.05 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 157 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 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 157 " distance=2.03 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 331 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS G 605 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.02 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.04 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.04 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.04 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.04 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS I 605 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.02 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " " BMA T 3 " - " MAN T 4 " BETA1-4 " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A 601 " - " ASN A 301 " " NAG A 602 " - " ASN A 88 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 234 " " NAG A 606 " - " ASN A 276 " " NAG A 607 " - " ASN A 295 " " NAG A 608 " - " ASN A 386 " " NAG A 609 " - " ASN A 448 " " NAG A 610 " - " ASN A 355 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG E 601 " - " ASN E 301 " " NAG E 602 " - " ASN E 88 " " NAG E 603 " - " ASN E 160 " " NAG E 604 " - " ASN E 197 " " NAG E 605 " - " ASN E 234 " " NAG E 606 " - " ASN E 276 " " NAG E 607 " - " ASN E 295 " " NAG E 608 " - " ASN E 339 " " NAG E 609 " - " ASN E 386 " " NAG E 610 " - " ASN E 448 " " NAG E 611 " - " ASN E 392 " " NAG F 601 " - " ASN F 301 " " NAG F 602 " - " ASN F 88 " " NAG F 603 " - " ASN F 160 " " NAG F 604 " - " ASN F 197 " " NAG F 605 " - " ASN F 234 " " NAG F 606 " - " ASN F 276 " " NAG F 607 " - " ASN F 295 " " NAG F 608 " - " ASN F 339 " " NAG F 609 " - " ASN F 386 " " NAG F 610 " - " ASN F 448 " " NAG F 611 " - " ASN F 355 " " NAG F 612 " - " ASN F 392 " " NAG G 701 " - " ASN G 611 " " NAG G 702 " - " ASN G 618 " " NAG G 703 " - " ASN G 637 " " NAG I 701 " - " ASN I 611 " " NAG I 702 " - " ASN I 618 " " NAG I 703 " - " ASN I 637 " " NAG O 1 " - " ASN A 332 " " NAG P 1 " - " ASN A 156 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN E 332 " " NAG S 1 " - " ASN E 156 " " NAG T 1 " - " ASN E 262 " " NAG U 1 " - " ASN F 332 " " NAG V 1 " - " ASN F 156 " " NAG W 1 " - " ASN F 262 " Time building additional restraints: 5.57 Conformation dependent library (CDL) restraints added in 2.4 seconds 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4756 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 35 sheets defined 23.0% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 99 through 116 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 354 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.179A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.847A pdb=" N THR C 87 " --> pdb=" O ASP C 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 30 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.648A pdb=" N GLU D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.706A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 removed outlier: 3.619A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 117 removed outlier: 3.578A pdb=" N GLN E 103 " --> pdb=" O ASN E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.722A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 199 removed outlier: 4.022A pdb=" N THR E 198 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 354 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.151A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 484 removed outlier: 3.777A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 60 through 65 removed outlier: 4.510A pdb=" N GLY J 65 " --> pdb=" O ASP J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'M' and resid 26 through 30 removed outlier: 3.503A pdb=" N ILE M 27C" --> pdb=" O THR M 26 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR M 30 " --> pdb=" O ASP M 27B" (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.648A pdb=" N GLU M 83 " --> pdb=" O ALA M 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 523 through 528 removed outlier: 4.383A pdb=" N GLY G 527 " --> pdb=" O GLY G 524 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 536 through 543 removed outlier: 3.856A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 596 Processing helix chain 'G' and resid 618 through 625 Processing helix chain 'G' and resid 627 through 635 Processing helix chain 'G' and resid 638 through 662 Processing helix chain 'F' and resid 96 through 98 No H-bonds generated for 'chain 'F' and resid 96 through 98' Processing helix chain 'F' and resid 99 through 117 Processing helix chain 'F' and resid 195 through 198 Processing helix chain 'F' and resid 335 through 354 Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 387 through 391 Processing helix chain 'F' and resid 425 through 429 removed outlier: 4.106A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 474 through 484 removed outlier: 4.256A pdb=" N ASN F 478 " --> pdb=" O ASP F 474 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'N' and resid 26 through 30 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.629A pdb=" N GLU N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 544 removed outlier: 3.650A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 573 through 596 Processing helix chain 'I' and resid 618 through 625 Processing helix chain 'I' and resid 627 through 635 Processing helix chain 'I' and resid 638 through 662 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.168A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (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 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.552A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 283 through 312 removed outlier: 6.873A pdb=" N ASN A 301 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N VAL A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 469 Processing sheet with id=AA8, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'C' and resid 34 through 39 removed outlier: 6.887A pdb=" N MET C 34 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LEU C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 57 through 59 current: chain 'C' and resid 100H through 103 Processing sheet with id=AB1, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AB2, first strand: chain 'D' and resid 33 through 38 removed outlier: 6.563A pdb=" N TRP D 35 " --> pdb=" O MET D 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 44 through 48 current: chain 'D' and resid 96 through 98 Processing sheet with id=AB3, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.575A pdb=" N VAL E 36 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR G 606 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AB5, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB7, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AB8, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.424A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 7.271A pdb=" N ASN E 301 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N VAL E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323 current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 465 through 469 Processing sheet with id=AC1, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'J' and resid 34 through 39 removed outlier: 6.997A pdb=" N MET J 34 " --> pdb=" O LEU J 50 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LEU J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 100H through 103 Processing sheet with id=AC3, first strand: chain 'M' and resid 19 through 23 Processing sheet with id=AC4, first strand: chain 'M' and resid 45 through 48 removed outlier: 6.369A pdb=" N TRP M 35 " --> pdb=" O MET M 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.384A pdb=" N VAL F 36 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR I 606 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.623A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AC8, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AC9, first strand: chain 'F' and resid 121 through 122 removed outlier: 4.378A pdb=" N ILE F 201 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 171 through 177 Processing sheet with id=AD2, first strand: chain 'F' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 259 through 261 current: chain 'F' and resid 284 through 298 removed outlier: 7.977A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 329 through 334 current: chain 'F' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 381 through 385 current: chain 'F' and resid 465 through 469 Processing sheet with id=AD3, first strand: chain 'F' and resid 304 through 312 removed outlier: 6.506A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 3 through 8 removed outlier: 3.849A pdb=" N GLY K 16 " --> pdb=" O SER K 82B" (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 34 through 39 removed outlier: 6.103A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 57 through 59 current: chain 'K' and resid 100H through 103 Processing sheet with id=AD6, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AD7, first strand: chain 'N' and resid 33 through 38 removed outlier: 6.579A pdb=" N TRP N 35 " --> pdb=" O MET N 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 45 through 48 current: chain 'N' and resid 96 through 98 Processing sheet with id=AD8, first strand: chain 'L' and resid 50 through 51 599 hydrogen bonds defined for protein. 1602 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: 6.01 Time building geometry restraints manager: 6.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6505 1.35 - 1.47: 5209 1.47 - 1.59: 8813 1.59 - 1.72: 0 1.72 - 1.84: 180 Bond restraints: 20707 Sorted by residual: bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.16e+00 bond pdb=" C1 NAG F 608 " pdb=" O5 NAG F 608 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.15e+00 bond pdb=" C ASP A 78 " pdb=" N PRO A 79 " ideal model delta sigma weight residual 1.335 1.361 -0.027 1.19e-02 7.06e+03 5.10e+00 bond pdb=" N THR F 163 " pdb=" CA THR F 163 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 5.04e+00 bond pdb=" CG1 ILE A 307 " pdb=" CD1 ILE A 307 " ideal model delta sigma weight residual 1.513 1.429 0.084 3.90e-02 6.57e+02 4.67e+00 ... (remaining 20702 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 27130 2.28 - 4.55: 891 4.55 - 6.83: 92 6.83 - 9.10: 7 9.10 - 11.38: 2 Bond angle restraints: 28122 Sorted by residual: angle pdb=" C UNK L 52 " pdb=" N UNK L 53 " pdb=" CA UNK L 53 " ideal model delta sigma weight residual 121.70 130.73 -9.03 1.80e+00 3.09e-01 2.52e+01 angle pdb=" C UNK H 100 " pdb=" N UNK H 101 " pdb=" CA UNK H 101 " ideal model delta sigma weight residual 121.70 129.40 -7.70 1.80e+00 3.09e-01 1.83e+01 angle pdb=" C UNK H 13 " pdb=" N UNK H 14 " pdb=" CA UNK H 14 " ideal model delta sigma weight residual 121.70 129.22 -7.52 1.80e+00 3.09e-01 1.74e+01 angle pdb=" N UNK L 88 " pdb=" CA UNK L 88 " pdb=" C UNK L 88 " ideal model delta sigma weight residual 110.74 99.36 11.38 3.00e+00 1.11e-01 1.44e+01 angle pdb=" C UNK H 54 " pdb=" N UNK H 55 " pdb=" CA UNK H 55 " ideal model delta sigma weight residual 121.70 128.51 -6.81 1.80e+00 3.09e-01 1.43e+01 ... (remaining 28117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.94: 12728 21.94 - 43.88: 336 43.88 - 65.82: 99 65.82 - 87.75: 30 87.75 - 109.69: 8 Dihedral angle restraints: 13201 sinusoidal: 5817 harmonic: 7384 Sorted by residual: dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 155.97 -62.97 1 1.00e+01 1.00e-02 5.24e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 155.60 -62.60 1 1.00e+01 1.00e-02 5.18e+01 dihedral pdb=" CB CYS F 378 " pdb=" SG CYS F 378 " pdb=" SG CYS F 445 " pdb=" CB CYS F 445 " ideal model delta sinusoidal sigma weight residual -86.00 -126.04 40.04 1 1.00e+01 1.00e-02 2.25e+01 ... (remaining 13198 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2553 0.062 - 0.124: 700 0.124 - 0.187: 88 0.187 - 0.249: 10 0.249 - 0.311: 4 Chirality restraints: 3355 Sorted by residual: chirality pdb=" C1 NAG F 604 " pdb=" ND2 ASN F 197 " pdb=" C2 NAG F 604 " pdb=" O5 NAG F 604 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" C5 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C6 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" C1 NAG E 608 " pdb=" ND2 ASN E 339 " pdb=" C2 NAG E 608 " pdb=" O5 NAG E 608 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 3352 not shown) Planarity restraints: 3571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 159 " 0.030 2.00e-02 2.50e+03 2.51e-02 1.11e+01 pdb=" CG PHE A 159 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE A 159 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 159 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 159 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 159 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 159 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 476 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.05e+01 pdb=" C ARG A 476 " 0.056 2.00e-02 2.50e+03 pdb=" O ARG A 476 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP A 477 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 476 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.32e+00 pdb=" C ARG F 476 " -0.053 2.00e-02 2.50e+03 pdb=" O ARG F 476 " 0.020 2.00e-02 2.50e+03 pdb=" N ASP F 477 " 0.018 2.00e-02 2.50e+03 ... (remaining 3568 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1228 2.73 - 3.27: 19634 3.27 - 3.81: 33099 3.81 - 4.36: 41045 4.36 - 4.90: 68305 Nonbonded interactions: 163311 Sorted by model distance: nonbonded pdb=" NH1 ARG F 350 " pdb=" O THR F 357 " model vdw 2.185 3.120 nonbonded pdb=" O ALA A 266 " pdb=" ND2 ASN A 289 " model vdw 2.191 3.120 nonbonded pdb=" OD1 ASP F 477 " pdb=" NH1 ARG F 480 " model vdw 2.224 3.120 nonbonded pdb=" OD1 ASP F 107 " pdb=" NZ LYS I 574 " model vdw 2.239 3.120 nonbonded pdb=" OD1 ASP E 107 " pdb=" NZ LYS G 574 " model vdw 2.252 3.120 ... (remaining 163306 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and (resid 33 through 185 or resid 189 through 504 or resid 601 throu \ gh 610)) selection = (chain 'F' and (resid 33 through 504 or resid 601 through 610)) } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'M' selection = chain 'N' } ncs_group { reference = (chain 'H' and resid 4 through 113) selection = chain 'L' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'Q' selection = chain 'T' } 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: 6.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 46.410 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 20707 Z= 0.358 Angle : 0.952 11.377 28122 Z= 0.514 Chirality : 0.056 0.311 3355 Planarity : 0.005 0.066 3520 Dihedral : 11.615 109.693 8328 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.20 % Allowed : 0.74 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.16), residues: 2290 helix: 0.73 (0.24), residues: 416 sheet: 0.82 (0.21), residues: 583 loop : 0.40 (0.16), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 479 HIS 0.020 0.002 HIS E 105 PHE 0.058 0.004 PHE A 159 TYR 0.031 0.003 TYR G 643 ARG 0.013 0.001 ARG J 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 841 time to evaluate : 2.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 HIS cc_start: 0.8023 (t70) cc_final: 0.7749 (t70) REVERT: A 107 ASP cc_start: 0.8813 (t70) cc_final: 0.8501 (t70) REVERT: A 110 SER cc_start: 0.9045 (t) cc_final: 0.8778 (p) REVERT: A 114 GLN cc_start: 0.8911 (tp40) cc_final: 0.8590 (tm-30) REVERT: A 128 THR cc_start: 0.7577 (m) cc_final: 0.7328 (p) REVERT: A 133 ASN cc_start: 0.8363 (t0) cc_final: 0.8156 (t0) REVERT: A 134 TYR cc_start: 0.9303 (t80) cc_final: 0.9101 (t80) REVERT: A 217 TYR cc_start: 0.7009 (m-80) cc_final: 0.6352 (m-80) REVERT: A 280 ASN cc_start: 0.7976 (p0) cc_final: 0.7690 (p0) REVERT: A 315 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7308 (mp10) REVERT: A 340 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8612 (mm-30) REVERT: A 468 PHE cc_start: 0.8862 (m-80) cc_final: 0.8586 (m-80) REVERT: C 56 LEU cc_start: 0.8651 (mt) cc_final: 0.8338 (mt) REVERT: C 66 ARG cc_start: 0.7900 (mtm-85) cc_final: 0.7229 (mtm-85) REVERT: C 91 TYR cc_start: 0.8627 (m-80) cc_final: 0.8224 (m-80) REVERT: B 577 GLN cc_start: 0.8708 (mt0) cc_final: 0.8461 (mt0) REVERT: B 624 ASP cc_start: 0.8728 (m-30) cc_final: 0.8455 (m-30) REVERT: B 625 ASN cc_start: 0.8817 (m-40) cc_final: 0.7818 (m110) REVERT: B 653 GLN cc_start: 0.9008 (tt0) cc_final: 0.8266 (tm-30) REVERT: E 99 ASN cc_start: 0.8988 (t0) cc_final: 0.8626 (t0) REVERT: E 106 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8560 (mt-10) REVERT: E 150 MET cc_start: 0.8092 (mmm) cc_final: 0.7549 (mmm) REVERT: E 199 SER cc_start: 0.8265 (p) cc_final: 0.7884 (t) REVERT: E 232 LYS cc_start: 0.7145 (mtmt) cc_final: 0.6741 (ptpp) REVERT: E 302 ASN cc_start: 0.8216 (m-40) cc_final: 0.7821 (p0) REVERT: E 325 HIS cc_start: 0.6227 (t70) cc_final: 0.5797 (t-90) REVERT: E 349 LEU cc_start: 0.9472 (mt) cc_final: 0.9127 (pp) REVERT: E 359 ILE cc_start: 0.7709 (mt) cc_final: 0.6993 (mm) REVERT: E 395 TRP cc_start: 0.5013 (m-90) cc_final: 0.3409 (m-90) REVERT: J 2 VAL cc_start: 0.8319 (t) cc_final: 0.7695 (t) REVERT: J 32 PHE cc_start: 0.8633 (m-80) cc_final: 0.8381 (m-10) REVERT: J 94 THR cc_start: 0.8107 (m) cc_final: 0.7048 (p) REVERT: J 102 PHE cc_start: 0.8627 (m-80) cc_final: 0.8141 (m-80) REVERT: M 35 TRP cc_start: 0.7117 (m100) cc_final: 0.6405 (m100) REVERT: M 62 PHE cc_start: 0.7576 (m-80) cc_final: 0.7116 (m-80) REVERT: M 75 ILE cc_start: 0.9150 (mt) cc_final: 0.8655 (mt) REVERT: M 86 TYR cc_start: 0.8242 (m-80) cc_final: 0.7719 (m-10) REVERT: M 91 TYR cc_start: 0.8738 (t80) cc_final: 0.8242 (t80) REVERT: G 581 LEU cc_start: 0.9363 (mt) cc_final: 0.8947 (mm) REVERT: G 584 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8477 (mt-10) REVERT: G 615 SER cc_start: 0.9366 (t) cc_final: 0.8929 (m) REVERT: G 650 GLN cc_start: 0.8723 (tp40) cc_final: 0.8407 (tm-30) REVERT: G 652 GLN cc_start: 0.8908 (mm-40) cc_final: 0.8468 (pt0) REVERT: G 654 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8062 (mt-10) REVERT: G 656 ASN cc_start: 0.8848 (m-40) cc_final: 0.8594 (m-40) REVERT: F 103 GLN cc_start: 0.7954 (mt0) cc_final: 0.7350 (tt0) REVERT: F 114 GLN cc_start: 0.8503 (tp40) cc_final: 0.7808 (mm-40) REVERT: F 116 LEU cc_start: 0.8750 (mt) cc_final: 0.8409 (mt) REVERT: F 161 MET cc_start: 0.7135 (mmm) cc_final: 0.6935 (mmm) REVERT: F 172 VAL cc_start: 0.9236 (t) cc_final: 0.8961 (t) REVERT: F 195 ASN cc_start: 0.8816 (p0) cc_final: 0.8415 (t0) REVERT: F 202 THR cc_start: 0.8975 (m) cc_final: 0.8744 (m) REVERT: F 275 GLU cc_start: 0.8607 (tt0) cc_final: 0.8350 (tm-30) REVERT: F 319 TYR cc_start: 0.8196 (p90) cc_final: 0.7807 (p90) REVERT: F 342 LEU cc_start: 0.8219 (tp) cc_final: 0.7443 (tp) REVERT: F 368 ASP cc_start: 0.8780 (m-30) cc_final: 0.8361 (p0) REVERT: F 434 MET cc_start: 0.8690 (tmm) cc_final: 0.8234 (tmm) REVERT: F 449 ILE cc_start: 0.8746 (mt) cc_final: 0.8454 (tt) REVERT: F 492 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8483 (mp0) REVERT: K 32 PHE cc_start: 0.8922 (m-80) cc_final: 0.8463 (m-10) REVERT: K 34 MET cc_start: 0.9218 (mtp) cc_final: 0.8868 (mpp) REVERT: K 45 LEU cc_start: 0.8706 (mt) cc_final: 0.8484 (mp) REVERT: K 64 LYS cc_start: 0.8445 (mttt) cc_final: 0.8236 (mtmt) REVERT: K 80 LEU cc_start: 0.8970 (tp) cc_final: 0.8396 (tp) REVERT: K 105 GLN cc_start: 0.7457 (mt0) cc_final: 0.6558 (mp10) REVERT: N 32 TYR cc_start: 0.8947 (m-80) cc_final: 0.8286 (m-80) REVERT: N 47 MET cc_start: 0.8482 (mmt) cc_final: 0.7953 (mmm) REVERT: N 50 ASP cc_start: 0.8765 (m-30) cc_final: 0.7856 (m-30) REVERT: N 95 GLN cc_start: 0.8214 (mp10) cc_final: 0.7815 (mt0) REVERT: I 653 GLN cc_start: 0.9042 (tt0) cc_final: 0.8673 (tt0) outliers start: 4 outliers final: 1 residues processed: 845 average time/residue: 0.3545 time to fit residues: 442.4769 Evaluate side-chains 500 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 499 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 211 optimal weight: 7.9990 chunk 189 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 195 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN E 66 HIS E 185 ASN E 249 HIS E 478 ASN J 39 GLN ** J 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN M 39 HIS ** G 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 HIS F 99 ASN F 478 ASN K 13 GLN K 100BGLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 20707 Z= 0.441 Angle : 0.817 9.246 28122 Z= 0.412 Chirality : 0.049 0.266 3355 Planarity : 0.005 0.059 3520 Dihedral : 8.505 75.407 4066 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.15 % Allowed : 2.95 % Favored : 96.90 % 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: 0.57 (0.17), residues: 2290 helix: 1.20 (0.26), residues: 409 sheet: 0.26 (0.20), residues: 647 loop : 0.29 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP D 35 HIS 0.009 0.002 HIS A 249 PHE 0.031 0.003 PHE F 391 TYR 0.034 0.003 TYR K 100G ARG 0.011 0.001 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 513 time to evaluate : 2.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.8907 (m-80) cc_final: 0.8701 (m-80) REVERT: A 80 ASN cc_start: 0.8184 (t0) cc_final: 0.7677 (p0) REVERT: A 95 MET cc_start: 0.8733 (ptm) cc_final: 0.8354 (ppp) REVERT: A 99 ASN cc_start: 0.8768 (OUTLIER) cc_final: 0.8430 (t0) REVERT: A 107 ASP cc_start: 0.8935 (t70) cc_final: 0.8513 (t70) REVERT: A 110 SER cc_start: 0.9012 (t) cc_final: 0.8750 (p) REVERT: A 114 GLN cc_start: 0.9045 (tp40) cc_final: 0.8697 (tt0) REVERT: A 150 MET cc_start: 0.9348 (mmm) cc_final: 0.8942 (mmp) REVERT: A 340 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8664 (mm-30) REVERT: C 18 LEU cc_start: 0.8894 (tp) cc_final: 0.8639 (tp) REVERT: C 72 ASP cc_start: 0.8920 (p0) cc_final: 0.8663 (p0) REVERT: C 91 TYR cc_start: 0.8488 (m-80) cc_final: 0.8132 (m-80) REVERT: C 101 ASP cc_start: 0.9335 (p0) cc_final: 0.9083 (p0) REVERT: D 32 TYR cc_start: 0.8754 (m-80) cc_final: 0.8519 (m-80) REVERT: B 573 ILE cc_start: 0.9511 (mm) cc_final: 0.9176 (mm) REVERT: B 589 ASP cc_start: 0.9255 (m-30) cc_final: 0.9034 (m-30) REVERT: B 595 ILE cc_start: 0.9444 (tt) cc_final: 0.9176 (tt) REVERT: B 624 ASP cc_start: 0.9047 (m-30) cc_final: 0.8729 (m-30) REVERT: B 650 GLN cc_start: 0.9469 (tp40) cc_final: 0.9022 (tp40) REVERT: B 653 GLN cc_start: 0.9173 (tt0) cc_final: 0.8383 (tm-30) REVERT: E 104 MET cc_start: 0.9476 (tpp) cc_final: 0.9173 (tpp) REVERT: E 106 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8601 (mt-10) REVERT: E 150 MET cc_start: 0.8337 (mmm) cc_final: 0.7165 (mmt) REVERT: E 162 THR cc_start: 0.9369 (p) cc_final: 0.9138 (p) REVERT: E 173 TYR cc_start: 0.8635 (m-80) cc_final: 0.8129 (m-80) REVERT: E 191 TYR cc_start: 0.8407 (m-80) cc_final: 0.6399 (m-80) REVERT: E 199 SER cc_start: 0.8653 (p) cc_final: 0.8433 (t) REVERT: E 217 TYR cc_start: 0.8005 (m-10) cc_final: 0.7694 (m-80) REVERT: E 302 ASN cc_start: 0.8149 (m-40) cc_final: 0.7749 (p0) REVERT: E 328 MET cc_start: 0.8094 (mtp) cc_final: 0.7511 (tpp) REVERT: E 368 ASP cc_start: 0.8342 (p0) cc_final: 0.7395 (p0) REVERT: E 370 GLU cc_start: 0.9441 (mp0) cc_final: 0.9092 (mp0) REVERT: E 434 MET cc_start: 0.7388 (tmm) cc_final: 0.7014 (tmm) REVERT: J 32 PHE cc_start: 0.8258 (m-80) cc_final: 0.8019 (m-80) REVERT: J 105 GLN cc_start: 0.8218 (pp30) cc_final: 0.7991 (pp30) REVERT: M 53 GLN cc_start: 0.8611 (mp10) cc_final: 0.8125 (mp10) REVERT: M 97 ILE cc_start: 0.9262 (tp) cc_final: 0.9059 (tp) REVERT: G 543 ASN cc_start: 0.8869 (t0) cc_final: 0.8519 (t0) REVERT: G 573 ILE cc_start: 0.8805 (tp) cc_final: 0.8557 (tp) REVERT: G 581 LEU cc_start: 0.9368 (mt) cc_final: 0.9141 (mm) REVERT: G 601 LYS cc_start: 0.9043 (mppt) cc_final: 0.8788 (mtmm) REVERT: G 647 GLU cc_start: 0.8457 (tt0) cc_final: 0.8235 (tt0) REVERT: G 650 GLN cc_start: 0.8740 (tp40) cc_final: 0.8534 (tm-30) REVERT: G 652 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8531 (pt0) REVERT: G 654 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8244 (mt-10) REVERT: G 656 ASN cc_start: 0.9084 (m-40) cc_final: 0.8771 (m-40) REVERT: F 95 MET cc_start: 0.9324 (ppp) cc_final: 0.9079 (ppp) REVERT: F 100 MET cc_start: 0.9044 (mtm) cc_final: 0.8745 (mtt) REVERT: F 104 MET cc_start: 0.8755 (ttt) cc_final: 0.8502 (ttt) REVERT: F 112 TRP cc_start: 0.8557 (t-100) cc_final: 0.8033 (t-100) REVERT: F 114 GLN cc_start: 0.8559 (tp40) cc_final: 0.7820 (mm-40) REVERT: F 161 MET cc_start: 0.7938 (mmm) cc_final: 0.7662 (mmm) REVERT: F 319 TYR cc_start: 0.8512 (p90) cc_final: 0.8193 (p90) REVERT: F 320 PHE cc_start: 0.8107 (t80) cc_final: 0.7842 (t80) REVERT: F 342 LEU cc_start: 0.8254 (tp) cc_final: 0.7870 (tp) REVERT: F 368 ASP cc_start: 0.8762 (m-30) cc_final: 0.8407 (p0) REVERT: F 426 MET cc_start: 0.8015 (mtp) cc_final: 0.7436 (mtp) REVERT: F 434 MET cc_start: 0.8533 (tmm) cc_final: 0.8065 (tmm) REVERT: F 474 ASP cc_start: 0.7788 (t0) cc_final: 0.6935 (t0) REVERT: F 477 ASP cc_start: 0.9181 (m-30) cc_final: 0.8909 (m-30) REVERT: F 490 LYS cc_start: 0.8946 (tttm) cc_final: 0.8559 (ttmm) REVERT: F 492 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8427 (mp0) REVERT: K 32 PHE cc_start: 0.8926 (m-80) cc_final: 0.8410 (m-10) REVERT: K 34 MET cc_start: 0.9302 (mtp) cc_final: 0.8800 (mpp) REVERT: K 64 LYS cc_start: 0.8728 (mttt) cc_final: 0.8508 (mtmm) REVERT: K 97 MET cc_start: 0.8331 (tmm) cc_final: 0.7341 (tmm) REVERT: K 105 GLN cc_start: 0.7988 (mt0) cc_final: 0.6748 (mp10) REVERT: N 45 LYS cc_start: 0.9064 (tttt) cc_final: 0.8595 (tttp) REVERT: N 47 MET cc_start: 0.8548 (mmt) cc_final: 0.7751 (mmm) REVERT: N 95 GLN cc_start: 0.8148 (mp10) cc_final: 0.7884 (mp10) REVERT: I 585 HIS cc_start: 0.8803 (m-70) cc_final: 0.8334 (m170) REVERT: I 586 TYR cc_start: 0.9018 (t80) cc_final: 0.8717 (t80) REVERT: I 589 ASP cc_start: 0.9379 (m-30) cc_final: 0.9146 (m-30) REVERT: I 621 GLU cc_start: 0.8181 (tp30) cc_final: 0.7937 (tp30) REVERT: I 646 LEU cc_start: 0.9520 (mt) cc_final: 0.9204 (mt) outliers start: 3 outliers final: 0 residues processed: 514 average time/residue: 0.3542 time to fit residues: 275.5400 Evaluate side-chains 363 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 362 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 126 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 227 optimal weight: 1.9990 chunk 245 optimal weight: 20.0000 chunk 202 optimal weight: 3.9990 chunk 225 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 182 optimal weight: 2.9990 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 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN E 99 ASN E 188 ASN J 39 GLN ** G 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20707 Z= 0.266 Angle : 0.640 7.912 28122 Z= 0.329 Chirality : 0.045 0.263 3355 Planarity : 0.004 0.074 3520 Dihedral : 7.353 56.733 4066 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.17), residues: 2290 helix: 1.22 (0.26), residues: 421 sheet: 0.20 (0.20), residues: 629 loop : 0.14 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 427 HIS 0.009 0.001 HIS A 249 PHE 0.025 0.002 PHE F 159 TYR 0.015 0.002 TYR A 173 ARG 0.013 0.001 ARG N 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 492 time to evaluate : 2.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8247 (t0) cc_final: 0.7716 (p0) REVERT: A 107 ASP cc_start: 0.8925 (t70) cc_final: 0.8564 (t70) REVERT: A 110 SER cc_start: 0.9092 (t) cc_final: 0.8830 (p) REVERT: A 114 GLN cc_start: 0.9038 (tp40) cc_final: 0.8711 (tt0) REVERT: A 150 MET cc_start: 0.9339 (mmm) cc_final: 0.8920 (mmp) REVERT: A 340 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8571 (mm-30) REVERT: A 384 TYR cc_start: 0.6250 (m-80) cc_final: 0.5261 (m-80) REVERT: C 101 ASP cc_start: 0.9345 (p0) cc_final: 0.8992 (p0) REVERT: D 91 TYR cc_start: 0.8651 (t80) cc_final: 0.7314 (t80) REVERT: B 573 ILE cc_start: 0.9405 (mm) cc_final: 0.8795 (mm) REVERT: B 579 ARG cc_start: 0.8582 (mtm-85) cc_final: 0.7975 (mtm-85) REVERT: B 589 ASP cc_start: 0.9239 (m-30) cc_final: 0.8967 (m-30) REVERT: B 595 ILE cc_start: 0.9423 (tt) cc_final: 0.9215 (tt) REVERT: B 608 VAL cc_start: 0.9368 (t) cc_final: 0.9052 (m) REVERT: B 624 ASP cc_start: 0.9037 (m-30) cc_final: 0.8707 (m-30) REVERT: B 650 GLN cc_start: 0.9494 (tp40) cc_final: 0.9041 (tp40) REVERT: B 653 GLN cc_start: 0.9214 (tt0) cc_final: 0.8489 (tm-30) REVERT: E 106 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8542 (mt-10) REVERT: E 150 MET cc_start: 0.8346 (mmm) cc_final: 0.7466 (mmt) REVERT: E 173 TYR cc_start: 0.8614 (m-80) cc_final: 0.8307 (m-10) REVERT: E 199 SER cc_start: 0.8631 (p) cc_final: 0.8406 (t) REVERT: E 302 ASN cc_start: 0.8144 (m-40) cc_final: 0.7754 (p0) REVERT: E 328 MET cc_start: 0.8222 (mtp) cc_final: 0.7695 (tpp) REVERT: E 368 ASP cc_start: 0.8320 (p0) cc_final: 0.7701 (p0) REVERT: E 434 MET cc_start: 0.7393 (tmm) cc_final: 0.6927 (tmm) REVERT: J 43 LYS cc_start: 0.9050 (mmtt) cc_final: 0.8773 (pttp) REVERT: M 53 GLN cc_start: 0.8780 (mp10) cc_final: 0.8235 (mp10) REVERT: M 91 TYR cc_start: 0.8930 (t80) cc_final: 0.8303 (t80) REVERT: M 103 ARG cc_start: 0.8550 (mmm160) cc_final: 0.8338 (mmm160) REVERT: G 543 ASN cc_start: 0.8835 (t0) cc_final: 0.8528 (t0) REVERT: G 581 LEU cc_start: 0.9351 (mt) cc_final: 0.9044 (mm) REVERT: G 601 LYS cc_start: 0.9058 (mppt) cc_final: 0.8730 (mtmm) REVERT: G 648 GLU cc_start: 0.8190 (pp20) cc_final: 0.7928 (tm-30) REVERT: G 652 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8595 (pt0) REVERT: G 654 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8529 (mt-10) REVERT: G 656 ASN cc_start: 0.9043 (m-40) cc_final: 0.8756 (m-40) REVERT: F 100 MET cc_start: 0.8886 (mtm) cc_final: 0.8544 (mtt) REVERT: F 107 ASP cc_start: 0.8680 (m-30) cc_final: 0.8391 (m-30) REVERT: F 112 TRP cc_start: 0.8428 (t-100) cc_final: 0.7801 (t-100) REVERT: F 114 GLN cc_start: 0.8569 (tp40) cc_final: 0.7803 (mm-40) REVERT: F 161 MET cc_start: 0.7835 (mmm) cc_final: 0.7522 (mmm) REVERT: F 319 TYR cc_start: 0.8578 (p90) cc_final: 0.8184 (p90) REVERT: F 320 PHE cc_start: 0.8067 (t80) cc_final: 0.7794 (t80) REVERT: F 349 LEU cc_start: 0.9190 (mt) cc_final: 0.8988 (mt) REVERT: F 368 ASP cc_start: 0.8710 (m-30) cc_final: 0.8462 (p0) REVERT: F 426 MET cc_start: 0.7876 (mtp) cc_final: 0.7434 (mtp) REVERT: F 434 MET cc_start: 0.8400 (tmm) cc_final: 0.8076 (tmm) REVERT: F 492 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8931 (tt0) REVERT: K 91 TYR cc_start: 0.8268 (m-10) cc_final: 0.7940 (m-10) REVERT: K 105 GLN cc_start: 0.7566 (mt0) cc_final: 0.6510 (mp10) REVERT: N 45 LYS cc_start: 0.9014 (tttt) cc_final: 0.8479 (tttp) REVERT: N 46 LEU cc_start: 0.9194 (tp) cc_final: 0.8835 (tp) REVERT: N 47 MET cc_start: 0.8620 (mmt) cc_final: 0.7858 (mmt) REVERT: N 95 GLN cc_start: 0.8140 (mp10) cc_final: 0.7867 (mp10) REVERT: I 530 MET cc_start: 0.9041 (mtm) cc_final: 0.8837 (mtm) REVERT: I 584 GLU cc_start: 0.9095 (tm-30) cc_final: 0.8780 (tm-30) REVERT: I 585 HIS cc_start: 0.8813 (m-70) cc_final: 0.8294 (m170) REVERT: I 586 TYR cc_start: 0.9072 (t80) cc_final: 0.8782 (t80) REVERT: I 621 GLU cc_start: 0.8121 (tp30) cc_final: 0.7891 (tp30) REVERT: I 642 ILE cc_start: 0.9810 (mt) cc_final: 0.9582 (mt) REVERT: I 646 LEU cc_start: 0.9412 (mt) cc_final: 0.9156 (mt) outliers start: 0 outliers final: 0 residues processed: 492 average time/residue: 0.3248 time to fit residues: 245.5729 Evaluate side-chains 377 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 224 optimal weight: 0.9990 chunk 170 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 228 optimal weight: 30.0000 chunk 241 optimal weight: 20.0000 chunk 119 optimal weight: 7.9990 chunk 216 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN D 37 GLN G 577 GLN ** G 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 HIS ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 352 HIS F 478 ASN N 6 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20707 Z= 0.267 Angle : 0.625 7.283 28122 Z= 0.319 Chirality : 0.044 0.277 3355 Planarity : 0.004 0.039 3520 Dihedral : 6.531 46.197 4066 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.17), residues: 2290 helix: 1.02 (0.26), residues: 429 sheet: 0.23 (0.20), residues: 665 loop : -0.02 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 479 HIS 0.009 0.001 HIS A 249 PHE 0.022 0.002 PHE F 391 TYR 0.015 0.002 TYR A 134 ARG 0.010 0.001 ARG G 588 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 459 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8290 (t0) cc_final: 0.7754 (p0) REVERT: A 95 MET cc_start: 0.8677 (ptm) cc_final: 0.8026 (ppp) REVERT: A 107 ASP cc_start: 0.8965 (t70) cc_final: 0.8606 (t70) REVERT: A 110 SER cc_start: 0.9097 (t) cc_final: 0.8849 (p) REVERT: A 114 GLN cc_start: 0.9049 (tp40) cc_final: 0.8667 (tt0) REVERT: A 150 MET cc_start: 0.9459 (mmm) cc_final: 0.9143 (mmm) REVERT: A 340 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8569 (mm-30) REVERT: A 422 GLN cc_start: 0.8445 (mm-40) cc_final: 0.8030 (mm-40) REVERT: C 18 LEU cc_start: 0.8960 (tp) cc_final: 0.8720 (tp) REVERT: C 101 ASP cc_start: 0.9324 (p0) cc_final: 0.9012 (p0) REVERT: D 91 TYR cc_start: 0.8562 (t80) cc_final: 0.7099 (t80) REVERT: B 573 ILE cc_start: 0.9367 (mm) cc_final: 0.8812 (tp) REVERT: B 589 ASP cc_start: 0.9271 (m-30) cc_final: 0.8936 (m-30) REVERT: B 595 ILE cc_start: 0.9402 (tt) cc_final: 0.9123 (tt) REVERT: B 608 VAL cc_start: 0.9379 (t) cc_final: 0.9087 (m) REVERT: B 626 MET cc_start: 0.8749 (ttm) cc_final: 0.8360 (ttm) REVERT: B 630 GLN cc_start: 0.9072 (mt0) cc_final: 0.8390 (mt0) REVERT: B 650 GLN cc_start: 0.9486 (tp40) cc_final: 0.9012 (tp40) REVERT: B 653 GLN cc_start: 0.9215 (tt0) cc_final: 0.8523 (tm-30) REVERT: E 106 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8528 (mt-10) REVERT: E 134 TYR cc_start: 0.7535 (t80) cc_final: 0.7110 (t80) REVERT: E 150 MET cc_start: 0.8481 (mmm) cc_final: 0.7463 (mmm) REVERT: E 173 TYR cc_start: 0.8634 (m-80) cc_final: 0.8319 (m-10) REVERT: E 302 ASN cc_start: 0.8071 (m-40) cc_final: 0.7761 (p0) REVERT: E 328 MET cc_start: 0.8227 (mtp) cc_final: 0.7564 (mpp) REVERT: E 368 ASP cc_start: 0.8361 (p0) cc_final: 0.7709 (p0) REVERT: E 434 MET cc_start: 0.7405 (tmm) cc_final: 0.7101 (tmm) REVERT: J 75 LYS cc_start: 0.8990 (mptt) cc_final: 0.8780 (pttm) REVERT: J 77 THR cc_start: 0.8092 (m) cc_final: 0.7565 (m) REVERT: M 53 GLN cc_start: 0.8872 (mp10) cc_final: 0.8283 (mp10) REVERT: M 91 TYR cc_start: 0.8891 (t80) cc_final: 0.8188 (t80) REVERT: M 97 ILE cc_start: 0.9255 (tp) cc_final: 0.9031 (tp) REVERT: G 543 ASN cc_start: 0.8810 (t0) cc_final: 0.8529 (t0) REVERT: G 574 LYS cc_start: 0.8536 (mptt) cc_final: 0.8234 (pttt) REVERT: G 601 LYS cc_start: 0.8990 (mppt) cc_final: 0.8701 (mtmm) REVERT: G 648 GLU cc_start: 0.8279 (pp20) cc_final: 0.7822 (pp20) REVERT: G 652 GLN cc_start: 0.8911 (mm-40) cc_final: 0.8559 (pt0) REVERT: G 656 ASN cc_start: 0.9029 (m-40) cc_final: 0.8725 (m-40) REVERT: F 100 MET cc_start: 0.8940 (mtm) cc_final: 0.8659 (mtt) REVERT: F 107 ASP cc_start: 0.8647 (m-30) cc_final: 0.8321 (m-30) REVERT: F 112 TRP cc_start: 0.8382 (t-100) cc_final: 0.7872 (t-100) REVERT: F 114 GLN cc_start: 0.8605 (tp40) cc_final: 0.7864 (mm-40) REVERT: F 161 MET cc_start: 0.7902 (mmm) cc_final: 0.7487 (mmm) REVERT: F 319 TYR cc_start: 0.8632 (p90) cc_final: 0.8241 (p90) REVERT: F 320 PHE cc_start: 0.8146 (t80) cc_final: 0.7737 (t80) REVERT: F 368 ASP cc_start: 0.8717 (m-30) cc_final: 0.8460 (p0) REVERT: F 414 LEU cc_start: 0.9125 (mt) cc_final: 0.8705 (mp) REVERT: F 426 MET cc_start: 0.7836 (mtp) cc_final: 0.7582 (mtp) REVERT: F 434 MET cc_start: 0.8342 (tmm) cc_final: 0.8100 (tmm) REVERT: F 492 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8854 (tt0) REVERT: K 1 GLU cc_start: 0.6536 (tp30) cc_final: 0.6273 (tp30) REVERT: K 3 GLN cc_start: 0.8684 (mt0) cc_final: 0.8425 (tm-30) REVERT: K 91 TYR cc_start: 0.8409 (m-10) cc_final: 0.7895 (m-10) REVERT: K 105 GLN cc_start: 0.7642 (mt0) cc_final: 0.6511 (mp10) REVERT: N 45 LYS cc_start: 0.9029 (tttt) cc_final: 0.8701 (tttp) REVERT: N 95 GLN cc_start: 0.8139 (mp10) cc_final: 0.7877 (mp10) REVERT: I 530 MET cc_start: 0.9090 (mtm) cc_final: 0.8663 (mtm) REVERT: I 584 GLU cc_start: 0.9083 (tm-30) cc_final: 0.8813 (tm-30) REVERT: I 586 TYR cc_start: 0.9069 (t80) cc_final: 0.8734 (t80) REVERT: I 621 GLU cc_start: 0.8080 (tp30) cc_final: 0.7844 (tp30) REVERT: I 642 ILE cc_start: 0.9798 (mt) cc_final: 0.9581 (mt) REVERT: I 646 LEU cc_start: 0.9392 (mt) cc_final: 0.9140 (mt) outliers start: 0 outliers final: 0 residues processed: 459 average time/residue: 0.3246 time to fit residues: 230.0334 Evaluate side-chains 360 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 201 optimal weight: 0.1980 chunk 137 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 179 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 206 optimal weight: 7.9990 chunk 167 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 216 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 99 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN C 3 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN B 616 ASN ** G 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 HIS F 82 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 185 ASN F 352 HIS K 76 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 20707 Z= 0.396 Angle : 0.702 7.700 28122 Z= 0.356 Chirality : 0.046 0.284 3355 Planarity : 0.004 0.044 3520 Dihedral : 6.615 55.736 4066 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.05 % Allowed : 2.46 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.17), residues: 2290 helix: 0.93 (0.26), residues: 414 sheet: 0.12 (0.21), residues: 638 loop : -0.24 (0.17), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 112 HIS 0.008 0.001 HIS A 249 PHE 0.023 0.002 PHE F 391 TYR 0.019 0.002 TYR K 27 ARG 0.011 0.001 ARG G 588 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 414 time to evaluate : 2.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8084 (t0) cc_final: 0.7644 (p0) REVERT: A 100 MET cc_start: 0.8621 (mtm) cc_final: 0.8331 (mtp) REVERT: A 107 ASP cc_start: 0.8989 (t70) cc_final: 0.8650 (t70) REVERT: A 110 SER cc_start: 0.9148 (t) cc_final: 0.8937 (p) REVERT: A 114 GLN cc_start: 0.9105 (tp40) cc_final: 0.8738 (tt0) REVERT: A 150 MET cc_start: 0.9500 (mmm) cc_final: 0.9061 (mmm) REVERT: A 340 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8604 (mm-30) REVERT: A 424 ILE cc_start: 0.9410 (mp) cc_final: 0.8778 (mp) REVERT: A 434 MET cc_start: 0.8921 (tmm) cc_final: 0.8331 (tmm) REVERT: C 32 PHE cc_start: 0.8065 (m-80) cc_final: 0.7801 (m-80) REVERT: C 50 LEU cc_start: 0.9598 (tt) cc_final: 0.9391 (tt) REVERT: C 101 ASP cc_start: 0.9368 (p0) cc_final: 0.9024 (p0) REVERT: D 91 TYR cc_start: 0.8552 (t80) cc_final: 0.7380 (t80) REVERT: B 573 ILE cc_start: 0.9321 (mm) cc_final: 0.8949 (tp) REVERT: B 579 ARG cc_start: 0.8632 (mtm-85) cc_final: 0.8115 (mtm-85) REVERT: B 589 ASP cc_start: 0.9314 (m-30) cc_final: 0.9035 (m-30) REVERT: B 595 ILE cc_start: 0.9453 (tt) cc_final: 0.9137 (tt) REVERT: B 608 VAL cc_start: 0.9402 (t) cc_final: 0.9122 (m) REVERT: B 621 GLU cc_start: 0.8454 (tp30) cc_final: 0.8090 (tp30) REVERT: B 650 GLN cc_start: 0.9490 (tp40) cc_final: 0.9207 (tp40) REVERT: B 653 GLN cc_start: 0.9218 (tt0) cc_final: 0.8427 (tm-30) REVERT: B 657 GLU cc_start: 0.8835 (mt-10) cc_final: 0.7601 (mt-10) REVERT: E 106 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8542 (mt-10) REVERT: E 150 MET cc_start: 0.8498 (mmm) cc_final: 0.7458 (mmm) REVERT: E 328 MET cc_start: 0.8290 (mtp) cc_final: 0.7540 (mmm) REVERT: E 425 ASN cc_start: 0.8114 (p0) cc_final: 0.7801 (p0) REVERT: E 434 MET cc_start: 0.7594 (tmm) cc_final: 0.7177 (tmm) REVERT: E 475 MET cc_start: 0.8819 (mmp) cc_final: 0.8479 (mmm) REVERT: J 43 LYS cc_start: 0.9053 (mmmt) cc_final: 0.8525 (pttp) REVERT: J 52 ASP cc_start: 0.9322 (p0) cc_final: 0.8980 (p0) REVERT: J 72 ASP cc_start: 0.8682 (t70) cc_final: 0.8381 (p0) REVERT: M 53 GLN cc_start: 0.8895 (mp10) cc_final: 0.8299 (mp10) REVERT: M 97 ILE cc_start: 0.9251 (tp) cc_final: 0.8940 (tp) REVERT: G 543 ASN cc_start: 0.8913 (t0) cc_final: 0.8622 (t0) REVERT: G 581 LEU cc_start: 0.9411 (mt) cc_final: 0.9056 (mm) REVERT: G 601 LYS cc_start: 0.9103 (mppt) cc_final: 0.8591 (mtmm) REVERT: G 648 GLU cc_start: 0.8442 (pp20) cc_final: 0.8196 (pp20) REVERT: G 652 GLN cc_start: 0.8966 (mm-40) cc_final: 0.8646 (pt0) REVERT: G 656 ASN cc_start: 0.9075 (m-40) cc_final: 0.8859 (m-40) REVERT: F 100 MET cc_start: 0.8892 (mtm) cc_final: 0.8601 (mtt) REVERT: F 107 ASP cc_start: 0.8655 (m-30) cc_final: 0.8297 (m-30) REVERT: F 112 TRP cc_start: 0.8653 (t-100) cc_final: 0.7954 (t-100) REVERT: F 114 GLN cc_start: 0.8591 (tp40) cc_final: 0.7807 (mm-40) REVERT: F 319 TYR cc_start: 0.8661 (p90) cc_final: 0.8354 (p90) REVERT: F 368 ASP cc_start: 0.8771 (m-30) cc_final: 0.8468 (p0) REVERT: F 376 PHE cc_start: 0.7171 (t80) cc_final: 0.6648 (t80) REVERT: F 414 LEU cc_start: 0.9134 (mt) cc_final: 0.8735 (mp) REVERT: F 434 MET cc_start: 0.8342 (tmm) cc_final: 0.8096 (tmm) REVERT: F 492 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8399 (mp0) REVERT: K 1 GLU cc_start: 0.6802 (tp30) cc_final: 0.6490 (tp30) REVERT: K 46 GLU cc_start: 0.8818 (tp30) cc_final: 0.8483 (tp30) REVERT: K 64 LYS cc_start: 0.8863 (mtmt) cc_final: 0.8460 (mttp) REVERT: K 91 TYR cc_start: 0.8567 (m-10) cc_final: 0.8051 (m-10) REVERT: K 105 GLN cc_start: 0.7756 (mt0) cc_final: 0.7403 (mt0) REVERT: N 46 LEU cc_start: 0.9181 (tp) cc_final: 0.8955 (tp) REVERT: N 47 MET cc_start: 0.8587 (mmt) cc_final: 0.8020 (mmm) REVERT: N 95 GLN cc_start: 0.8160 (mp10) cc_final: 0.7938 (mp10) REVERT: I 530 MET cc_start: 0.9101 (mtm) cc_final: 0.8855 (mtp) REVERT: I 584 GLU cc_start: 0.9075 (tm-30) cc_final: 0.8737 (tm-30) REVERT: I 586 TYR cc_start: 0.9122 (t80) cc_final: 0.8855 (t80) REVERT: I 589 ASP cc_start: 0.9412 (m-30) cc_final: 0.9191 (m-30) REVERT: I 621 GLU cc_start: 0.8079 (tp30) cc_final: 0.7821 (tp30) REVERT: I 646 LEU cc_start: 0.9425 (mt) cc_final: 0.9157 (mt) outliers start: 1 outliers final: 0 residues processed: 414 average time/residue: 0.3153 time to fit residues: 202.6571 Evaluate side-chains 328 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 81 optimal weight: 6.9990 chunk 217 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 241 optimal weight: 20.0000 chunk 200 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 577 GLN ** G 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 658 GLN F 72 HIS ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20707 Z= 0.238 Angle : 0.610 7.192 28122 Z= 0.313 Chirality : 0.044 0.265 3355 Planarity : 0.004 0.050 3520 Dihedral : 6.189 57.287 4066 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.17), residues: 2290 helix: 1.15 (0.27), residues: 414 sheet: 0.25 (0.21), residues: 639 loop : -0.27 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 479 HIS 0.015 0.001 HIS F 374 PHE 0.022 0.002 PHE F 391 TYR 0.022 0.002 TYR E 217 ARG 0.011 0.001 ARG G 588 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 437 time to evaluate : 2.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8154 (t0) cc_final: 0.7696 (p0) REVERT: A 100 MET cc_start: 0.8545 (mtm) cc_final: 0.8254 (mtp) REVERT: A 107 ASP cc_start: 0.8932 (t70) cc_final: 0.8604 (t70) REVERT: A 114 GLN cc_start: 0.9110 (tp40) cc_final: 0.8736 (tt0) REVERT: A 150 MET cc_start: 0.9426 (mmm) cc_final: 0.8969 (mmm) REVERT: A 340 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8546 (mm-30) REVERT: A 424 ILE cc_start: 0.9358 (mp) cc_final: 0.8913 (mp) REVERT: A 434 MET cc_start: 0.8870 (tmm) cc_final: 0.8306 (tmm) REVERT: C 32 PHE cc_start: 0.8067 (m-80) cc_final: 0.7807 (m-80) REVERT: C 91 TYR cc_start: 0.8449 (m-80) cc_final: 0.8103 (m-80) REVERT: C 101 ASP cc_start: 0.9393 (p0) cc_final: 0.8977 (p0) REVERT: D 49 TYR cc_start: 0.8741 (p90) cc_final: 0.8483 (p90) REVERT: D 53 GLN cc_start: 0.9104 (tp40) cc_final: 0.8469 (tp40) REVERT: D 91 TYR cc_start: 0.8541 (t80) cc_final: 0.7273 (t80) REVERT: B 573 ILE cc_start: 0.9265 (mm) cc_final: 0.9008 (mm) REVERT: B 579 ARG cc_start: 0.8520 (mtm-85) cc_final: 0.8000 (mtm-85) REVERT: B 589 ASP cc_start: 0.9307 (m-30) cc_final: 0.9009 (m-30) REVERT: B 595 ILE cc_start: 0.9391 (tt) cc_final: 0.9058 (tt) REVERT: B 608 VAL cc_start: 0.9410 (t) cc_final: 0.9178 (m) REVERT: B 621 GLU cc_start: 0.8334 (tp30) cc_final: 0.7984 (tp30) REVERT: B 630 GLN cc_start: 0.8997 (mt0) cc_final: 0.8555 (mt0) REVERT: B 650 GLN cc_start: 0.9433 (tp40) cc_final: 0.8970 (tp40) REVERT: B 653 GLN cc_start: 0.9202 (tt0) cc_final: 0.8348 (tm-30) REVERT: B 657 GLU cc_start: 0.8831 (mt-10) cc_final: 0.7526 (mt-10) REVERT: E 40 TYR cc_start: 0.9047 (t80) cc_final: 0.8744 (t80) REVERT: E 100 MET cc_start: 0.8411 (mtm) cc_final: 0.8207 (ptp) REVERT: E 106 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8508 (mt-10) REVERT: E 173 TYR cc_start: 0.8500 (m-80) cc_final: 0.8168 (m-10) REVERT: E 328 MET cc_start: 0.8396 (mtp) cc_final: 0.8076 (mmm) REVERT: E 368 ASP cc_start: 0.8431 (p0) cc_final: 0.7794 (p0) REVERT: E 425 ASN cc_start: 0.8189 (p0) cc_final: 0.7834 (p0) REVERT: E 434 MET cc_start: 0.7579 (tmm) cc_final: 0.7205 (tmm) REVERT: J 43 LYS cc_start: 0.9041 (mmmt) cc_final: 0.8495 (pttp) REVERT: J 52 ASP cc_start: 0.9288 (p0) cc_final: 0.8927 (p0) REVERT: J 72 ASP cc_start: 0.8867 (t70) cc_final: 0.8658 (t0) REVERT: M 53 GLN cc_start: 0.8859 (mp10) cc_final: 0.8249 (mp10) REVERT: M 91 TYR cc_start: 0.8939 (t80) cc_final: 0.8255 (t80) REVERT: G 543 ASN cc_start: 0.8880 (t0) cc_final: 0.8638 (t0) REVERT: G 574 LYS cc_start: 0.8520 (mptt) cc_final: 0.8131 (pttt) REVERT: G 581 LEU cc_start: 0.9369 (mt) cc_final: 0.9016 (mm) REVERT: G 601 LYS cc_start: 0.9003 (mppt) cc_final: 0.8582 (mtmm) REVERT: G 615 SER cc_start: 0.9282 (t) cc_final: 0.8936 (m) REVERT: G 630 GLN cc_start: 0.9012 (mt0) cc_final: 0.8668 (mt0) REVERT: G 648 GLU cc_start: 0.8438 (pp20) cc_final: 0.8200 (pp20) REVERT: G 652 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8600 (pt0) REVERT: G 656 ASN cc_start: 0.8934 (m-40) cc_final: 0.8723 (m-40) REVERT: F 78 ASP cc_start: 0.8301 (p0) cc_final: 0.8003 (t70) REVERT: F 100 MET cc_start: 0.8947 (mtm) cc_final: 0.8664 (mtt) REVERT: F 107 ASP cc_start: 0.8589 (m-30) cc_final: 0.8248 (m-30) REVERT: F 112 TRP cc_start: 0.8596 (t-100) cc_final: 0.7825 (t-100) REVERT: F 114 GLN cc_start: 0.8584 (tp40) cc_final: 0.7759 (mm-40) REVERT: F 161 MET cc_start: 0.8207 (mmm) cc_final: 0.7188 (mmm) REVERT: F 319 TYR cc_start: 0.8655 (p90) cc_final: 0.8391 (p90) REVERT: F 368 ASP cc_start: 0.8755 (m-30) cc_final: 0.8519 (p0) REVERT: F 376 PHE cc_start: 0.7103 (t80) cc_final: 0.6833 (t80) REVERT: F 414 LEU cc_start: 0.9136 (mt) cc_final: 0.8726 (mp) REVERT: F 492 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8883 (tt0) REVERT: K 64 LYS cc_start: 0.8905 (mtmt) cc_final: 0.8605 (mttp) REVERT: K 91 TYR cc_start: 0.8511 (m-10) cc_final: 0.7956 (m-10) REVERT: K 105 GLN cc_start: 0.7715 (mt0) cc_final: 0.7361 (mt0) REVERT: N 46 LEU cc_start: 0.9137 (tp) cc_final: 0.8501 (tp) REVERT: N 53 GLN cc_start: 0.7984 (mp10) cc_final: 0.7533 (mp10) REVERT: N 95 GLN cc_start: 0.8126 (mp10) cc_final: 0.7891 (mp10) REVERT: I 530 MET cc_start: 0.9062 (mtm) cc_final: 0.8745 (mtp) REVERT: I 584 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8785 (tm-30) REVERT: I 586 TYR cc_start: 0.9097 (t80) cc_final: 0.8801 (t80) REVERT: I 589 ASP cc_start: 0.9395 (m-30) cc_final: 0.9134 (m-30) REVERT: I 621 GLU cc_start: 0.8061 (tp30) cc_final: 0.7818 (tp30) REVERT: I 646 LEU cc_start: 0.9392 (mt) cc_final: 0.9146 (mt) outliers start: 0 outliers final: 0 residues processed: 437 average time/residue: 0.3161 time to fit residues: 213.5609 Evaluate side-chains 346 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 233 optimal weight: 30.0000 chunk 27 optimal weight: 10.0000 chunk 137 optimal weight: 9.9990 chunk 176 optimal weight: 0.2980 chunk 136 optimal weight: 0.8980 chunk 203 optimal weight: 7.9990 chunk 135 optimal weight: 4.9990 chunk 240 optimal weight: 40.0000 chunk 150 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 352 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 577 GLN ** G 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20707 Z= 0.315 Angle : 0.644 7.591 28122 Z= 0.329 Chirality : 0.045 0.376 3355 Planarity : 0.004 0.057 3520 Dihedral : 6.284 58.096 4066 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.05 % Allowed : 1.48 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.17), residues: 2290 helix: 1.10 (0.27), residues: 414 sheet: 0.11 (0.20), residues: 651 loop : -0.41 (0.17), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 479 HIS 0.010 0.001 HIS F 374 PHE 0.022 0.002 PHE F 391 TYR 0.021 0.002 TYR J 100G ARG 0.014 0.001 ARG G 588 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 415 time to evaluate : 2.301 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 80 ASN cc_start: 0.8185 (t0) cc_final: 0.7787 (p0) REVERT: A 100 MET cc_start: 0.8622 (mtm) cc_final: 0.8262 (mtp) REVERT: A 107 ASP cc_start: 0.8944 (t70) cc_final: 0.8622 (t70) REVERT: A 114 GLN cc_start: 0.9106 (tp40) cc_final: 0.8739 (tt0) REVERT: A 150 MET cc_start: 0.9280 (mmm) cc_final: 0.8817 (mmm) REVERT: A 340 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8571 (mm-30) REVERT: A 352 HIS cc_start: 0.8500 (m90) cc_final: 0.8139 (m90) REVERT: A 424 ILE cc_start: 0.9350 (mp) cc_final: 0.9082 (mp) REVERT: A 434 MET cc_start: 0.8967 (tmm) cc_final: 0.8363 (tmm) REVERT: C 32 PHE cc_start: 0.8034 (m-80) cc_final: 0.7786 (m-80) REVERT: C 46 GLU cc_start: 0.8740 (tt0) cc_final: 0.7873 (tp30) REVERT: C 48 VAL cc_start: 0.8921 (t) cc_final: 0.8676 (t) REVERT: C 50 LEU cc_start: 0.9559 (tt) cc_final: 0.9314 (tt) REVERT: C 91 TYR cc_start: 0.8352 (m-80) cc_final: 0.8014 (m-80) REVERT: C 101 ASP cc_start: 0.9390 (p0) cc_final: 0.9003 (p0) REVERT: D 91 TYR cc_start: 0.8482 (t80) cc_final: 0.7398 (t80) REVERT: B 579 ARG cc_start: 0.8489 (mtm-85) cc_final: 0.8011 (mtm-85) REVERT: B 589 ASP cc_start: 0.9329 (m-30) cc_final: 0.9041 (m-30) REVERT: B 608 VAL cc_start: 0.9410 (t) cc_final: 0.9139 (m) REVERT: B 621 GLU cc_start: 0.8370 (tp30) cc_final: 0.8032 (tp30) REVERT: B 630 GLN cc_start: 0.9074 (mt0) cc_final: 0.8493 (mt0) REVERT: B 650 GLN cc_start: 0.9503 (tp40) cc_final: 0.9154 (tp40) REVERT: B 653 GLN cc_start: 0.9204 (tt0) cc_final: 0.8628 (tm-30) REVERT: B 657 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8265 (mt-10) REVERT: E 100 MET cc_start: 0.8566 (mtm) cc_final: 0.8300 (ptp) REVERT: E 104 MET cc_start: 0.9379 (mmm) cc_final: 0.9146 (tpt) REVERT: E 106 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8517 (mt-10) REVERT: E 107 ASP cc_start: 0.8455 (m-30) cc_final: 0.8158 (m-30) REVERT: E 134 TYR cc_start: 0.7509 (t80) cc_final: 0.7069 (t80) REVERT: E 173 TYR cc_start: 0.8510 (m-80) cc_final: 0.8138 (m-10) REVERT: E 328 MET cc_start: 0.8518 (mtp) cc_final: 0.8304 (mtt) REVERT: E 368 ASP cc_start: 0.8483 (p0) cc_final: 0.7776 (p0) REVERT: E 425 ASN cc_start: 0.8237 (p0) cc_final: 0.7873 (p0) REVERT: E 434 MET cc_start: 0.7643 (tmm) cc_final: 0.7283 (tmm) REVERT: J 43 LYS cc_start: 0.9028 (mmmt) cc_final: 0.8451 (pttp) REVERT: J 52 ASP cc_start: 0.9333 (p0) cc_final: 0.9065 (p0) REVERT: M 53 GLN cc_start: 0.8901 (mp10) cc_final: 0.8287 (mp10) REVERT: M 91 TYR cc_start: 0.8915 (t80) cc_final: 0.8204 (t80) REVERT: M 97 ILE cc_start: 0.9251 (tp) cc_final: 0.8831 (tp) REVERT: G 543 ASN cc_start: 0.8920 (t0) cc_final: 0.8674 (t0) REVERT: G 574 LYS cc_start: 0.8608 (mptt) cc_final: 0.8221 (pttt) REVERT: G 581 LEU cc_start: 0.9401 (mt) cc_final: 0.8998 (mm) REVERT: G 601 LYS cc_start: 0.8976 (mppt) cc_final: 0.8507 (mtmm) REVERT: G 615 SER cc_start: 0.9288 (t) cc_final: 0.8977 (m) REVERT: G 648 GLU cc_start: 0.8516 (pp20) cc_final: 0.8244 (pp20) REVERT: G 652 GLN cc_start: 0.8978 (mm-40) cc_final: 0.8606 (pt0) REVERT: F 78 ASP cc_start: 0.8294 (p0) cc_final: 0.8012 (t70) REVERT: F 100 MET cc_start: 0.8917 (mtm) cc_final: 0.8630 (mtt) REVERT: F 107 ASP cc_start: 0.8590 (m-30) cc_final: 0.8245 (m-30) REVERT: F 112 TRP cc_start: 0.8725 (t-100) cc_final: 0.7670 (t-100) REVERT: F 114 GLN cc_start: 0.8536 (tp40) cc_final: 0.7720 (mm-40) REVERT: F 319 TYR cc_start: 0.8676 (p90) cc_final: 0.8387 (p90) REVERT: F 368 ASP cc_start: 0.8734 (m-30) cc_final: 0.8498 (p0) REVERT: F 376 PHE cc_start: 0.7225 (t80) cc_final: 0.6891 (t80) REVERT: F 426 MET cc_start: 0.8182 (mtp) cc_final: 0.7807 (mtp) REVERT: F 434 MET cc_start: 0.8216 (tmm) cc_final: 0.7802 (tmm) REVERT: F 492 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8814 (tt0) REVERT: K 64 LYS cc_start: 0.8929 (mtmt) cc_final: 0.8621 (mttp) REVERT: K 91 TYR cc_start: 0.8647 (m-10) cc_final: 0.8065 (m-10) REVERT: K 105 GLN cc_start: 0.7793 (mt0) cc_final: 0.7499 (mt0) REVERT: N 47 MET cc_start: 0.8195 (mmt) cc_final: 0.7984 (mmm) REVERT: N 50 ASP cc_start: 0.8880 (m-30) cc_final: 0.8588 (m-30) REVERT: N 53 GLN cc_start: 0.8260 (mp10) cc_final: 0.7601 (mp10) REVERT: N 95 GLN cc_start: 0.8122 (mp10) cc_final: 0.7904 (mp10) REVERT: I 530 MET cc_start: 0.9073 (mtm) cc_final: 0.8702 (mtp) REVERT: I 584 GLU cc_start: 0.9057 (tm-30) cc_final: 0.8797 (tm-30) REVERT: I 586 TYR cc_start: 0.9110 (t80) cc_final: 0.8841 (t80) REVERT: I 589 ASP cc_start: 0.9405 (m-30) cc_final: 0.9154 (m-30) REVERT: I 621 GLU cc_start: 0.8073 (tp30) cc_final: 0.7824 (tp30) REVERT: I 646 LEU cc_start: 0.9427 (mt) cc_final: 0.9160 (mt) outliers start: 1 outliers final: 0 residues processed: 415 average time/residue: 0.3189 time to fit residues: 205.6553 Evaluate side-chains 332 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 149 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 143 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 189 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20707 Z= 0.246 Angle : 0.614 7.814 28122 Z= 0.315 Chirality : 0.044 0.280 3355 Planarity : 0.004 0.084 3520 Dihedral : 6.165 57.310 4066 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.17), residues: 2290 helix: 1.04 (0.27), residues: 416 sheet: 0.20 (0.21), residues: 623 loop : -0.46 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 427 HIS 0.013 0.001 HIS F 374 PHE 0.021 0.002 PHE F 391 TYR 0.017 0.002 TYR J 100G ARG 0.014 0.001 ARG G 588 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 424 time to evaluate : 2.121 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: A 80 ASN cc_start: 0.8209 (t0) cc_final: 0.7813 (p0) REVERT: A 100 MET cc_start: 0.8575 (mtm) cc_final: 0.8224 (mtp) REVERT: A 107 ASP cc_start: 0.8931 (t70) cc_final: 0.8614 (t70) REVERT: A 114 GLN cc_start: 0.9108 (tp40) cc_final: 0.8743 (tt0) REVERT: A 150 MET cc_start: 0.9144 (mmm) cc_final: 0.8831 (mtp) REVERT: A 340 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8552 (mm-30) REVERT: A 352 HIS cc_start: 0.8485 (m90) cc_final: 0.8150 (m90) REVERT: A 424 ILE cc_start: 0.9361 (mp) cc_final: 0.9097 (mp) REVERT: A 434 MET cc_start: 0.8908 (tmm) cc_final: 0.8336 (tmm) REVERT: C 18 LEU cc_start: 0.9035 (tp) cc_final: 0.8816 (tp) REVERT: C 32 PHE cc_start: 0.8070 (m-80) cc_final: 0.7800 (m-80) REVERT: C 46 GLU cc_start: 0.8752 (tt0) cc_final: 0.7902 (tp30) REVERT: C 48 VAL cc_start: 0.8867 (t) cc_final: 0.8620 (t) REVERT: C 82 MET cc_start: 0.8776 (pmm) cc_final: 0.8552 (pmm) REVERT: C 91 TYR cc_start: 0.8429 (m-80) cc_final: 0.8124 (m-80) REVERT: C 97 MET cc_start: 0.9002 (ptm) cc_final: 0.8770 (ptm) REVERT: C 101 ASP cc_start: 0.9404 (p0) cc_final: 0.9011 (p0) REVERT: D 91 TYR cc_start: 0.8461 (t80) cc_final: 0.7321 (t80) REVERT: B 573 ILE cc_start: 0.9200 (mm) cc_final: 0.8928 (tp) REVERT: B 579 ARG cc_start: 0.8486 (mtm-85) cc_final: 0.7975 (mtm-85) REVERT: B 589 ASP cc_start: 0.9340 (m-30) cc_final: 0.9027 (m-30) REVERT: B 595 ILE cc_start: 0.9311 (tt) cc_final: 0.8989 (tt) REVERT: B 608 VAL cc_start: 0.9422 (t) cc_final: 0.9177 (m) REVERT: B 621 GLU cc_start: 0.8346 (tp30) cc_final: 0.8015 (tp30) REVERT: B 630 GLN cc_start: 0.9030 (mt0) cc_final: 0.8454 (mt0) REVERT: B 650 GLN cc_start: 0.9475 (tp40) cc_final: 0.9018 (tp40) REVERT: B 653 GLN cc_start: 0.9158 (tt0) cc_final: 0.8622 (tm-30) REVERT: B 657 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8268 (mt-10) REVERT: E 104 MET cc_start: 0.9387 (mmm) cc_final: 0.9089 (tpt) REVERT: E 106 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8515 (mt-10) REVERT: E 134 TYR cc_start: 0.7524 (t80) cc_final: 0.7106 (t80) REVERT: E 168 LYS cc_start: 0.9108 (mptt) cc_final: 0.8738 (mmtt) REVERT: E 173 TYR cc_start: 0.8507 (m-80) cc_final: 0.8155 (m-10) REVERT: E 217 TYR cc_start: 0.7926 (m-80) cc_final: 0.7296 (m-80) REVERT: E 328 MET cc_start: 0.8733 (mtp) cc_final: 0.8331 (mtm) REVERT: E 368 ASP cc_start: 0.8492 (p0) cc_final: 0.7732 (p0) REVERT: E 425 ASN cc_start: 0.8322 (p0) cc_final: 0.7892 (p0) REVERT: E 434 MET cc_start: 0.7624 (tmm) cc_final: 0.7264 (tmm) REVERT: J 38 ARG cc_start: 0.8339 (ptm-80) cc_final: 0.7948 (ptm160) REVERT: J 43 LYS cc_start: 0.9012 (mmmt) cc_final: 0.8447 (pttp) REVERT: J 52 ASP cc_start: 0.9339 (p0) cc_final: 0.9066 (p0) REVERT: M 53 GLN cc_start: 0.8880 (mp10) cc_final: 0.8250 (mp10) REVERT: M 91 TYR cc_start: 0.8876 (t80) cc_final: 0.8223 (t80) REVERT: M 97 ILE cc_start: 0.9193 (tp) cc_final: 0.8942 (tp) REVERT: M 103 ARG cc_start: 0.9070 (mmm160) cc_final: 0.8686 (mmm160) REVERT: G 540 GLN cc_start: 0.8842 (mp10) cc_final: 0.8555 (mt0) REVERT: G 543 ASN cc_start: 0.8888 (t0) cc_final: 0.8670 (t0) REVERT: G 581 LEU cc_start: 0.9384 (mt) cc_final: 0.8971 (mm) REVERT: G 601 LYS cc_start: 0.9009 (mppt) cc_final: 0.8676 (mtmm) REVERT: G 615 SER cc_start: 0.9282 (t) cc_final: 0.8957 (m) REVERT: G 648 GLU cc_start: 0.8540 (pp20) cc_final: 0.8262 (pp20) REVERT: G 650 GLN cc_start: 0.8703 (tp-100) cc_final: 0.8125 (tp-100) REVERT: G 652 GLN cc_start: 0.8945 (mm-40) cc_final: 0.8620 (pt0) REVERT: G 654 GLU cc_start: 0.8666 (mt-10) cc_final: 0.7857 (mt-10) REVERT: G 657 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8729 (mt-10) REVERT: F 78 ASP cc_start: 0.8288 (p0) cc_final: 0.8059 (t70) REVERT: F 100 MET cc_start: 0.8953 (mtm) cc_final: 0.8630 (mtt) REVERT: F 107 ASP cc_start: 0.8609 (m-30) cc_final: 0.8264 (m-30) REVERT: F 114 GLN cc_start: 0.8554 (tp40) cc_final: 0.7778 (mm-40) REVERT: F 319 TYR cc_start: 0.8665 (p90) cc_final: 0.8368 (p90) REVERT: F 368 ASP cc_start: 0.8828 (m-30) cc_final: 0.8546 (p0) REVERT: F 376 PHE cc_start: 0.7364 (t80) cc_final: 0.7070 (t80) REVERT: F 434 MET cc_start: 0.8241 (tmm) cc_final: 0.7855 (tmm) REVERT: F 492 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8858 (tt0) REVERT: K 1 GLU cc_start: 0.7799 (pp20) cc_final: 0.7567 (pp20) REVERT: K 46 GLU cc_start: 0.8773 (tp30) cc_final: 0.8544 (tp30) REVERT: K 64 LYS cc_start: 0.8938 (mtmt) cc_final: 0.8481 (mttp) REVERT: K 91 TYR cc_start: 0.8606 (m-10) cc_final: 0.7903 (m-10) REVERT: K 105 GLN cc_start: 0.7766 (mt0) cc_final: 0.7467 (mt0) REVERT: N 46 LEU cc_start: 0.9071 (tp) cc_final: 0.8810 (tp) REVERT: N 50 ASP cc_start: 0.8816 (m-30) cc_final: 0.8597 (m-30) REVERT: N 53 GLN cc_start: 0.8363 (mp10) cc_final: 0.7718 (mp10) REVERT: N 95 GLN cc_start: 0.8053 (mp10) cc_final: 0.7829 (mp10) REVERT: I 530 MET cc_start: 0.9057 (mtm) cc_final: 0.8667 (mtp) REVERT: I 584 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8786 (tm-30) REVERT: I 586 TYR cc_start: 0.9109 (t80) cc_final: 0.8841 (t80) REVERT: I 589 ASP cc_start: 0.9379 (m-30) cc_final: 0.9115 (m-30) REVERT: I 621 GLU cc_start: 0.8063 (tp30) cc_final: 0.7840 (tp30) REVERT: I 646 LEU cc_start: 0.9393 (mt) cc_final: 0.9158 (mt) REVERT: I 648 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8224 (tm-30) outliers start: 0 outliers final: 0 residues processed: 424 average time/residue: 0.3185 time to fit residues: 208.7741 Evaluate side-chains 338 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 2.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 219 optimal weight: 0.0470 chunk 230 optimal weight: 30.0000 chunk 210 optimal weight: 4.9990 chunk 224 optimal weight: 0.7980 chunk 135 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 202 optimal weight: 6.9990 chunk 212 optimal weight: 8.9990 chunk 223 optimal weight: 4.9990 overall best weight: 2.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 658 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.5494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20707 Z= 0.293 Angle : 0.639 8.411 28122 Z= 0.328 Chirality : 0.045 0.237 3355 Planarity : 0.004 0.055 3520 Dihedral : 6.123 51.954 4066 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.17), residues: 2290 helix: 0.95 (0.27), residues: 416 sheet: 0.13 (0.21), residues: 623 loop : -0.53 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 427 HIS 0.009 0.001 HIS F 374 PHE 0.029 0.002 PHE B 522 TYR 0.026 0.002 TYR K 100G ARG 0.015 0.001 ARG G 588 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 2.243 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 80 ASN cc_start: 0.8238 (t0) cc_final: 0.7841 (p0) REVERT: A 100 MET cc_start: 0.8623 (mtm) cc_final: 0.8250 (mtp) REVERT: A 107 ASP cc_start: 0.8959 (t70) cc_final: 0.8636 (t70) REVERT: A 114 GLN cc_start: 0.9146 (tp40) cc_final: 0.8775 (tt0) REVERT: A 133 ASN cc_start: 0.8409 (t0) cc_final: 0.8183 (t0) REVERT: A 150 MET cc_start: 0.9017 (mmm) cc_final: 0.8752 (mtp) REVERT: A 201 ILE cc_start: 0.8783 (tt) cc_final: 0.8550 (tp) REVERT: A 340 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8570 (mm-30) REVERT: A 352 HIS cc_start: 0.8496 (m90) cc_final: 0.8191 (m90) REVERT: A 424 ILE cc_start: 0.9378 (mp) cc_final: 0.9111 (mp) REVERT: A 434 MET cc_start: 0.8927 (tmm) cc_final: 0.8381 (tmm) REVERT: C 32 PHE cc_start: 0.8049 (m-80) cc_final: 0.7743 (m-80) REVERT: C 46 GLU cc_start: 0.8723 (tt0) cc_final: 0.7866 (tp30) REVERT: C 48 VAL cc_start: 0.8914 (t) cc_final: 0.8668 (t) REVERT: C 91 TYR cc_start: 0.8427 (m-80) cc_final: 0.8115 (m-80) REVERT: C 97 MET cc_start: 0.8945 (ptm) cc_final: 0.8680 (ptm) REVERT: C 101 ASP cc_start: 0.9383 (p0) cc_final: 0.9031 (p0) REVERT: D 91 TYR cc_start: 0.8451 (t80) cc_final: 0.7404 (t80) REVERT: B 589 ASP cc_start: 0.9330 (m-30) cc_final: 0.9008 (m-30) REVERT: B 595 ILE cc_start: 0.9309 (tt) cc_final: 0.8985 (tt) REVERT: B 608 VAL cc_start: 0.9410 (t) cc_final: 0.9189 (m) REVERT: B 621 GLU cc_start: 0.8369 (tp30) cc_final: 0.8048 (tp30) REVERT: B 630 GLN cc_start: 0.9080 (mt0) cc_final: 0.8520 (mt0) REVERT: B 650 GLN cc_start: 0.9475 (tp40) cc_final: 0.9161 (tp40) REVERT: B 653 GLN cc_start: 0.9179 (tt0) cc_final: 0.8625 (tm-30) REVERT: B 657 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8370 (mt-10) REVERT: E 104 MET cc_start: 0.9436 (mmm) cc_final: 0.9099 (tpt) REVERT: E 106 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8521 (mt-10) REVERT: E 168 LYS cc_start: 0.9102 (mptt) cc_final: 0.8745 (mmtt) REVERT: E 217 TYR cc_start: 0.7912 (m-80) cc_final: 0.7214 (m-80) REVERT: E 328 MET cc_start: 0.8784 (mtp) cc_final: 0.8390 (mtp) REVERT: E 368 ASP cc_start: 0.8499 (p0) cc_final: 0.7704 (p0) REVERT: E 425 ASN cc_start: 0.8313 (p0) cc_final: 0.7848 (p0) REVERT: E 434 MET cc_start: 0.7588 (tmm) cc_final: 0.7216 (tmm) REVERT: J 38 ARG cc_start: 0.8325 (ptm-80) cc_final: 0.7966 (ptm160) REVERT: J 52 ASP cc_start: 0.9357 (p0) cc_final: 0.9123 (p0) REVERT: M 53 GLN cc_start: 0.8865 (mp10) cc_final: 0.8234 (mp10) REVERT: M 91 TYR cc_start: 0.8868 (t80) cc_final: 0.8227 (t80) REVERT: M 97 ILE cc_start: 0.9196 (tp) cc_final: 0.8886 (tp) REVERT: M 103 ARG cc_start: 0.9133 (mmm160) cc_final: 0.8725 (mmm160) REVERT: G 543 ASN cc_start: 0.8945 (t0) cc_final: 0.8690 (t0) REVERT: G 601 LYS cc_start: 0.9078 (mppt) cc_final: 0.8624 (mtmm) REVERT: G 615 SER cc_start: 0.9276 (t) cc_final: 0.8976 (m) REVERT: G 648 GLU cc_start: 0.8595 (pp20) cc_final: 0.8339 (pp20) REVERT: G 650 GLN cc_start: 0.8722 (tp-100) cc_final: 0.8189 (tp-100) REVERT: G 652 GLN cc_start: 0.8941 (mm-40) cc_final: 0.8713 (pt0) REVERT: G 654 GLU cc_start: 0.8668 (mt-10) cc_final: 0.7918 (mt-10) REVERT: G 657 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8726 (mt-10) REVERT: G 658 GLN cc_start: 0.8863 (tm130) cc_final: 0.8576 (tm-30) REVERT: F 78 ASP cc_start: 0.8225 (p0) cc_final: 0.7987 (t70) REVERT: F 100 MET cc_start: 0.8928 (mtm) cc_final: 0.8600 (mtt) REVERT: F 107 ASP cc_start: 0.8611 (m-30) cc_final: 0.8270 (m-30) REVERT: F 112 TRP cc_start: 0.8640 (t-100) cc_final: 0.7605 (t-100) REVERT: F 114 GLN cc_start: 0.8552 (tp40) cc_final: 0.7781 (mm-40) REVERT: F 319 TYR cc_start: 0.8707 (p90) cc_final: 0.8396 (p90) REVERT: F 368 ASP cc_start: 0.8856 (m-30) cc_final: 0.8584 (p0) REVERT: F 376 PHE cc_start: 0.7320 (t80) cc_final: 0.7062 (t80) REVERT: F 434 MET cc_start: 0.8187 (tmm) cc_final: 0.7817 (tmm) REVERT: F 492 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8838 (tt0) REVERT: K 1 GLU cc_start: 0.7926 (pp20) cc_final: 0.7713 (pp20) REVERT: K 46 GLU cc_start: 0.8811 (tp30) cc_final: 0.8588 (tp30) REVERT: K 69 ILE cc_start: 0.8839 (tt) cc_final: 0.8428 (pt) REVERT: K 82 MET cc_start: 0.8208 (mmp) cc_final: 0.7825 (mmp) REVERT: K 91 TYR cc_start: 0.8633 (m-10) cc_final: 0.8037 (m-80) REVERT: K 105 GLN cc_start: 0.7782 (mt0) cc_final: 0.7568 (mt0) REVERT: N 50 ASP cc_start: 0.8915 (m-30) cc_final: 0.8664 (m-30) REVERT: N 53 GLN cc_start: 0.8492 (mp10) cc_final: 0.7884 (mp10) REVERT: N 95 GLN cc_start: 0.8064 (mp10) cc_final: 0.7837 (mp10) REVERT: I 530 MET cc_start: 0.9068 (mtm) cc_final: 0.8474 (mtp) REVERT: I 584 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8747 (tm-30) REVERT: I 586 TYR cc_start: 0.9124 (t80) cc_final: 0.8899 (t80) REVERT: I 589 ASP cc_start: 0.9375 (m-30) cc_final: 0.9111 (m-30) REVERT: I 621 GLU cc_start: 0.8071 (tp30) cc_final: 0.7851 (tp30) REVERT: I 626 MET cc_start: 0.8185 (ttt) cc_final: 0.5918 (ttt) REVERT: I 646 LEU cc_start: 0.9433 (mt) cc_final: 0.9185 (mt) REVERT: I 648 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8225 (tm-30) outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.3147 time to fit residues: 198.6211 Evaluate side-chains 331 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 147 optimal weight: 6.9990 chunk 237 optimal weight: 30.0000 chunk 144 optimal weight: 5.9990 chunk 112 optimal weight: 0.0170 chunk 165 optimal weight: 8.9990 chunk 249 optimal weight: 30.0000 chunk 229 optimal weight: 40.0000 chunk 198 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 577 GLN ** G 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 658 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.5562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20707 Z= 0.234 Angle : 0.620 8.764 28122 Z= 0.318 Chirality : 0.044 0.228 3355 Planarity : 0.004 0.057 3520 Dihedral : 5.909 53.342 4066 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.18), residues: 2290 helix: 1.04 (0.27), residues: 416 sheet: 0.18 (0.21), residues: 621 loop : -0.57 (0.17), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 427 HIS 0.008 0.001 HIS F 374 PHE 0.024 0.002 PHE B 522 TYR 0.028 0.002 TYR K 100G ARG 0.015 0.001 ARG G 588 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 2.266 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: A 80 ASN cc_start: 0.8243 (t0) cc_final: 0.7848 (p0) REVERT: A 100 MET cc_start: 0.8572 (mtm) cc_final: 0.8220 (mtp) REVERT: A 107 ASP cc_start: 0.8958 (t70) cc_final: 0.8626 (t70) REVERT: A 114 GLN cc_start: 0.9136 (tp40) cc_final: 0.8757 (tt0) REVERT: A 150 MET cc_start: 0.8954 (mmm) cc_final: 0.8689 (mtp) REVERT: A 340 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8549 (mm-30) REVERT: A 352 HIS cc_start: 0.8490 (m90) cc_final: 0.8195 (m90) REVERT: A 424 ILE cc_start: 0.9366 (mp) cc_final: 0.9109 (mp) REVERT: A 434 MET cc_start: 0.8940 (tmm) cc_final: 0.8413 (tmm) REVERT: C 32 PHE cc_start: 0.8043 (m-80) cc_final: 0.7745 (m-80) REVERT: C 46 GLU cc_start: 0.8753 (tt0) cc_final: 0.7911 (tp30) REVERT: C 48 VAL cc_start: 0.8874 (t) cc_final: 0.8619 (t) REVERT: C 91 TYR cc_start: 0.8410 (m-80) cc_final: 0.8143 (m-80) REVERT: C 101 ASP cc_start: 0.9400 (p0) cc_final: 0.9036 (p0) REVERT: D 91 TYR cc_start: 0.8500 (t80) cc_final: 0.7353 (t80) REVERT: B 579 ARG cc_start: 0.8532 (mtm-85) cc_final: 0.8075 (mtm-85) REVERT: B 589 ASP cc_start: 0.9331 (m-30) cc_final: 0.9027 (m-30) REVERT: B 608 VAL cc_start: 0.9416 (t) cc_final: 0.9156 (m) REVERT: B 621 GLU cc_start: 0.8327 (tp30) cc_final: 0.7994 (tp30) REVERT: B 630 GLN cc_start: 0.9036 (mt0) cc_final: 0.8478 (mt0) REVERT: B 650 GLN cc_start: 0.9489 (tp40) cc_final: 0.9145 (tp40) REVERT: B 653 GLN cc_start: 0.9158 (tt0) cc_final: 0.8632 (tm-30) REVERT: B 657 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8280 (mt-10) REVERT: E 104 MET cc_start: 0.9416 (mmm) cc_final: 0.9163 (tpt) REVERT: E 106 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8534 (mt-10) REVERT: E 168 LYS cc_start: 0.9109 (mptt) cc_final: 0.8742 (mmtt) REVERT: E 319 TYR cc_start: 0.9150 (p90) cc_final: 0.8615 (p90) REVERT: E 328 MET cc_start: 0.8786 (mtp) cc_final: 0.8411 (mtp) REVERT: E 368 ASP cc_start: 0.8420 (p0) cc_final: 0.7637 (p0) REVERT: E 370 GLU cc_start: 0.9267 (mp0) cc_final: 0.9047 (mp0) REVERT: E 425 ASN cc_start: 0.8352 (p0) cc_final: 0.8062 (p0) REVERT: E 434 MET cc_start: 0.7514 (tmm) cc_final: 0.7200 (tmm) REVERT: J 38 ARG cc_start: 0.8303 (ptm-80) cc_final: 0.7921 (ptm160) REVERT: J 52 ASP cc_start: 0.9341 (p0) cc_final: 0.9108 (p0) REVERT: J 72 ASP cc_start: 0.9024 (t0) cc_final: 0.8819 (t0) REVERT: M 53 GLN cc_start: 0.8877 (mp10) cc_final: 0.8272 (mp10) REVERT: M 91 TYR cc_start: 0.8869 (t80) cc_final: 0.8192 (t80) REVERT: M 97 ILE cc_start: 0.9201 (tp) cc_final: 0.8691 (tp) REVERT: M 103 ARG cc_start: 0.9153 (mmm160) cc_final: 0.8734 (mmm160) REVERT: G 543 ASN cc_start: 0.8878 (t0) cc_final: 0.8673 (t0) REVERT: G 581 LEU cc_start: 0.9382 (mt) cc_final: 0.9071 (mm) REVERT: G 601 LYS cc_start: 0.9086 (mppt) cc_final: 0.8626 (mtmm) REVERT: G 615 SER cc_start: 0.9273 (t) cc_final: 0.8966 (m) REVERT: G 648 GLU cc_start: 0.8604 (pp20) cc_final: 0.8323 (pp20) REVERT: G 650 GLN cc_start: 0.8709 (tp-100) cc_final: 0.8171 (tp-100) REVERT: G 652 GLN cc_start: 0.8938 (mm-40) cc_final: 0.8618 (pt0) REVERT: G 654 GLU cc_start: 0.8659 (mt-10) cc_final: 0.7898 (mt-10) REVERT: G 657 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8716 (mt-10) REVERT: G 658 GLN cc_start: 0.8861 (tm130) cc_final: 0.8555 (tm-30) REVERT: F 78 ASP cc_start: 0.8272 (p0) cc_final: 0.8024 (t70) REVERT: F 100 MET cc_start: 0.8928 (mtm) cc_final: 0.8594 (mtt) REVERT: F 104 MET cc_start: 0.9094 (ttt) cc_final: 0.8805 (ttt) REVERT: F 107 ASP cc_start: 0.8603 (m-30) cc_final: 0.8313 (m-30) REVERT: F 112 TRP cc_start: 0.8736 (t-100) cc_final: 0.7650 (t-100) REVERT: F 114 GLN cc_start: 0.8557 (tp40) cc_final: 0.7782 (mm-40) REVERT: F 315 GLN cc_start: 0.8751 (mp10) cc_final: 0.8549 (mp10) REVERT: F 319 TYR cc_start: 0.8674 (p90) cc_final: 0.8351 (p90) REVERT: F 368 ASP cc_start: 0.8889 (m-30) cc_final: 0.8610 (p0) REVERT: F 376 PHE cc_start: 0.7308 (t80) cc_final: 0.7107 (t80) REVERT: F 434 MET cc_start: 0.8377 (tmm) cc_final: 0.7923 (tmm) REVERT: F 492 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8868 (tt0) REVERT: K 46 GLU cc_start: 0.8796 (tp30) cc_final: 0.8594 (tp30) REVERT: K 91 TYR cc_start: 0.8562 (m-10) cc_final: 0.7830 (m-10) REVERT: K 105 GLN cc_start: 0.7720 (mt0) cc_final: 0.7393 (mt0) REVERT: N 47 MET cc_start: 0.7814 (mmt) cc_final: 0.7592 (mmp) REVERT: N 50 ASP cc_start: 0.8930 (m-30) cc_final: 0.8615 (m-30) REVERT: N 53 GLN cc_start: 0.8499 (mp10) cc_final: 0.7887 (mp10) REVERT: N 95 GLN cc_start: 0.8058 (mp10) cc_final: 0.7830 (mp10) REVERT: I 530 MET cc_start: 0.9117 (mtm) cc_final: 0.8647 (mtp) REVERT: I 584 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8766 (tm-30) REVERT: I 586 TYR cc_start: 0.9085 (t80) cc_final: 0.8874 (t80) REVERT: I 589 ASP cc_start: 0.9370 (m-30) cc_final: 0.9111 (m-30) REVERT: I 603 ILE cc_start: 0.9679 (mm) cc_final: 0.9365 (tp) REVERT: I 621 GLU cc_start: 0.8053 (tp30) cc_final: 0.7835 (tp30) REVERT: I 626 MET cc_start: 0.8166 (ttt) cc_final: 0.7492 (ttt) REVERT: I 646 LEU cc_start: 0.9404 (mt) cc_final: 0.9170 (mt) REVERT: I 648 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8213 (tm-30) outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 0.3178 time to fit residues: 203.7426 Evaluate side-chains 336 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 157 optimal weight: 10.0000 chunk 211 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 182 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 55 optimal weight: 0.0570 chunk 198 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 203 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 overall best weight: 2.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** G 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 658 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.077635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.063845 restraints weight = 89147.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.065725 restraints weight = 48630.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.066953 restraints weight = 31507.364| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 20707 Z= 0.254 Angle : 0.621 8.444 28122 Z= 0.319 Chirality : 0.044 0.219 3355 Planarity : 0.004 0.055 3520 Dihedral : 5.835 55.503 4066 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.18), residues: 2290 helix: 1.04 (0.27), residues: 417 sheet: 0.11 (0.21), residues: 623 loop : -0.58 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 427 HIS 0.007 0.001 HIS F 374 PHE 0.022 0.002 PHE B 522 TYR 0.026 0.002 TYR K 100G ARG 0.015 0.001 ARG G 588 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4781.69 seconds wall clock time: 88 minutes 21.98 seconds (5301.98 seconds total)