Starting phenix.real_space_refine on Sun Aug 24 16:02:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f9m_28945/08_2025/8f9m_28945.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f9m_28945/08_2025/8f9m_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 { model { file = "/net/cci-nas-00/data/ceres_data/8f9m_28945/08_2025/8f9m_28945.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f9m_28945/08_2025/8f9m_28945.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f9m_28945/08_2025/8f9m_28945.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f9m_28945/08_2025/8f9m_28945.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.22, per 1000 atoms: 0.21 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: 1.43 Conformation dependent library (CDL) restraints added in 559.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.67 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: 2.50 Time building geometry restraints manager: 1.88 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 610)) selection = (chain 'F' and resid 33 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: 4.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 15.440 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.940 ------------------------------------------------------------------------------- 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 20810 Z= 0.269 Angle : 0.972 11.377 28392 Z= 0.517 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.013 0.001 ARG J 83 TYR 0.031 0.003 TYR G 643 PHE 0.058 0.004 PHE A 159 TRP 0.026 0.002 TRP F 479 HIS 0.020 0.002 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00581 (20707) covalent geometry : angle 0.95217 (28122) SS BOND : bond 0.00522 ( 39) SS BOND : angle 1.65394 ( 78) hydrogen bonds : bond 0.13549 ( 599) hydrogen bonds : angle 6.88758 ( 1602) link_ALPHA1-3 : bond 0.00253 ( 2) link_ALPHA1-3 : angle 1.61176 ( 6) link_BETA1-4 : bond 0.00298 ( 11) link_BETA1-4 : angle 1.78374 ( 33) link_NAG-ASN : bond 0.00484 ( 51) link_NAG-ASN : angle 2.52667 ( 153) *********************** 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 : 0.479 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: 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: 0.7746 (t70) REVERT: A 107 ASP cc_start: 0.8813 (t70) cc_final: 0.8499 (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: 0.8158 (t0) REVERT: A 217 TYR cc_start: 0.7009 (m-80) cc_final: 0.6339 (m-80) REVERT: A 280 ASN cc_start: 0.7976 (p0) cc_final: 0.7701 (p0) REVERT: A 315 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7309 (mp10) REVERT: A 340 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8612 (mm-30) REVERT: C 56 LEU cc_start: 0.8651 (mt) cc_final: 0.8333 (mt) REVERT: C 91 TYR cc_start: 0.8627 (m-80) cc_final: 0.8192 (m-10) REVERT: B 577 GLN cc_start: 0.8708 (mt0) cc_final: 0.8458 (mt0) REVERT: B 624 ASP cc_start: 0.8728 (m-30) cc_final: 0.8445 (m-30) 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: 0.8558 (mt-10) REVERT: E 150 MET cc_start: 0.8092 (mmm) cc_final: 0.7550 (mmm) REVERT: E 199 SER cc_start: 0.8265 (p) cc_final: 0.7888 (t) REVERT: E 210 PHE cc_start: 0.8782 (m-80) cc_final: 0.8495 (m-10) REVERT: E 232 LYS cc_start: 0.7145 (mtmt) cc_final: 0.6739 (ptpp) REVERT: E 302 ASN cc_start: 0.8216 (m-40) cc_final: 0.7819 (p0) REVERT: E 325 HIS cc_start: 0.6227 (t70) cc_final: 0.5796 (t-90) REVERT: E 349 LEU cc_start: 0.9472 (mt) cc_final: 0.9126 (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: E 477 ASP cc_start: 0.8850 (m-30) cc_final: 0.8647 (m-30) REVERT: J 2 VAL cc_start: 0.8319 (t) cc_final: 0.7661 (t) REVERT: J 32 PHE cc_start: 0.8633 (m-80) cc_final: 0.8371 (m-10) REVERT: J 94 THR cc_start: 0.8107 (m) cc_final: 0.6921 (p) REVERT: J 102 PHE cc_start: 0.8627 (m-80) cc_final: 0.8195 (m-80) REVERT: M 35 TRP cc_start: 0.7117 (m100) cc_final: 0.6403 (m100) REVERT: M 62 PHE cc_start: 0.7576 (m-80) cc_final: 0.7112 (m-80) REVERT: M 75 ILE cc_start: 0.9150 (mt) cc_final: 0.8653 (mt) REVERT: M 86 TYR cc_start: 0.8242 (m-80) cc_final: 0.7720 (m-10) REVERT: M 91 TYR cc_start: 0.8738 (t80) cc_final: 0.8239 (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: 0.8478 (mt-10) REVERT: G 615 SER cc_start: 0.9366 (t) cc_final: 0.8928 (m) REVERT: G 650 GLN cc_start: 0.8723 (tp40) cc_final: 0.8429 (tm-30) REVERT: G 652 GLN cc_start: 0.8908 (mm-40) cc_final: 0.8473 (pt0) REVERT: G 654 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8061 (mt-10) REVERT: G 656 ASN cc_start: 0.8848 (m-40) cc_final: 0.8589 (m-40) REVERT: F 103 GLN cc_start: 0.7954 (mt0) cc_final: 0.7353 (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: 0.8414 (mt) REVERT: F 172 VAL cc_start: 0.9236 (t) cc_final: 0.8952 (t) REVERT: F 195 ASN cc_start: 0.8816 (p0) cc_final: 0.8414 (t0) REVERT: F 202 THR cc_start: 0.8975 (m) cc_final: 0.8742 (m) REVERT: F 275 GLU cc_start: 0.8607 (tt0) cc_final: 0.8348 (tm-30) REVERT: F 319 TYR cc_start: 0.8196 (p90) cc_final: 0.7804 (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: 0.8229 (tmm) REVERT: F 449 ILE cc_start: 0.8746 (mt) cc_final: 0.8461 (tt) REVERT: F 478 ASN cc_start: 0.9173 (m-40) cc_final: 0.8708 (m110) REVERT: F 492 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8481 (mp0) REVERT: K 32 PHE cc_start: 0.8922 (m-80) cc_final: 0.8465 (m-10) REVERT: K 34 MET cc_start: 0.9218 (mtp) cc_final: 0.8870 (mpp) REVERT: K 45 LEU cc_start: 0.8706 (mt) cc_final: 0.8485 (mp) REVERT: K 64 LYS cc_start: 0.8445 (mttt) cc_final: 0.8232 (mtmt) REVERT: K 80 LEU cc_start: 0.8970 (tp) cc_final: 0.8400 (tp) REVERT: K 105 GLN cc_start: 0.7457 (mt0) cc_final: 0.6560 (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: 0.7858 (m-30) REVERT: N 95 GLN cc_start: 0.8214 (mp10) cc_final: 0.7818 (mt0) REVERT: I 653 GLN cc_start: 0.9042 (tt0) cc_final: 0.8694 (tt0) outliers start: 4 outliers final: 1 residues processed: 845 average time/residue: 0.1408 time to fit residues: 176.8796 Evaluate side-chains 492 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 491 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 247 optimal weight: 20.0000 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 478 ASN B 616 ASN E 66 HIS E 249 HIS M 38 GLN M 39 HIS ** G 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 HIS F 99 ASN K 100BGLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.080626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.066645 restraints weight = 87233.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.068587 restraints weight = 46944.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.069819 restraints weight = 30124.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.070685 restraints weight = 21840.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.071240 restraints weight = 17215.048| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20810 Z= 0.208 Angle : 0.750 12.266 28392 Z= 0.373 Chirality : 0.047 0.266 3355 Planarity : 0.005 0.060 3520 Dihedral : 8.221 75.414 4066 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.15 % Allowed : 2.66 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.17), residues: 2290 helix: 1.32 (0.26), residues: 411 sheet: 0.32 (0.20), residues: 630 loop : 0.41 (0.17), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 83 TYR 0.031 0.002 TYR K 100G PHE 0.025 0.002 PHE F 391 TRP 0.026 0.002 TRP D 35 HIS 0.010 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00450 (20707) covalent geometry : angle 0.71865 (28122) SS BOND : bond 0.00391 ( 39) SS BOND : angle 0.95700 ( 78) hydrogen bonds : bond 0.04778 ( 599) hydrogen bonds : angle 5.75066 ( 1602) link_ALPHA1-3 : bond 0.00840 ( 2) link_ALPHA1-3 : angle 2.53945 ( 6) link_BETA1-4 : bond 0.00272 ( 11) link_BETA1-4 : angle 1.90722 ( 33) link_NAG-ASN : bond 0.00620 ( 51) link_NAG-ASN : angle 2.82658 ( 153) *********************** 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 551 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 548 time to evaluate : 0.734 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: A 39 TYR cc_start: 0.8590 (m-80) cc_final: 0.8354 (m-80) REVERT: A 80 ASN cc_start: 0.8131 (t0) cc_final: 0.7609 (p0) REVERT: A 95 MET cc_start: 0.8528 (ptm) cc_final: 0.8202 (ppp) REVERT: A 99 ASN cc_start: 0.8665 (OUTLIER) cc_final: 0.8375 (t0) REVERT: A 107 ASP cc_start: 0.8879 (t70) cc_final: 0.8514 (t70) REVERT: A 110 SER cc_start: 0.9045 (t) cc_final: 0.8810 (p) REVERT: A 150 MET cc_start: 0.9287 (mmm) cc_final: 0.8931 (mmp) REVERT: A 217 TYR cc_start: 0.7007 (m-80) cc_final: 0.6669 (m-80) REVERT: A 338 TRP cc_start: 0.9311 (t-100) cc_final: 0.8985 (t-100) REVERT: A 340 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8555 (mm-30) REVERT: C 46 GLU cc_start: 0.8657 (tt0) cc_final: 0.8079 (tp30) REVERT: C 91 TYR cc_start: 0.8439 (m-80) cc_final: 0.8155 (m-80) REVERT: C 101 ASP cc_start: 0.9235 (p0) cc_final: 0.8869 (p0) REVERT: B 538 THR cc_start: 0.9538 (p) cc_final: 0.8610 (p) REVERT: B 542 ARG cc_start: 0.8638 (mtm-85) cc_final: 0.7505 (mtm110) REVERT: B 573 ILE cc_start: 0.9432 (mm) cc_final: 0.9077 (mm) REVERT: B 595 ILE cc_start: 0.9413 (tt) cc_final: 0.9173 (tt) REVERT: B 621 GLU cc_start: 0.7925 (tp30) cc_final: 0.7701 (tp30) REVERT: B 624 ASP cc_start: 0.8835 (m-30) cc_final: 0.8508 (m-30) REVERT: B 650 GLN cc_start: 0.9423 (tp40) cc_final: 0.9075 (tp40) REVERT: B 653 GLN cc_start: 0.9077 (tt0) cc_final: 0.8303 (tm-30) REVERT: E 104 MET cc_start: 0.9427 (tpp) cc_final: 0.8874 (tpp) REVERT: E 106 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8548 (pt0) REVERT: E 150 MET cc_start: 0.8162 (mmm) cc_final: 0.7227 (mmm) REVERT: E 173 TYR cc_start: 0.8516 (m-80) cc_final: 0.8058 (m-80) REVERT: E 191 TYR cc_start: 0.8262 (m-80) cc_final: 0.6392 (m-80) REVERT: E 199 SER cc_start: 0.8683 (p) cc_final: 0.8407 (t) REVERT: E 210 PHE cc_start: 0.8920 (m-80) cc_final: 0.8604 (m-10) REVERT: E 217 TYR cc_start: 0.8191 (m-10) cc_final: 0.7362 (m-10) REVERT: E 302 ASN cc_start: 0.8119 (m-40) cc_final: 0.7801 (p0) REVERT: E 325 HIS cc_start: 0.6327 (t70) cc_final: 0.5977 (t70) REVERT: E 349 LEU cc_start: 0.9174 (mt) cc_final: 0.8797 (pp) REVERT: E 359 ILE cc_start: 0.7707 (mt) cc_final: 0.6822 (mm) REVERT: E 368 ASP cc_start: 0.8353 (p0) cc_final: 0.7677 (p0) REVERT: E 395 TRP cc_start: 0.5095 (m-90) cc_final: 0.3797 (m-90) REVERT: E 434 MET cc_start: 0.7235 (tmm) cc_final: 0.6932 (tmm) REVERT: E 435 TYR cc_start: 0.8063 (t80) cc_final: 0.7492 (t80) REVERT: J 64 LYS cc_start: 0.8884 (ptmt) cc_final: 0.8524 (mtpt) REVERT: J 105 GLN cc_start: 0.8100 (pp30) cc_final: 0.7890 (pp30) REVERT: M 53 GLN cc_start: 0.8342 (mp10) cc_final: 0.8137 (mp10) REVERT: M 91 TYR cc_start: 0.8949 (t80) cc_final: 0.8392 (t80) REVERT: G 543 ASN cc_start: 0.8754 (t0) cc_final: 0.8517 (t0) REVERT: G 544 LEU cc_start: 0.9339 (mt) cc_final: 0.9081 (mp) REVERT: G 647 GLU cc_start: 0.8204 (tt0) cc_final: 0.7613 (tt0) REVERT: G 654 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8270 (mt-10) REVERT: G 656 ASN cc_start: 0.9138 (m-40) cc_final: 0.8862 (m-40) REVERT: F 100 MET cc_start: 0.8937 (mtm) cc_final: 0.8613 (mtt) REVERT: F 104 MET cc_start: 0.8708 (ttt) cc_final: 0.8442 (ttt) REVERT: F 112 TRP cc_start: 0.8390 (t-100) cc_final: 0.7917 (t60) REVERT: F 114 GLN cc_start: 0.8586 (tp40) cc_final: 0.7860 (mp10) REVERT: F 161 MET cc_start: 0.7864 (mmp) cc_final: 0.7260 (mmm) REVERT: F 202 THR cc_start: 0.8765 (m) cc_final: 0.8554 (m) REVERT: F 319 TYR cc_start: 0.8425 (p90) cc_final: 0.8110 (p90) REVERT: F 342 LEU cc_start: 0.8114 (tp) cc_final: 0.7636 (tp) REVERT: F 368 ASP cc_start: 0.8633 (m-30) cc_final: 0.8386 (p0) REVERT: F 426 MET cc_start: 0.7987 (mtp) cc_final: 0.7302 (mtp) REVERT: F 490 LYS cc_start: 0.8808 (tttm) cc_final: 0.8560 (ttmm) REVERT: F 492 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8536 (mp0) REVERT: K 32 PHE cc_start: 0.8863 (m-80) cc_final: 0.8344 (m-10) REVERT: K 64 LYS cc_start: 0.8649 (mttt) cc_final: 0.8367 (mtmm) REVERT: K 97 MET cc_start: 0.8260 (tmm) cc_final: 0.7377 (tmm) REVERT: K 100 LEU cc_start: 0.8932 (mt) cc_final: 0.8540 (mt) REVERT: K 105 GLN cc_start: 0.7760 (mt0) cc_final: 0.6690 (mp10) REVERT: N 45 LYS cc_start: 0.8967 (tttt) cc_final: 0.8532 (tttp) REVERT: N 47 MET cc_start: 0.8438 (mmt) cc_final: 0.7772 (mmm) REVERT: N 95 GLN cc_start: 0.7990 (mp10) cc_final: 0.7744 (mp10) REVERT: I 530 MET cc_start: 0.8896 (mtm) cc_final: 0.8693 (mtm) REVERT: I 585 HIS cc_start: 0.8453 (m-70) cc_final: 0.8148 (m170) REVERT: I 621 GLU cc_start: 0.7952 (tp30) cc_final: 0.7722 (tp30) REVERT: I 626 MET cc_start: 0.7874 (ttt) cc_final: 0.6862 (ttt) REVERT: I 646 LEU cc_start: 0.9492 (mt) cc_final: 0.9266 (mt) outliers start: 3 outliers final: 0 residues processed: 549 average time/residue: 0.1360 time to fit residues: 113.9764 Evaluate side-chains 389 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 388 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 161 optimal weight: 0.0670 chunk 115 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 164 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 231 optimal weight: 30.0000 chunk 159 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 overall best weight: 2.5724 ------------------------------------------------------------------------------- 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** A 478 ASN C 81 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 ASN E 188 ASN ** G 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 HIS K 13 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.079174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.065024 restraints weight = 88484.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.066939 restraints weight = 47617.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.068188 restraints weight = 30607.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.069035 restraints weight = 22177.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.069613 restraints weight = 17535.900| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20810 Z= 0.198 Angle : 0.690 21.759 28392 Z= 0.341 Chirality : 0.047 0.735 3355 Planarity : 0.004 0.054 3520 Dihedral : 7.337 58.955 4066 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.17), residues: 2290 helix: 0.85 (0.26), residues: 435 sheet: 0.31 (0.20), residues: 623 loop : 0.17 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 588 TYR 0.019 0.002 TYR I 586 PHE 0.019 0.002 PHE J 29 TRP 0.021 0.002 TRP E 479 HIS 0.009 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00425 (20707) covalent geometry : angle 0.64647 (28122) SS BOND : bond 0.00393 ( 39) SS BOND : angle 0.88647 ( 78) hydrogen bonds : bond 0.04349 ( 599) hydrogen bonds : angle 5.57525 ( 1602) link_ALPHA1-3 : bond 0.00904 ( 2) link_ALPHA1-3 : angle 1.81866 ( 6) link_BETA1-4 : bond 0.00320 ( 11) link_BETA1-4 : angle 1.74286 ( 33) link_NAG-ASN : bond 0.00561 ( 51) link_NAG-ASN : angle 3.23037 ( 153) *********************** 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 500 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 500 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8161 (t0) cc_final: 0.7643 (p0) REVERT: A 95 MET cc_start: 0.8590 (ptm) cc_final: 0.8127 (ppp) REVERT: A 107 ASP cc_start: 0.8871 (t70) cc_final: 0.8490 (t70) REVERT: A 110 SER cc_start: 0.9109 (t) cc_final: 0.8850 (p) REVERT: A 114 GLN cc_start: 0.8974 (tp40) cc_final: 0.8637 (tt0) REVERT: A 150 MET cc_start: 0.9317 (mmm) cc_final: 0.8900 (mmp) REVERT: A 340 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8539 (mm-30) REVERT: C 57 THR cc_start: 0.9013 (p) cc_final: 0.8556 (t) REVERT: C 101 ASP cc_start: 0.9214 (p0) cc_final: 0.8805 (p0) REVERT: D 49 TYR cc_start: 0.9036 (p90) cc_final: 0.8797 (p90) REVERT: B 573 ILE cc_start: 0.9328 (mm) cc_final: 0.8725 (mm) REVERT: B 589 ASP cc_start: 0.9169 (m-30) cc_final: 0.8949 (m-30) REVERT: B 595 ILE cc_start: 0.9423 (tt) cc_final: 0.9198 (tt) REVERT: B 608 VAL cc_start: 0.9480 (t) cc_final: 0.9223 (m) REVERT: B 624 ASP cc_start: 0.8835 (m-30) cc_final: 0.8578 (m-30) REVERT: B 626 MET cc_start: 0.7467 (ttm) cc_final: 0.7160 (ttm) REVERT: B 650 GLN cc_start: 0.9445 (tp40) cc_final: 0.9041 (tp40) REVERT: B 653 GLN cc_start: 0.9091 (tt0) cc_final: 0.8419 (tm-30) REVERT: E 100 MET cc_start: 0.8471 (mtm) cc_final: 0.8256 (mtm) REVERT: E 104 MET cc_start: 0.9376 (tpp) cc_final: 0.9053 (tpp) REVERT: E 106 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8549 (mt-10) REVERT: E 173 TYR cc_start: 0.8521 (m-80) cc_final: 0.8045 (m-80) REVERT: E 199 SER cc_start: 0.8654 (p) cc_final: 0.8418 (t) REVERT: E 203 GLN cc_start: 0.8368 (tp40) cc_final: 0.7796 (tp40) REVERT: E 302 ASN cc_start: 0.8145 (m-40) cc_final: 0.7800 (p0) REVERT: E 349 LEU cc_start: 0.9211 (mt) cc_final: 0.8797 (pp) REVERT: E 359 ILE cc_start: 0.7801 (mt) cc_final: 0.7576 (mm) REVERT: E 368 ASP cc_start: 0.8305 (p0) cc_final: 0.7647 (p0) REVERT: E 434 MET cc_start: 0.7192 (tmm) cc_final: 0.6750 (tmm) REVERT: E 435 TYR cc_start: 0.7980 (t80) cc_final: 0.7577 (t80) REVERT: J 43 LYS cc_start: 0.9027 (mmtt) cc_final: 0.8798 (pttp) REVERT: J 91 TYR cc_start: 0.8001 (m-80) cc_final: 0.6921 (m-80) REVERT: J 105 GLN cc_start: 0.8147 (pp30) cc_final: 0.7342 (pp30) REVERT: M 53 GLN cc_start: 0.8624 (mp10) cc_final: 0.8100 (mp10) REVERT: M 91 TYR cc_start: 0.8983 (t80) cc_final: 0.8371 (t80) REVERT: M 97 ILE cc_start: 0.9270 (tp) cc_final: 0.9064 (tp) REVERT: G 543 ASN cc_start: 0.8681 (t0) cc_final: 0.8441 (t0) REVERT: G 573 ILE cc_start: 0.9159 (tp) cc_final: 0.8857 (tp) REVERT: G 648 GLU cc_start: 0.8006 (pp20) cc_final: 0.7706 (tm-30) REVERT: G 650 GLN cc_start: 0.8677 (tp-100) cc_final: 0.8336 (tm-30) REVERT: G 654 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8121 (mt-10) REVERT: G 656 ASN cc_start: 0.9190 (m-40) cc_final: 0.8890 (m-40) REVERT: F 95 MET cc_start: 0.9280 (ppp) cc_final: 0.9023 (ppp) REVERT: F 100 MET cc_start: 0.8885 (mtm) cc_final: 0.8611 (mtt) REVERT: F 107 ASP cc_start: 0.8603 (m-30) cc_final: 0.8339 (m-30) REVERT: F 112 TRP cc_start: 0.8500 (t-100) cc_final: 0.7825 (t-100) REVERT: F 114 GLN cc_start: 0.8580 (tp40) cc_final: 0.7822 (mm-40) REVERT: F 161 MET cc_start: 0.8069 (mmp) cc_final: 0.7113 (mmm) REVERT: F 319 TYR cc_start: 0.8457 (p90) cc_final: 0.8213 (p90) REVERT: F 426 MET cc_start: 0.7826 (mtp) cc_final: 0.7209 (mtp) REVERT: K 32 PHE cc_start: 0.8760 (m-80) cc_final: 0.8381 (m-80) REVERT: K 34 MET cc_start: 0.7913 (mpp) cc_final: 0.7639 (mpp) REVERT: K 64 LYS cc_start: 0.8708 (mttt) cc_final: 0.8474 (mtmm) REVERT: K 105 GLN cc_start: 0.7463 (mt0) cc_final: 0.6516 (mp10) REVERT: N 45 LYS cc_start: 0.8957 (tttt) cc_final: 0.8357 (tttp) REVERT: N 46 LEU cc_start: 0.9199 (tp) cc_final: 0.8813 (tp) REVERT: N 47 MET cc_start: 0.8649 (mmt) cc_final: 0.7804 (mmt) REVERT: N 95 GLN cc_start: 0.7991 (mp10) cc_final: 0.7772 (mp10) REVERT: I 586 TYR cc_start: 0.8929 (t80) cc_final: 0.8545 (t80) REVERT: I 626 MET cc_start: 0.7814 (ttt) cc_final: 0.7010 (ttt) outliers start: 0 outliers final: 0 residues processed: 500 average time/residue: 0.1326 time to fit residues: 101.8909 Evaluate side-chains 376 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 218 optimal weight: 0.8980 chunk 234 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 95 optimal weight: 0.2980 chunk 147 optimal weight: 5.9990 chunk 138 optimal weight: 20.0000 chunk 197 optimal weight: 10.0000 chunk 205 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 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 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN C 3 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN G 577 GLN ** G 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 658 GLN F 72 HIS F 185 ASN F 352 HIS ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 585 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.078091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.064246 restraints weight = 87802.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.066142 restraints weight = 47133.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.067403 restraints weight = 30247.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.068265 restraints weight = 21810.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.068794 restraints weight = 17156.927| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20810 Z= 0.223 Angle : 0.693 19.861 28392 Z= 0.342 Chirality : 0.046 0.523 3355 Planarity : 0.004 0.044 3520 Dihedral : 6.640 47.723 4066 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.17), residues: 2290 helix: 1.05 (0.26), residues: 417 sheet: 0.24 (0.20), residues: 642 loop : 0.04 (0.17), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG N 54 TYR 0.018 0.002 TYR A 134 PHE 0.028 0.002 PHE F 391 TRP 0.024 0.002 TRP E 479 HIS 0.008 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00486 (20707) covalent geometry : angle 0.65162 (28122) SS BOND : bond 0.00396 ( 39) SS BOND : angle 0.85725 ( 78) hydrogen bonds : bond 0.04269 ( 599) hydrogen bonds : angle 5.58691 ( 1602) link_ALPHA1-3 : bond 0.00543 ( 2) link_ALPHA1-3 : angle 2.00193 ( 6) link_BETA1-4 : bond 0.00234 ( 11) link_BETA1-4 : angle 1.80728 ( 33) link_NAG-ASN : bond 0.00578 ( 51) link_NAG-ASN : angle 3.12075 ( 153) *********************** 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 455 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8266 (t0) cc_final: 0.7732 (p0) REVERT: A 95 MET cc_start: 0.8675 (ptm) cc_final: 0.8012 (ppp) REVERT: A 107 ASP cc_start: 0.8936 (t70) cc_final: 0.8574 (t70) REVERT: A 110 SER cc_start: 0.9123 (t) cc_final: 0.8887 (p) REVERT: A 114 GLN cc_start: 0.9029 (tp40) cc_final: 0.8651 (tt0) REVERT: A 150 MET cc_start: 0.9305 (mmm) cc_final: 0.8822 (mmp) REVERT: A 340 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8537 (mm-30) REVERT: A 422 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8082 (mm-40) REVERT: A 424 ILE cc_start: 0.9400 (mp) cc_final: 0.8741 (mp) REVERT: A 434 MET cc_start: 0.9038 (tmm) cc_final: 0.8342 (tmm) REVERT: C 91 TYR cc_start: 0.8525 (m-80) cc_final: 0.8313 (m-80) REVERT: C 101 ASP cc_start: 0.9283 (p0) cc_final: 0.8893 (p0) REVERT: D 91 TYR cc_start: 0.8752 (t80) cc_final: 0.7748 (t80) REVERT: B 538 THR cc_start: 0.9577 (p) cc_final: 0.8689 (p) REVERT: B 542 ARG cc_start: 0.8676 (mtp-110) cc_final: 0.7852 (mtm110) REVERT: B 573 ILE cc_start: 0.9429 (mm) cc_final: 0.8916 (mm) REVERT: B 589 ASP cc_start: 0.9197 (m-30) cc_final: 0.8957 (m-30) REVERT: B 595 ILE cc_start: 0.9401 (tt) cc_final: 0.9072 (tt) REVERT: B 608 VAL cc_start: 0.9463 (t) cc_final: 0.9236 (m) REVERT: B 626 MET cc_start: 0.7607 (ttm) cc_final: 0.6095 (ttm) REVERT: B 650 GLN cc_start: 0.9455 (tp40) cc_final: 0.8982 (tp40) REVERT: B 653 GLN cc_start: 0.9120 (tt0) cc_final: 0.8489 (tm-30) REVERT: E 106 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8520 (mt-10) REVERT: E 150 MET cc_start: 0.7845 (mmm) cc_final: 0.7597 (mmm) REVERT: E 173 TYR cc_start: 0.8549 (m-80) cc_final: 0.8226 (m-10) REVERT: E 217 TYR cc_start: 0.8027 (m-10) cc_final: 0.7520 (m-10) REVERT: E 349 LEU cc_start: 0.9227 (mt) cc_final: 0.8789 (pp) REVERT: E 359 ILE cc_start: 0.7830 (mt) cc_final: 0.7419 (mm) REVERT: E 368 ASP cc_start: 0.8384 (p0) cc_final: 0.7684 (p0) REVERT: E 434 MET cc_start: 0.7417 (tmm) cc_final: 0.7111 (tmm) REVERT: E 449 ILE cc_start: 0.9308 (mp) cc_final: 0.9096 (tp) REVERT: J 52 ASP cc_start: 0.9188 (p0) cc_final: 0.8824 (p0) REVERT: J 91 TYR cc_start: 0.8005 (m-80) cc_final: 0.6924 (m-80) REVERT: M 53 GLN cc_start: 0.8809 (mp10) cc_final: 0.8304 (mp10) REVERT: M 91 TYR cc_start: 0.8981 (t80) cc_final: 0.8307 (t80) REVERT: G 543 ASN cc_start: 0.8743 (t0) cc_final: 0.8479 (t0) REVERT: G 574 LYS cc_start: 0.8576 (mptt) cc_final: 0.8326 (pttt) REVERT: G 650 GLN cc_start: 0.8668 (tp-100) cc_final: 0.8389 (tm-30) REVERT: G 652 GLN cc_start: 0.8531 (pt0) cc_final: 0.8232 (pt0) REVERT: G 654 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8180 (mt-10) REVERT: G 656 ASN cc_start: 0.9121 (m-40) cc_final: 0.8873 (m-40) REVERT: F 78 ASP cc_start: 0.8634 (p0) cc_final: 0.8302 (p0) REVERT: F 100 MET cc_start: 0.8900 (mtm) cc_final: 0.8637 (mtt) REVERT: F 107 ASP cc_start: 0.8630 (m-30) cc_final: 0.8354 (m-30) REVERT: F 112 TRP cc_start: 0.8578 (t-100) cc_final: 0.7838 (t-100) REVERT: F 114 GLN cc_start: 0.8718 (tp40) cc_final: 0.7944 (mm-40) REVERT: F 319 TYR cc_start: 0.8502 (p90) cc_final: 0.8238 (p90) REVERT: F 368 ASP cc_start: 0.8116 (p0) cc_final: 0.7864 (p0) REVERT: F 376 PHE cc_start: 0.7080 (t80) cc_final: 0.6832 (t80) REVERT: F 414 LEU cc_start: 0.9105 (mt) cc_final: 0.8770 (mp) REVERT: F 426 MET cc_start: 0.7814 (mtp) cc_final: 0.7235 (mtp) REVERT: K 3 GLN cc_start: 0.8669 (mt0) cc_final: 0.8442 (tm-30) REVERT: K 32 PHE cc_start: 0.8783 (m-80) cc_final: 0.8450 (m-80) REVERT: K 34 MET cc_start: 0.8022 (mpp) cc_final: 0.7664 (mpp) REVERT: K 64 LYS cc_start: 0.8817 (mttt) cc_final: 0.8575 (mtmm) REVERT: K 91 TYR cc_start: 0.8183 (m-10) cc_final: 0.7863 (m-10) REVERT: K 105 GLN cc_start: 0.7621 (mt0) cc_final: 0.6554 (mp10) REVERT: N 45 LYS cc_start: 0.8983 (tttt) cc_final: 0.8643 (tttp) REVERT: N 95 GLN cc_start: 0.7995 (mp10) cc_final: 0.7791 (mp10) REVERT: I 626 MET cc_start: 0.7795 (ttt) cc_final: 0.7294 (ttt) REVERT: I 642 ILE cc_start: 0.9834 (mt) cc_final: 0.9619 (mt) outliers start: 0 outliers final: 0 residues processed: 455 average time/residue: 0.1309 time to fit residues: 92.4084 Evaluate side-chains 349 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 67 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 chunk 148 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 352 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN A 478 ASN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 577 GLN F 72 HIS F 82 GLN ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 585 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.075662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.061701 restraints weight = 90042.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.063525 restraints weight = 49253.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.064750 restraints weight = 32143.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.065554 restraints weight = 23508.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.066111 restraints weight = 18813.166| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 20810 Z= 0.314 Angle : 0.799 20.213 28392 Z= 0.391 Chirality : 0.048 0.472 3355 Planarity : 0.005 0.062 3520 Dihedral : 6.844 52.355 4066 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.05 % Allowed : 1.82 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.17), residues: 2290 helix: 0.65 (0.26), residues: 414 sheet: 0.01 (0.21), residues: 612 loop : -0.31 (0.16), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 588 TYR 0.026 0.003 TYR J 27 PHE 0.029 0.003 PHE F 391 TRP 0.045 0.002 TRP E 395 HIS 0.008 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00679 (20707) covalent geometry : angle 0.75942 (28122) SS BOND : bond 0.00495 ( 39) SS BOND : angle 0.98528 ( 78) hydrogen bonds : bond 0.04664 ( 599) hydrogen bonds : angle 5.89867 ( 1602) link_ALPHA1-3 : bond 0.00656 ( 2) link_ALPHA1-3 : angle 2.03549 ( 6) link_BETA1-4 : bond 0.00470 ( 11) link_BETA1-4 : angle 2.40306 ( 33) link_NAG-ASN : bond 0.00675 ( 51) link_NAG-ASN : angle 3.23339 ( 153) *********************** 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 419 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 418 time to evaluate : 0.606 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: A 80 ASN cc_start: 0.8064 (t0) cc_final: 0.7614 (p0) REVERT: A 107 ASP cc_start: 0.8948 (t70) cc_final: 0.8649 (t70) REVERT: A 114 GLN cc_start: 0.9076 (tp40) cc_final: 0.8676 (tt0) REVERT: A 150 MET cc_start: 0.9279 (mmm) cc_final: 0.8953 (mmp) REVERT: A 340 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8555 (mm-30) REVERT: A 424 ILE cc_start: 0.9414 (mp) cc_final: 0.8836 (mp) REVERT: A 434 MET cc_start: 0.9097 (tmm) cc_final: 0.8478 (tmm) REVERT: C 91 TYR cc_start: 0.8531 (m-80) cc_final: 0.8147 (m-80) REVERT: C 100 TYR cc_start: 0.8433 (p90) cc_final: 0.8099 (p90) REVERT: C 101 ASP cc_start: 0.9244 (p0) cc_final: 0.8891 (p0) REVERT: D 91 TYR cc_start: 0.8766 (t80) cc_final: 0.7908 (t80) REVERT: B 538 THR cc_start: 0.9551 (p) cc_final: 0.8689 (p) REVERT: B 542 ARG cc_start: 0.8644 (mtp-110) cc_final: 0.7754 (mtm110) REVERT: B 573 ILE cc_start: 0.9329 (mm) cc_final: 0.8978 (mm) REVERT: B 589 ASP cc_start: 0.9249 (m-30) cc_final: 0.8984 (m-30) REVERT: B 650 GLN cc_start: 0.9453 (tp40) cc_final: 0.9162 (tp40) REVERT: B 653 GLN cc_start: 0.9072 (tt0) cc_final: 0.8409 (tm-30) REVERT: B 657 GLU cc_start: 0.8527 (mt-10) cc_final: 0.7369 (mt-10) REVERT: E 100 MET cc_start: 0.8627 (mtm) cc_final: 0.8299 (ptp) REVERT: E 106 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8607 (mt-10) REVERT: E 173 TYR cc_start: 0.8511 (m-80) cc_final: 0.8139 (m-10) REVERT: E 217 TYR cc_start: 0.8203 (m-10) cc_final: 0.7936 (m-10) REVERT: E 368 ASP cc_start: 0.8446 (p0) cc_final: 0.7689 (p0) REVERT: E 370 GLU cc_start: 0.9354 (mp0) cc_final: 0.9146 (mp0) REVERT: E 425 ASN cc_start: 0.8108 (p0) cc_final: 0.7806 (p0) REVERT: E 434 MET cc_start: 0.7508 (tmm) cc_final: 0.7096 (tmm) REVERT: E 475 MET cc_start: 0.8489 (mmm) cc_final: 0.8090 (mmm) REVERT: J 43 LYS cc_start: 0.9032 (mmmt) cc_final: 0.8584 (pttp) REVERT: J 52 ASP cc_start: 0.9276 (p0) cc_final: 0.8986 (p0) REVERT: J 91 TYR cc_start: 0.8220 (m-80) cc_final: 0.7121 (m-80) REVERT: M 53 GLN cc_start: 0.8788 (mp10) cc_final: 0.8267 (mp10) REVERT: M 97 ILE cc_start: 0.9299 (tp) cc_final: 0.8843 (tp) REVERT: G 650 GLN cc_start: 0.8660 (tp-100) cc_final: 0.8390 (tp-100) REVERT: G 656 ASN cc_start: 0.9169 (m-40) cc_final: 0.8961 (m-40) REVERT: F 78 ASP cc_start: 0.8641 (p0) cc_final: 0.8400 (p0) REVERT: F 100 MET cc_start: 0.8888 (mtm) cc_final: 0.8651 (mtt) REVERT: F 107 ASP cc_start: 0.8581 (m-30) cc_final: 0.8253 (m-30) REVERT: F 112 TRP cc_start: 0.8752 (t-100) cc_final: 0.7966 (t-100) REVERT: F 114 GLN cc_start: 0.8622 (tp40) cc_final: 0.7837 (mm-40) REVERT: F 319 TYR cc_start: 0.8655 (p90) cc_final: 0.8264 (p90) REVERT: F 368 ASP cc_start: 0.8107 (p0) cc_final: 0.7884 (p0) REVERT: F 376 PHE cc_start: 0.7351 (t80) cc_final: 0.6999 (t80) REVERT: F 414 LEU cc_start: 0.9138 (mt) cc_final: 0.8755 (mp) REVERT: K 1 GLU cc_start: 0.6643 (tp30) cc_final: 0.6407 (tp30) REVERT: K 32 PHE cc_start: 0.8842 (m-80) cc_final: 0.8503 (m-80) REVERT: K 34 MET cc_start: 0.8295 (mpp) cc_final: 0.7623 (mpp) REVERT: K 64 LYS cc_start: 0.8936 (mttt) cc_final: 0.8666 (mtmm) REVERT: K 91 TYR cc_start: 0.8350 (m-10) cc_final: 0.7950 (m-10) REVERT: K 105 GLN cc_start: 0.7764 (mt0) cc_final: 0.7523 (mt0) REVERT: N 45 LYS cc_start: 0.9028 (tttt) cc_final: 0.8629 (tttp) REVERT: I 586 TYR cc_start: 0.9105 (t80) cc_final: 0.8670 (t80) REVERT: I 626 MET cc_start: 0.7747 (ttt) cc_final: 0.7266 (ttt) outliers start: 1 outliers final: 0 residues processed: 418 average time/residue: 0.1232 time to fit residues: 80.3820 Evaluate side-chains 324 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 101 optimal weight: 5.9990 chunk 230 optimal weight: 30.0000 chunk 145 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 120 optimal weight: 8.9990 chunk 86 optimal weight: 20.0000 chunk 150 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 chunk 192 optimal weight: 2.9990 chunk 219 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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** ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 577 GLN F 72 HIS F 352 HIS K 3 GLN ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 585 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.077463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.063327 restraints weight = 88673.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.065172 restraints weight = 48558.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.066422 restraints weight = 31732.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.067229 restraints weight = 23266.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.067804 restraints weight = 18700.053| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 20810 Z= 0.184 Angle : 0.678 20.451 28392 Z= 0.332 Chirality : 0.045 0.452 3355 Planarity : 0.004 0.049 3520 Dihedral : 6.386 55.950 4066 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.10 % Allowed : 2.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.17), residues: 2290 helix: 0.94 (0.26), residues: 412 sheet: 0.04 (0.20), residues: 664 loop : -0.30 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 588 TYR 0.017 0.002 TYR E 177 PHE 0.028 0.002 PHE A 468 TRP 0.038 0.002 TRP E 395 HIS 0.007 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00406 (20707) covalent geometry : angle 0.63827 (28122) SS BOND : bond 0.00358 ( 39) SS BOND : angle 0.83399 ( 78) hydrogen bonds : bond 0.04201 ( 599) hydrogen bonds : angle 5.60003 ( 1602) link_ALPHA1-3 : bond 0.00798 ( 2) link_ALPHA1-3 : angle 1.57304 ( 6) link_BETA1-4 : bond 0.00350 ( 11) link_BETA1-4 : angle 1.91994 ( 33) link_NAG-ASN : bond 0.00502 ( 51) link_NAG-ASN : angle 3.01592 ( 153) *********************** 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 429 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 427 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8139 (t0) cc_final: 0.7698 (p0) REVERT: A 95 MET cc_start: 0.8651 (ptm) cc_final: 0.7925 (ppp) REVERT: A 107 ASP cc_start: 0.8929 (t70) cc_final: 0.8558 (t70) REVERT: A 114 GLN cc_start: 0.9067 (tp40) cc_final: 0.8654 (tt0) REVERT: A 150 MET cc_start: 0.9247 (mmm) cc_final: 0.8946 (mmp) REVERT: A 352 HIS cc_start: 0.8423 (m90) cc_final: 0.8149 (m-70) REVERT: C 46 GLU cc_start: 0.8654 (tt0) cc_final: 0.7822 (tp30) REVERT: C 91 TYR cc_start: 0.8613 (m-80) cc_final: 0.8137 (m-80) REVERT: C 100 TYR cc_start: 0.8451 (p90) cc_final: 0.8151 (p90) REVERT: C 101 ASP cc_start: 0.9264 (p0) cc_final: 0.8744 (p0) REVERT: D 91 TYR cc_start: 0.8735 (t80) cc_final: 0.7845 (t80) REVERT: B 573 ILE cc_start: 0.9281 (mm) cc_final: 0.8957 (mm) REVERT: B 589 ASP cc_start: 0.9197 (m-30) cc_final: 0.8946 (m-30) REVERT: B 590 GLN cc_start: 0.9003 (mm-40) cc_final: 0.8789 (mm-40) REVERT: B 595 ILE cc_start: 0.9329 (tt) cc_final: 0.8862 (tt) REVERT: B 621 GLU cc_start: 0.7855 (tp30) cc_final: 0.7523 (tp30) REVERT: B 630 GLN cc_start: 0.8850 (mt0) cc_final: 0.8650 (mt0) REVERT: B 650 GLN cc_start: 0.9400 (tp40) cc_final: 0.8939 (tp40) REVERT: B 653 GLN cc_start: 0.9067 (tt0) cc_final: 0.8624 (tm-30) REVERT: B 657 GLU cc_start: 0.8523 (mt-10) cc_final: 0.7933 (mt-10) REVERT: E 40 TYR cc_start: 0.8966 (t80) cc_final: 0.8705 (t80) REVERT: E 100 MET cc_start: 0.8474 (mtm) cc_final: 0.8257 (ptp) REVERT: E 104 MET cc_start: 0.9387 (tpp) cc_final: 0.9051 (tpp) REVERT: E 106 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8598 (mt-10) REVERT: E 114 GLN cc_start: 0.8997 (tt0) cc_final: 0.8776 (tt0) REVERT: E 173 TYR cc_start: 0.8405 (m-80) cc_final: 0.8101 (m-10) REVERT: E 217 TYR cc_start: 0.8001 (m-10) cc_final: 0.7798 (m-10) REVERT: E 368 ASP cc_start: 0.8453 (p0) cc_final: 0.7751 (p0) REVERT: E 425 ASN cc_start: 0.8173 (p0) cc_final: 0.7844 (p0) REVERT: E 434 MET cc_start: 0.7595 (tmm) cc_final: 0.7183 (tmm) REVERT: J 43 LYS cc_start: 0.9001 (mmmt) cc_final: 0.8546 (pttp) REVERT: J 52 ASP cc_start: 0.9246 (p0) cc_final: 0.8963 (p0) REVERT: J 90 TYR cc_start: 0.9029 (m-10) cc_final: 0.8742 (m-10) REVERT: J 91 TYR cc_start: 0.8217 (m-80) cc_final: 0.7136 (m-80) REVERT: M 53 GLN cc_start: 0.8736 (mp10) cc_final: 0.8300 (mp10) REVERT: M 91 TYR cc_start: 0.8981 (t80) cc_final: 0.8240 (t80) REVERT: M 97 ILE cc_start: 0.9251 (tp) cc_final: 0.8856 (tp) REVERT: G 574 LYS cc_start: 0.8582 (mptt) cc_final: 0.8332 (pttt) REVERT: G 615 SER cc_start: 0.9231 (t) cc_final: 0.8911 (m) REVERT: G 630 GLN cc_start: 0.8863 (mt0) cc_final: 0.8624 (mt0) REVERT: G 652 GLN cc_start: 0.8587 (pt0) cc_final: 0.8307 (pt0) REVERT: G 656 ASN cc_start: 0.9157 (m-40) cc_final: 0.8804 (m-40) REVERT: F 100 MET cc_start: 0.8876 (mtm) cc_final: 0.8656 (mtt) REVERT: F 104 MET cc_start: 0.9003 (ttt) cc_final: 0.8775 (ttt) REVERT: F 107 ASP cc_start: 0.8507 (m-30) cc_final: 0.8186 (m-30) REVERT: F 112 TRP cc_start: 0.8712 (t-100) cc_final: 0.7807 (t-100) REVERT: F 114 GLN cc_start: 0.8621 (tp40) cc_final: 0.7782 (mm-40) REVERT: F 319 TYR cc_start: 0.8587 (p90) cc_final: 0.8259 (p90) REVERT: F 368 ASP cc_start: 0.8044 (p0) cc_final: 0.7764 (p0) REVERT: F 434 MET cc_start: 0.8160 (tmm) cc_final: 0.7497 (tmm) REVERT: K 32 PHE cc_start: 0.8692 (m-80) cc_final: 0.8347 (m-80) REVERT: K 34 MET cc_start: 0.7868 (mpp) cc_final: 0.7638 (mpp) REVERT: K 64 LYS cc_start: 0.8935 (mttt) cc_final: 0.8666 (mtmm) REVERT: K 91 TYR cc_start: 0.8301 (m-10) cc_final: 0.7832 (m-10) REVERT: K 105 GLN cc_start: 0.7713 (mt0) cc_final: 0.7459 (mt0) REVERT: N 45 LYS cc_start: 0.8950 (tttt) cc_final: 0.8674 (ttpp) REVERT: N 46 LEU cc_start: 0.9102 (tp) cc_final: 0.8878 (tp) REVERT: N 53 GLN cc_start: 0.8151 (mp10) cc_final: 0.7570 (mp10) REVERT: I 530 MET cc_start: 0.8968 (mtm) cc_final: 0.8016 (mpp) REVERT: I 626 MET cc_start: 0.7470 (ttt) cc_final: 0.7202 (ttt) REVERT: I 646 LEU cc_start: 0.9406 (mt) cc_final: 0.9162 (mt) outliers start: 2 outliers final: 0 residues processed: 427 average time/residue: 0.1301 time to fit residues: 86.3490 Evaluate side-chains 342 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 16 optimal weight: 1.9990 chunk 205 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 178 optimal weight: 9.9990 chunk 166 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 231 optimal weight: 40.0000 chunk 230 optimal weight: 30.0000 chunk 68 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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** ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 325 HIS ** G 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN ** N 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 585 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.076050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.062030 restraints weight = 89449.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.063865 restraints weight = 48890.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.065090 restraints weight = 31861.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.065889 restraints weight = 23328.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.066472 restraints weight = 18687.549| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.5365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 20810 Z= 0.253 Angle : 0.727 20.254 28392 Z= 0.359 Chirality : 0.046 0.447 3355 Planarity : 0.004 0.062 3520 Dihedral : 6.569 58.487 4066 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.10 % Allowed : 1.57 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.17), residues: 2290 helix: 0.89 (0.26), residues: 407 sheet: 0.01 (0.20), residues: 654 loop : -0.43 (0.17), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 588 TYR 0.019 0.002 TYR K 100G PHE 0.025 0.002 PHE F 391 TRP 0.034 0.002 TRP E 395 HIS 0.007 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00553 (20707) covalent geometry : angle 0.68952 (28122) SS BOND : bond 0.00441 ( 39) SS BOND : angle 0.89885 ( 78) hydrogen bonds : bond 0.04414 ( 599) hydrogen bonds : angle 5.79341 ( 1602) link_ALPHA1-3 : bond 0.00504 ( 2) link_ALPHA1-3 : angle 1.71884 ( 6) link_BETA1-4 : bond 0.00281 ( 11) link_BETA1-4 : angle 2.11315 ( 33) link_NAG-ASN : bond 0.00508 ( 51) link_NAG-ASN : angle 3.04848 ( 153) *********************** 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 403 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 401 time to evaluate : 0.593 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: A 80 ASN cc_start: 0.8206 (t0) cc_final: 0.7774 (p0) REVERT: A 95 MET cc_start: 0.8792 (ptm) cc_final: 0.7982 (ppp) REVERT: A 107 ASP cc_start: 0.8941 (t70) cc_final: 0.8623 (t70) REVERT: A 114 GLN cc_start: 0.9114 (tp40) cc_final: 0.8691 (tt0) REVERT: A 150 MET cc_start: 0.9288 (mmm) cc_final: 0.8954 (mmp) REVERT: A 352 HIS cc_start: 0.8402 (m90) cc_final: 0.8103 (m90) REVERT: A 424 ILE cc_start: 0.9416 (mp) cc_final: 0.9164 (mp) REVERT: A 434 MET cc_start: 0.8963 (tmm) cc_final: 0.8350 (tmm) REVERT: C 46 GLU cc_start: 0.8616 (tt0) cc_final: 0.7743 (tp30) REVERT: C 48 VAL cc_start: 0.8889 (t) cc_final: 0.8675 (t) REVERT: C 101 ASP cc_start: 0.9301 (p0) cc_final: 0.8878 (p0) REVERT: D 91 TYR cc_start: 0.8690 (t80) cc_final: 0.7750 (t80) REVERT: B 538 THR cc_start: 0.9540 (p) cc_final: 0.8659 (p) REVERT: B 542 ARG cc_start: 0.8752 (mtm110) cc_final: 0.7640 (mtm110) REVERT: B 573 ILE cc_start: 0.9225 (mm) cc_final: 0.8988 (tp) REVERT: B 589 ASP cc_start: 0.9297 (m-30) cc_final: 0.9042 (m-30) REVERT: B 595 ILE cc_start: 0.9328 (tt) cc_final: 0.8913 (tt) REVERT: B 621 GLU cc_start: 0.8143 (tp30) cc_final: 0.7732 (tp30) REVERT: B 650 GLN cc_start: 0.9443 (tp40) cc_final: 0.9104 (tp40) REVERT: B 653 GLN cc_start: 0.9106 (tt0) cc_final: 0.8634 (tm-30) REVERT: B 657 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8024 (mt-10) REVERT: E 106 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8660 (mt-10) REVERT: E 114 GLN cc_start: 0.8955 (tt0) cc_final: 0.8752 (tt0) REVERT: E 150 MET cc_start: 0.7776 (mmm) cc_final: 0.7273 (mmm) REVERT: E 425 ASN cc_start: 0.8263 (p0) cc_final: 0.7904 (p0) REVERT: E 434 MET cc_start: 0.7551 (tmm) cc_final: 0.7219 (tmm) REVERT: J 52 ASP cc_start: 0.9328 (p0) cc_final: 0.9092 (p0) REVERT: J 91 TYR cc_start: 0.8375 (m-80) cc_final: 0.7207 (m-80) REVERT: M 53 GLN cc_start: 0.8900 (mp10) cc_final: 0.8388 (mp10) REVERT: M 91 TYR cc_start: 0.9011 (t80) cc_final: 0.8278 (t80) REVERT: M 97 ILE cc_start: 0.9231 (tp) cc_final: 0.8975 (tp) REVERT: M 103 ARG cc_start: 0.9090 (mmm160) cc_final: 0.8723 (mmm160) REVERT: G 615 SER cc_start: 0.9268 (t) cc_final: 0.8966 (m) REVERT: G 648 GLU cc_start: 0.8412 (pp20) cc_final: 0.8190 (pp20) REVERT: G 656 ASN cc_start: 0.9087 (m-40) cc_final: 0.8884 (m-40) REVERT: F 78 ASP cc_start: 0.8533 (p0) cc_final: 0.8139 (t70) REVERT: F 100 MET cc_start: 0.8918 (mtm) cc_final: 0.8647 (mtt) REVERT: F 104 MET cc_start: 0.9065 (ttt) cc_final: 0.8844 (ttt) REVERT: F 107 ASP cc_start: 0.8546 (m-30) cc_final: 0.8218 (m-30) REVERT: F 114 GLN cc_start: 0.8590 (tp40) cc_final: 0.7801 (mm-40) REVERT: F 319 TYR cc_start: 0.8659 (p90) cc_final: 0.8301 (p90) REVERT: F 368 ASP cc_start: 0.8080 (p0) cc_final: 0.7801 (p0) REVERT: F 376 PHE cc_start: 0.7497 (t80) cc_final: 0.7232 (t80) REVERT: F 434 MET cc_start: 0.8193 (tmm) cc_final: 0.7419 (tmm) REVERT: K 32 PHE cc_start: 0.8772 (m-80) cc_final: 0.8334 (m-80) REVERT: K 34 MET cc_start: 0.8152 (mpp) cc_final: 0.7657 (mpp) REVERT: K 64 LYS cc_start: 0.8990 (mttt) cc_final: 0.8637 (mtmm) REVERT: K 75 LYS cc_start: 0.9129 (mppt) cc_final: 0.8873 (mmtm) REVERT: K 91 TYR cc_start: 0.8518 (m-10) cc_final: 0.8036 (m-80) REVERT: N 45 LYS cc_start: 0.9014 (tttt) cc_final: 0.8756 (tttp) REVERT: N 46 LEU cc_start: 0.9196 (tp) cc_final: 0.8955 (tp) REVERT: N 50 ASP cc_start: 0.8854 (m-30) cc_final: 0.8624 (m-30) REVERT: N 53 GLN cc_start: 0.8399 (mp10) cc_final: 0.7810 (mp10) REVERT: I 626 MET cc_start: 0.7735 (ttt) cc_final: 0.7341 (ttt) REVERT: I 646 LEU cc_start: 0.9446 (mt) cc_final: 0.9224 (mt) outliers start: 2 outliers final: 0 residues processed: 402 average time/residue: 0.1290 time to fit residues: 81.1012 Evaluate side-chains 326 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 205 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 243 optimal weight: 20.0000 chunk 119 optimal weight: 9.9990 chunk 135 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 214 optimal weight: 20.0000 chunk 168 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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** ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 650 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** K 76 ASN K 82AHIS ** N 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 585 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.076057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.062153 restraints weight = 89585.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.063995 restraints weight = 48616.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.065224 restraints weight = 31561.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.066006 restraints weight = 23024.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.066592 restraints weight = 18488.379| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.5552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20810 Z= 0.240 Angle : 0.726 20.145 28392 Z= 0.357 Chirality : 0.046 0.447 3355 Planarity : 0.004 0.051 3520 Dihedral : 6.596 57.859 4066 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.05 % Allowed : 0.74 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.17), residues: 2290 helix: 0.83 (0.26), residues: 410 sheet: 0.00 (0.20), residues: 653 loop : -0.49 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 588 TYR 0.018 0.002 TYR K 100G PHE 0.025 0.002 PHE F 391 TRP 0.034 0.002 TRP E 395 HIS 0.006 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00525 (20707) covalent geometry : angle 0.68261 (28122) SS BOND : bond 0.00426 ( 39) SS BOND : angle 0.91739 ( 78) hydrogen bonds : bond 0.04357 ( 599) hydrogen bonds : angle 5.74804 ( 1602) link_ALPHA1-3 : bond 0.00643 ( 2) link_ALPHA1-3 : angle 1.62255 ( 6) link_BETA1-4 : bond 0.00294 ( 11) link_BETA1-4 : angle 2.01630 ( 33) link_NAG-ASN : bond 0.00605 ( 51) link_NAG-ASN : angle 3.27183 ( 153) *********************** 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 398 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 397 time to evaluate : 0.825 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: 0.8255 (t0) cc_final: 0.7860 (p0) REVERT: A 95 MET cc_start: 0.8721 (ptm) cc_final: 0.7879 (ppp) REVERT: A 107 ASP cc_start: 0.9031 (t70) cc_final: 0.8711 (t70) REVERT: A 114 GLN cc_start: 0.9137 (tp40) cc_final: 0.8717 (tt0) REVERT: A 150 MET cc_start: 0.9296 (mmm) cc_final: 0.8998 (mmm) REVERT: A 352 HIS cc_start: 0.8350 (m90) cc_final: 0.8061 (m90) REVERT: A 424 ILE cc_start: 0.9381 (mp) cc_final: 0.9158 (mp) REVERT: A 434 MET cc_start: 0.8985 (tmm) cc_final: 0.8332 (tmm) REVERT: C 46 GLU cc_start: 0.8573 (tt0) cc_final: 0.7709 (tp30) REVERT: C 48 VAL cc_start: 0.8807 (t) cc_final: 0.8584 (t) REVERT: C 84 ASP cc_start: 0.8136 (t0) cc_final: 0.7710 (t0) REVERT: C 101 ASP cc_start: 0.9270 (p0) cc_final: 0.8813 (p0) REVERT: D 49 TYR cc_start: 0.8825 (p90) cc_final: 0.8329 (p90) REVERT: D 53 GLN cc_start: 0.8947 (tp40) cc_final: 0.8322 (tp40) REVERT: D 91 TYR cc_start: 0.8670 (t80) cc_final: 0.7765 (t80) REVERT: B 589 ASP cc_start: 0.9307 (m-30) cc_final: 0.9014 (m-30) REVERT: B 595 ILE cc_start: 0.9318 (tt) cc_final: 0.8939 (tt) REVERT: B 621 GLU cc_start: 0.8144 (tp30) cc_final: 0.7821 (tp30) REVERT: B 625 ASN cc_start: 0.8116 (m110) cc_final: 0.7915 (m110) REVERT: B 630 GLN cc_start: 0.8887 (mt0) cc_final: 0.8396 (mt0) REVERT: B 650 GLN cc_start: 0.9434 (tp40) cc_final: 0.9085 (tp40) REVERT: B 653 GLN cc_start: 0.9081 (tt0) cc_final: 0.8613 (tm-30) REVERT: B 657 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8027 (mt-10) REVERT: E 100 MET cc_start: 0.8387 (mpp) cc_final: 0.8067 (mpp) REVERT: E 106 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8668 (mt-10) REVERT: E 349 LEU cc_start: 0.9132 (mp) cc_final: 0.8804 (mt) REVERT: E 368 ASP cc_start: 0.8516 (p0) cc_final: 0.7767 (p0) REVERT: E 425 ASN cc_start: 0.8372 (p0) cc_final: 0.7946 (p0) REVERT: E 434 MET cc_start: 0.7527 (tmm) cc_final: 0.7184 (tmm) REVERT: J 52 ASP cc_start: 0.9341 (p0) cc_final: 0.9076 (p0) REVERT: J 72 ASP cc_start: 0.8835 (t70) cc_final: 0.8588 (t0) REVERT: J 91 TYR cc_start: 0.8373 (m-80) cc_final: 0.7782 (m-80) REVERT: M 53 GLN cc_start: 0.8869 (mp10) cc_final: 0.8389 (mp10) REVERT: M 91 TYR cc_start: 0.8987 (t80) cc_final: 0.8256 (t80) REVERT: M 97 ILE cc_start: 0.9246 (tp) cc_final: 0.8781 (tp) REVERT: M 103 ARG cc_start: 0.9115 (mmm160) cc_final: 0.8724 (mmm160) REVERT: G 615 SER cc_start: 0.9258 (t) cc_final: 0.8954 (m) REVERT: G 652 GLN cc_start: 0.8543 (pt0) cc_final: 0.8205 (pt0) REVERT: G 656 ASN cc_start: 0.9112 (m-40) cc_final: 0.8857 (m-40) REVERT: F 78 ASP cc_start: 0.8492 (p0) cc_final: 0.8162 (t70) REVERT: F 100 MET cc_start: 0.8929 (mtm) cc_final: 0.8653 (mtt) REVERT: F 104 MET cc_start: 0.9074 (ttt) cc_final: 0.8839 (ttt) REVERT: F 107 ASP cc_start: 0.8547 (m-30) cc_final: 0.8213 (m-30) REVERT: F 112 TRP cc_start: 0.8677 (t-100) cc_final: 0.7700 (t-100) REVERT: F 114 GLN cc_start: 0.8556 (tp40) cc_final: 0.7681 (mm-40) REVERT: F 319 TYR cc_start: 0.8644 (p90) cc_final: 0.8288 (p90) REVERT: F 368 ASP cc_start: 0.8065 (p0) cc_final: 0.7769 (p0) REVERT: F 376 PHE cc_start: 0.7443 (t80) cc_final: 0.7219 (t80) REVERT: F 434 MET cc_start: 0.8159 (tmm) cc_final: 0.7407 (tmm) REVERT: K 32 PHE cc_start: 0.8849 (m-80) cc_final: 0.8437 (m-80) REVERT: K 34 MET cc_start: 0.7947 (mpp) cc_final: 0.7454 (mpp) REVERT: K 64 LYS cc_start: 0.9003 (mttt) cc_final: 0.8630 (mtmm) REVERT: K 75 LYS cc_start: 0.9126 (mppt) cc_final: 0.8867 (mmtm) REVERT: K 91 TYR cc_start: 0.8558 (m-10) cc_final: 0.8048 (m-80) REVERT: N 45 LYS cc_start: 0.8975 (tttt) cc_final: 0.8741 (ttpp) REVERT: N 46 LEU cc_start: 0.9160 (tp) cc_final: 0.8931 (tp) REVERT: N 53 GLN cc_start: 0.8443 (mp10) cc_final: 0.7864 (mp10) REVERT: I 530 MET cc_start: 0.8911 (mtm) cc_final: 0.7903 (mpp) REVERT: I 626 MET cc_start: 0.7561 (ttt) cc_final: 0.7309 (ttt) REVERT: I 646 LEU cc_start: 0.9434 (mt) cc_final: 0.9187 (mt) outliers start: 1 outliers final: 0 residues processed: 398 average time/residue: 0.1448 time to fit residues: 89.9740 Evaluate side-chains 320 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 31 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 197 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 159 optimal weight: 0.7980 chunk 213 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 chunk 4 optimal weight: 0.1980 chunk 12 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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** E 99 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** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 585 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.077305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.063452 restraints weight = 88714.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.065283 restraints weight = 48369.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.066494 restraints weight = 31509.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.067310 restraints weight = 23080.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.067867 restraints weight = 18437.864| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.5659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20810 Z= 0.176 Angle : 0.685 19.973 28392 Z= 0.338 Chirality : 0.045 0.438 3355 Planarity : 0.004 0.056 3520 Dihedral : 6.229 58.998 4066 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.15 % Allowed : 0.64 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.18), residues: 2290 helix: 0.85 (0.26), residues: 412 sheet: 0.11 (0.20), residues: 669 loop : -0.53 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 588 TYR 0.026 0.002 TYR K 100G PHE 0.025 0.002 PHE F 391 TRP 0.049 0.002 TRP E 395 HIS 0.007 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00391 (20707) covalent geometry : angle 0.64351 (28122) SS BOND : bond 0.00330 ( 39) SS BOND : angle 0.77182 ( 78) hydrogen bonds : bond 0.04183 ( 599) hydrogen bonds : angle 5.60048 ( 1602) link_ALPHA1-3 : bond 0.00942 ( 2) link_ALPHA1-3 : angle 1.66416 ( 6) link_BETA1-4 : bond 0.00375 ( 11) link_BETA1-4 : angle 1.86987 ( 33) link_NAG-ASN : bond 0.00582 ( 51) link_NAG-ASN : angle 3.13930 ( 153) *********************** 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 400 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 397 time to evaluate : 0.606 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: 0.8255 (t0) cc_final: 0.7876 (p0) REVERT: A 95 MET cc_start: 0.8731 (ptm) cc_final: 0.7203 (ppp) REVERT: A 114 GLN cc_start: 0.9134 (tp40) cc_final: 0.8718 (tt0) REVERT: A 150 MET cc_start: 0.9272 (mmm) cc_final: 0.8938 (mmm) REVERT: A 201 ILE cc_start: 0.9175 (tt) cc_final: 0.8962 (tp) REVERT: A 434 MET cc_start: 0.9000 (tmm) cc_final: 0.8438 (tmm) REVERT: C 46 GLU cc_start: 0.8536 (tt0) cc_final: 0.7671 (tp30) REVERT: C 61 ASP cc_start: 0.8081 (p0) cc_final: 0.7875 (t0) REVERT: C 84 ASP cc_start: 0.8272 (t0) cc_final: 0.7721 (t0) REVERT: C 101 ASP cc_start: 0.9231 (p0) cc_final: 0.8647 (p0) REVERT: D 49 TYR cc_start: 0.8703 (p90) cc_final: 0.8288 (p90) REVERT: D 53 GLN cc_start: 0.8802 (tp40) cc_final: 0.8127 (tp40) REVERT: D 91 TYR cc_start: 0.8694 (t80) cc_final: 0.7813 (t80) REVERT: B 538 THR cc_start: 0.9514 (p) cc_final: 0.8541 (p) REVERT: B 542 ARG cc_start: 0.8686 (mtm110) cc_final: 0.7549 (mtm110) REVERT: B 579 ARG cc_start: 0.8381 (mtm-85) cc_final: 0.7789 (mtp180) REVERT: B 589 ASP cc_start: 0.9264 (m-30) cc_final: 0.8989 (m-30) REVERT: B 595 ILE cc_start: 0.9305 (tt) cc_final: 0.8935 (tt) REVERT: B 621 GLU cc_start: 0.7818 (tp30) cc_final: 0.7433 (tp30) REVERT: B 650 GLN cc_start: 0.9387 (tp40) cc_final: 0.9054 (tp40) REVERT: B 653 GLN cc_start: 0.9032 (tt0) cc_final: 0.8575 (tm-30) REVERT: B 657 GLU cc_start: 0.8526 (mt-10) cc_final: 0.7958 (mt-10) REVERT: E 100 MET cc_start: 0.8341 (mpp) cc_final: 0.8116 (mpp) REVERT: E 106 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8576 (mt-10) REVERT: E 150 MET cc_start: 0.7670 (mmm) cc_final: 0.7312 (mmm) REVERT: E 259 LEU cc_start: 0.9470 (mt) cc_final: 0.9211 (mt) REVERT: E 328 MET cc_start: 0.8123 (mmm) cc_final: 0.7920 (mmt) REVERT: E 349 LEU cc_start: 0.9084 (mp) cc_final: 0.8773 (mt) REVERT: E 368 ASP cc_start: 0.8455 (p0) cc_final: 0.7609 (p0) REVERT: E 425 ASN cc_start: 0.8394 (p0) cc_final: 0.7975 (p0) REVERT: E 434 MET cc_start: 0.7562 (tmm) cc_final: 0.7298 (tmm) REVERT: J 43 LYS cc_start: 0.8976 (mmmt) cc_final: 0.8505 (pttp) REVERT: J 52 ASP cc_start: 0.9296 (p0) cc_final: 0.9050 (p0) REVERT: J 91 TYR cc_start: 0.8282 (m-80) cc_final: 0.7704 (m-80) REVERT: M 53 GLN cc_start: 0.8861 (mp10) cc_final: 0.8354 (mp10) REVERT: M 91 TYR cc_start: 0.8957 (t80) cc_final: 0.8359 (t80) REVERT: M 97 ILE cc_start: 0.9239 (tp) cc_final: 0.8731 (tp) REVERT: M 103 ARG cc_start: 0.9077 (mmm160) cc_final: 0.8690 (mmm160) REVERT: G 540 GLN cc_start: 0.8929 (mp10) cc_final: 0.8648 (mt0) REVERT: G 574 LYS cc_start: 0.8641 (mptt) cc_final: 0.8118 (pttt) REVERT: G 615 SER cc_start: 0.9226 (t) cc_final: 0.8919 (m) REVERT: G 652 GLN cc_start: 0.8530 (pt0) cc_final: 0.8189 (pt0) REVERT: G 656 ASN cc_start: 0.9008 (m-40) cc_final: 0.8790 (m-40) REVERT: F 78 ASP cc_start: 0.8422 (p0) cc_final: 0.8097 (t70) REVERT: F 100 MET cc_start: 0.8884 (mtm) cc_final: 0.8607 (mtt) REVERT: F 104 MET cc_start: 0.9078 (ttt) cc_final: 0.8829 (ttt) REVERT: F 107 ASP cc_start: 0.8540 (m-30) cc_final: 0.8209 (m-30) REVERT: F 114 GLN cc_start: 0.8589 (tp40) cc_final: 0.7807 (mm-40) REVERT: F 319 TYR cc_start: 0.8609 (p90) cc_final: 0.8299 (p90) REVERT: F 368 ASP cc_start: 0.7989 (p0) cc_final: 0.7733 (p0) REVERT: F 434 MET cc_start: 0.8182 (tmm) cc_final: 0.7360 (tmm) REVERT: K 32 PHE cc_start: 0.8774 (m-80) cc_final: 0.8465 (m-80) REVERT: K 34 MET cc_start: 0.7918 (mpp) cc_final: 0.7466 (mpp) REVERT: K 75 LYS cc_start: 0.9094 (mppt) cc_final: 0.8854 (mmtm) REVERT: K 91 TYR cc_start: 0.8417 (m-10) cc_final: 0.7792 (m-10) REVERT: N 45 LYS cc_start: 0.8946 (tttt) cc_final: 0.8711 (ttpp) REVERT: N 50 ASP cc_start: 0.8865 (m-30) cc_final: 0.8591 (m-30) REVERT: N 53 GLN cc_start: 0.8457 (mp10) cc_final: 0.7903 (mp10) REVERT: I 530 MET cc_start: 0.8875 (mtm) cc_final: 0.7972 (mpp) REVERT: I 626 MET cc_start: 0.7560 (ttt) cc_final: 0.7359 (ttt) REVERT: I 646 LEU cc_start: 0.9422 (mt) cc_final: 0.9192 (mt) outliers start: 3 outliers final: 0 residues processed: 398 average time/residue: 0.1302 time to fit residues: 80.9805 Evaluate side-chains 325 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 249 optimal weight: 30.0000 chunk 7 optimal weight: 7.9990 chunk 213 optimal weight: 10.0000 chunk 179 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 221 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 216 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 243 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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** E 99 ASN ** G 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 650 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 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 585 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.074720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.060993 restraints weight = 89725.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.062786 restraints weight = 48772.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.063989 restraints weight = 31694.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.064798 restraints weight = 23150.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.065258 restraints weight = 18425.310| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.5903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 20810 Z= 0.311 Angle : 0.801 20.025 28392 Z= 0.395 Chirality : 0.048 0.443 3355 Planarity : 0.005 0.052 3520 Dihedral : 6.704 50.071 4066 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.10 % Allowed : 0.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.17), residues: 2290 helix: 0.57 (0.26), residues: 416 sheet: -0.37 (0.20), residues: 679 loop : -0.65 (0.17), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 588 TYR 0.029 0.003 TYR E 217 PHE 0.026 0.002 PHE F 391 TRP 0.079 0.003 TRP B 614 HIS 0.008 0.002 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00682 (20707) covalent geometry : angle 0.76070 (28122) SS BOND : bond 0.00507 ( 39) SS BOND : angle 0.98995 ( 78) hydrogen bonds : bond 0.04720 ( 599) hydrogen bonds : angle 5.99755 ( 1602) link_ALPHA1-3 : bond 0.00451 ( 2) link_ALPHA1-3 : angle 1.76962 ( 6) link_BETA1-4 : bond 0.00274 ( 11) link_BETA1-4 : angle 2.20325 ( 33) link_NAG-ASN : bond 0.00629 ( 51) link_NAG-ASN : angle 3.32422 ( 153) ********************** 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 391 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 389 time to evaluate : 0.651 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: 0.8188 (t0) cc_final: 0.7883 (p0) REVERT: A 114 GLN cc_start: 0.9157 (tp40) cc_final: 0.8746 (tt0) REVERT: A 150 MET cc_start: 0.9270 (mmm) cc_final: 0.8946 (mmm) REVERT: A 340 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8536 (mm-30) REVERT: A 424 ILE cc_start: 0.9404 (mp) cc_final: 0.9186 (mp) REVERT: A 434 MET cc_start: 0.8992 (tmm) cc_final: 0.8379 (tmm) REVERT: C 84 ASP cc_start: 0.8631 (t0) cc_final: 0.7946 (t0) REVERT: C 101 ASP cc_start: 0.9303 (p0) cc_final: 0.8924 (p0) REVERT: D 91 TYR cc_start: 0.8668 (t80) cc_final: 0.7826 (t80) REVERT: B 538 THR cc_start: 0.9516 (p) cc_final: 0.8558 (p) REVERT: B 542 ARG cc_start: 0.8742 (mtm110) cc_final: 0.7663 (mtm110) REVERT: B 589 ASP cc_start: 0.9298 (m-30) cc_final: 0.9039 (m-30) REVERT: B 650 GLN cc_start: 0.9429 (tp40) cc_final: 0.9030 (tp40) REVERT: B 653 GLN cc_start: 0.9110 (tt0) cc_final: 0.8665 (tm-30) REVERT: B 657 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8118 (mt-10) REVERT: E 100 MET cc_start: 0.8319 (mpp) cc_final: 0.8042 (mpp) REVERT: E 106 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8556 (mt-10) REVERT: E 150 MET cc_start: 0.7802 (mmm) cc_final: 0.7068 (mmm) REVERT: E 173 TYR cc_start: 0.8384 (m-80) cc_final: 0.7974 (m-10) REVERT: E 328 MET cc_start: 0.8207 (mmm) cc_final: 0.7983 (mmp) REVERT: E 434 MET cc_start: 0.7593 (tmm) cc_final: 0.7272 (tmm) REVERT: J 43 LYS cc_start: 0.9026 (mmmt) cc_final: 0.8444 (pttp) REVERT: J 52 ASP cc_start: 0.9327 (p0) cc_final: 0.9082 (p0) REVERT: J 72 ASP cc_start: 0.8856 (t70) cc_final: 0.8633 (t0) REVERT: J 91 TYR cc_start: 0.8445 (m-80) cc_final: 0.7882 (m-80) REVERT: M 53 GLN cc_start: 0.8920 (mp10) cc_final: 0.8438 (mp10) REVERT: M 91 TYR cc_start: 0.9050 (t80) cc_final: 0.8427 (t80) REVERT: M 97 ILE cc_start: 0.9243 (tp) cc_final: 0.8741 (tp) REVERT: M 103 ARG cc_start: 0.9093 (mmm160) cc_final: 0.8694 (mmm160) REVERT: G 573 ILE cc_start: 0.9221 (mm) cc_final: 0.8950 (mm) REVERT: G 615 SER cc_start: 0.9262 (t) cc_final: 0.9013 (m) REVERT: G 648 GLU cc_start: 0.8482 (pp20) cc_final: 0.8224 (pp20) REVERT: G 656 ASN cc_start: 0.9098 (m-40) cc_final: 0.8895 (m-40) REVERT: F 78 ASP cc_start: 0.8348 (p0) cc_final: 0.7931 (t70) REVERT: F 100 MET cc_start: 0.8925 (mtm) cc_final: 0.8614 (mtt) REVERT: F 104 MET cc_start: 0.9097 (ttt) cc_final: 0.8863 (ttt) REVERT: F 107 ASP cc_start: 0.8568 (m-30) cc_final: 0.8251 (m-30) REVERT: F 114 GLN cc_start: 0.8560 (tp40) cc_final: 0.7758 (mm-40) REVERT: F 319 TYR cc_start: 0.8736 (p90) cc_final: 0.8309 (p90) REVERT: F 368 ASP cc_start: 0.8131 (p0) cc_final: 0.7894 (p0) REVERT: F 434 MET cc_start: 0.8211 (tmm) cc_final: 0.7402 (tmm) REVERT: K 32 PHE cc_start: 0.8815 (m-80) cc_final: 0.8434 (m-80) REVERT: K 34 MET cc_start: 0.8173 (mpp) cc_final: 0.7559 (mpp) REVERT: K 64 LYS cc_start: 0.9057 (mttt) cc_final: 0.8648 (mtmm) REVERT: K 75 LYS cc_start: 0.9109 (mppt) cc_final: 0.8841 (mmtm) REVERT: K 91 TYR cc_start: 0.8804 (m-10) cc_final: 0.8236 (m-80) REVERT: N 46 LEU cc_start: 0.9170 (tp) cc_final: 0.8812 (tp) REVERT: N 47 MET cc_start: 0.8337 (mmt) cc_final: 0.7661 (mmm) REVERT: N 53 GLN cc_start: 0.8538 (mp10) cc_final: 0.7920 (mp10) REVERT: I 530 MET cc_start: 0.8965 (mtm) cc_final: 0.7982 (mpp) REVERT: I 626 MET cc_start: 0.7711 (ttt) cc_final: 0.7394 (ttt) REVERT: I 646 LEU cc_start: 0.9465 (mt) cc_final: 0.9235 (mt) outliers start: 2 outliers final: 0 residues processed: 390 average time/residue: 0.1421 time to fit residues: 86.9935 Evaluate side-chains 307 residues out of total 2032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 7 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 244 optimal weight: 20.0000 chunk 204 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 209 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 287 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** G 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 650 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** I 585 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.076375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.062587 restraints weight = 88014.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.064438 restraints weight = 47760.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.065656 restraints weight = 30873.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.066500 restraints weight = 22460.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.067043 restraints weight = 17752.780| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.5958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20810 Z= 0.208 Angle : 0.723 19.759 28392 Z= 0.357 Chirality : 0.046 0.432 3355 Planarity : 0.004 0.054 3520 Dihedral : 6.365 43.316 4066 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.10 % Allowed : 0.34 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.17), residues: 2290 helix: 0.68 (0.26), residues: 416 sheet: -0.21 (0.21), residues: 633 loop : -0.66 (0.17), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 588 TYR 0.029 0.002 TYR K 100G PHE 0.024 0.002 PHE F 391 TRP 0.064 0.003 TRP B 614 HIS 0.007 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00462 (20707) covalent geometry : angle 0.68159 (28122) SS BOND : bond 0.00386 ( 39) SS BOND : angle 0.91969 ( 78) hydrogen bonds : bond 0.04460 ( 599) hydrogen bonds : angle 5.81884 ( 1602) link_ALPHA1-3 : bond 0.00721 ( 2) link_ALPHA1-3 : angle 1.58426 ( 6) link_BETA1-4 : bond 0.00323 ( 11) link_BETA1-4 : angle 1.96305 ( 33) link_NAG-ASN : bond 0.00565 ( 51) link_NAG-ASN : angle 3.18389 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3257.77 seconds wall clock time: 57 minutes 20.24 seconds (3440.24 seconds total)