Starting phenix.real_space_refine on Sun Jan 26 11:11:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t49_41024/01_2025/8t49_41024.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t49_41024/01_2025/8t49_41024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t49_41024/01_2025/8t49_41024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t49_41024/01_2025/8t49_41024.map" model { file = "/net/cci-nas-00/data/ceres_data/8t49_41024/01_2025/8t49_41024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t49_41024/01_2025/8t49_41024.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 15642 2.51 5 N 4140 2.21 5 O 5013 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 24939 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3445 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 21, 'TRANS': 412} Chain breaks: 4 Chain: "H" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 967 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "L" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 798 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} 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: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 950 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "T" 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: "U" 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: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 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 Restraints were copied for chains: G, I, O, P, W, a, K, J, Z, d, Y, c, M, N, E, F, X, b, Q, R Time building chain proxies: 13.85, per 1000 atoms: 0.56 Number of scatterers: 24939 At special positions: 0 Unit cell: (146.05, 149.5, 172.5, 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 144 16.00 O 5013 8.00 N 4140 7.00 C 15642 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, 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=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 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=2.03 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.04 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=2.03 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 ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN W 4 " - " MAN W 5 " " MAN a 4 " - " MAN a 5 " ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " " BMA W 3 " - " MAN W 4 " " BMA Y 3 " - " MAN Y 4 " " BMA a 3 " - " MAN a 4 " " BMA c 3 " - " MAN c 4 " ALPHA1-6 " BMA S 3 " - " MAN S 6 " " BMA W 3 " - " MAN W 6 " " BMA a 3 " - " MAN a 6 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " 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 339 " " NAG A 609 " - " ASN A 386 " " NAG A 610 " - " ASN A 448 " " NAG A 611 " - " ASN A 289 " " NAG A 612 " - " ASN A 241 " " NAG A 613 " - " ASN A 355 " " NAG A 614 " - " ASN A 392 " " 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 289 " " NAG E 612 " - " ASN E 241 " " NAG E 613 " - " ASN E 355 " " NAG E 614 " - " 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 289 " " NAG F 612 " - " ASN F 241 " " NAG F 613 " - " ASN F 355 " " NAG F 614 " - " 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 S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 156 " " NAG U 1 " - " ASN A 262 " " NAG V 1 " - " ASN H 60 " " NAG W 1 " - " ASN E 332 " " NAG X 1 " - " ASN E 156 " " NAG Y 1 " - " ASN E 262 " " NAG Z 1 " - " ASN O 60 " " NAG a 1 " - " ASN F 332 " " NAG b 1 " - " ASN F 156 " " NAG c 1 " - " ASN F 262 " " NAG d 1 " - " ASN P 60 " Time building additional restraints: 6.92 Conformation dependent library (CDL) restraints added in 3.0 seconds 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5562 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 45 sheets defined 20.7% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.17 Creating SS restraints... Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 117 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 removed outlier: 4.030A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) 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: 4.247A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 484 removed outlier: 4.227A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100B through 100F Processing helix chain 'L' and resid 26 through 30 removed outlier: 3.652A pdb=" N GLU L 29 " --> pdb=" O ASP L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 removed outlier: 4.085A pdb=" N GLU D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.441A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.585A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.667A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 354 removed outlier: 4.030A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.247A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 484 removed outlier: 4.227A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 65 No H-bonds generated for 'chain 'O' and resid 63 through 65' Processing helix chain 'O' and resid 73 through 75 No H-bonds generated for 'chain 'O' and resid 73 through 75' Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'O' and resid 100B through 100F Processing helix chain 'Q' and resid 26 through 30 removed outlier: 3.652A pdb=" N GLU Q 29 " --> pdb=" O ASP Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 83 Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 removed outlier: 4.084A pdb=" N GLU M 83 " --> pdb=" O ALA M 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 523 through 528 removed outlier: 4.441A 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: 3.585A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN G 543 " --> pdb=" O VAL G 539 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 596 Processing helix chain 'G' and resid 618 through 626 removed outlier: 3.668A pdb=" N MET G 626 " --> pdb=" O ILE G 622 " (cutoff:3.500A) 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 122 through 126 Processing helix chain 'F' and resid 195 through 198 Processing helix chain 'F' and resid 335 through 354 removed outlier: 4.030A pdb=" N HIS F 352 " --> pdb=" O GLN F 348 " (cutoff:3.500A) 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: 4.247A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 474 through 484 removed outlier: 4.227A pdb=" N ASN F 478 " --> pdb=" O ASP F 474 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 65 No H-bonds generated for 'chain 'P' and resid 63 through 65' Processing helix chain 'P' and resid 73 through 75 No H-bonds generated for 'chain 'P' and resid 73 through 75' Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'P' and resid 100B through 100F Processing helix chain 'R' and resid 26 through 30 removed outlier: 3.652A pdb=" N GLU R 29 " --> pdb=" O ASP R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 83 Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 4.085A pdb=" N GLU N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 523 through 528 removed outlier: 4.441A pdb=" N GLY I 527 " --> pdb=" O GLY I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 543 removed outlier: 3.585A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN I 543 " --> pdb=" O VAL I 539 " (cutoff:3.500A) Processing helix chain 'I' and resid 573 through 596 Processing helix chain 'I' and resid 618 through 626 removed outlier: 3.667A pdb=" N MET I 626 " --> pdb=" O ILE I 622 " (cutoff:3.500A) 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: 5.360A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.061A 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 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 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 201 through 203 removed outlier: 6.446A 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 284 through 312 removed outlier: 7.059A pdb=" N ASN A 301 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N VAL A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.276A 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 'H' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'H' and resid 34 through 39 removed outlier: 6.762A pdb=" N TRP H 35 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASN H 50 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100H through 103 Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AB2, first strand: chain 'L' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 12 current: chain 'L' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 97 through 98 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.807A pdb=" N GLY C 16 " --> pdb=" O SER C 82B" (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 34 through 39 removed outlier: 5.805A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (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=AB5, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AB6, first strand: chain 'D' and resid 33 through 38 removed outlier: 6.268A 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 45 through 48 current: chain 'D' and resid 95A through 98 Processing sheet with id=AB7, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.361A pdb=" N VAL G 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N VAL E 38 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR G 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N TYR E 40 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N CYS G 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AB9, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AC1, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'E' and resid 172 through 177 Processing sheet with id=AC3, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.446A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC4, 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: 7.059A pdb=" N ASN E 301 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N VAL E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.276A 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=AC5, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'O' and resid 34 through 39 removed outlier: 6.762A pdb=" N TRP O 35 " --> pdb=" O ASN O 50 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASN O 50 " --> pdb=" O TRP O 35 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 57 through 59 current: chain 'O' and resid 100H through 103 Processing sheet with id=AC7, first strand: chain 'Q' and resid 5 through 6 Processing sheet with id=AC8, first strand: chain 'Q' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 9 through 12 current: chain 'Q' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 45 through 48 current: chain 'Q' and resid 97 through 98 No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.807A pdb=" N GLY J 16 " --> pdb=" O SER J 82B" (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 34 through 39 removed outlier: 5.804A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (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=AD2, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=AD3, first strand: chain 'M' and resid 33 through 38 removed outlier: 6.268A pdb=" N TRP M 35 " --> pdb=" O MET M 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 45 through 48 current: chain 'M' and resid 95A through 98 Processing sheet with id=AD4, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.360A pdb=" N VAL I 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N VAL F 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR I 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N TYR F 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N CYS I 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AD6, first strand: chain 'F' and resid 75 through 76 Processing sheet with id=AD7, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'F' and resid 172 through 177 Processing sheet with id=AD9, first strand: chain 'F' and resid 201 through 203 removed outlier: 6.446A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AE1, 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 312 removed outlier: 7.059A pdb=" N ASN F 301 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N VAL F 323 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 315 through 323 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=AE2, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'P' and resid 34 through 39 removed outlier: 6.762A pdb=" N TRP P 35 " --> pdb=" O ASN P 50 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASN P 50 " --> pdb=" O TRP P 35 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TRP P 36 " --> pdb=" O ILE P 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 57 through 59 current: chain 'P' and resid 100H through 103 Processing sheet with id=AE4, first strand: chain 'R' and resid 5 through 6 Processing sheet with id=AE5, first strand: chain 'R' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 9 through 12 current: chain 'R' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 45 through 48 current: chain 'R' and resid 97 through 98 No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'K' and resid 3 through 7 removed outlier: 3.808A pdb=" N GLY K 16 " --> pdb=" O SER K 82B" (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 34 through 39 removed outlier: 5.804A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.290A 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=AE8, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AE9, first strand: chain 'N' and resid 33 through 38 removed outlier: 6.268A 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 95A through 98 720 hydrogen bonds defined for protein. 1782 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: 8.46 Time building geometry restraints manager: 7.91 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: 7833 1.35 - 1.47: 6705 1.47 - 1.60: 10716 1.60 - 1.72: 0 1.72 - 1.85: 198 Bond restraints: 25452 Sorted by residual: bond pdb=" C1 NAG V 2 " pdb=" O5 NAG V 2 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.59e+00 bond pdb=" C5 MAN S 5 " pdb=" O5 MAN S 5 " ideal model delta sigma weight residual 1.418 1.465 -0.047 2.00e-02 2.50e+03 5.57e+00 bond pdb=" C5 MAN W 5 " pdb=" O5 MAN W 5 " ideal model delta sigma weight residual 1.418 1.465 -0.047 2.00e-02 2.50e+03 5.53e+00 bond pdb=" C1 NAG Z 2 " pdb=" O5 NAG Z 2 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.53e+00 bond pdb=" C1 NAG d 2 " pdb=" O5 NAG d 2 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.49e+00 ... (remaining 25447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 32477 2.23 - 4.47: 1773 4.47 - 6.70: 265 6.70 - 8.93: 27 8.93 - 11.16: 12 Bond angle restraints: 34554 Sorted by residual: angle pdb=" N LEU Q 97 " pdb=" CA LEU Q 97 " pdb=" C LEU Q 97 " ideal model delta sigma weight residual 107.93 96.77 11.16 1.65e+00 3.67e-01 4.58e+01 angle pdb=" N LEU L 97 " pdb=" CA LEU L 97 " pdb=" C LEU L 97 " ideal model delta sigma weight residual 107.93 96.78 11.15 1.65e+00 3.67e-01 4.57e+01 angle pdb=" N LEU R 97 " pdb=" CA LEU R 97 " pdb=" C LEU R 97 " ideal model delta sigma weight residual 107.93 96.79 11.14 1.65e+00 3.67e-01 4.56e+01 angle pdb=" CA TRP H 47 " pdb=" CB TRP H 47 " pdb=" CG TRP H 47 " ideal model delta sigma weight residual 113.60 122.87 -9.27 1.90e+00 2.77e-01 2.38e+01 angle pdb=" CA TRP O 47 " pdb=" CB TRP O 47 " pdb=" CG TRP O 47 " ideal model delta sigma weight residual 113.60 122.87 -9.27 1.90e+00 2.77e-01 2.38e+01 ... (remaining 34549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.50: 15484 21.50 - 42.99: 513 42.99 - 64.49: 131 64.49 - 85.99: 81 85.99 - 107.49: 39 Dihedral angle restraints: 16248 sinusoidal: 7554 harmonic: 8694 Sorted by residual: dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -136.36 50.36 1 1.00e+01 1.00e-02 3.48e+01 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 92 " pdb=" CB CYS C 92 " ideal model delta sinusoidal sigma weight residual 93.00 45.62 47.38 1 1.00e+01 1.00e-02 3.10e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 52.92 40.08 1 1.00e+01 1.00e-02 2.25e+01 ... (remaining 16245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 3889 0.122 - 0.245: 231 0.245 - 0.367: 14 0.367 - 0.489: 0 0.489 - 0.611: 3 Chirality restraints: 4137 Sorted by residual: chirality pdb=" C1 NAG Z 1 " pdb=" ND2 ASN O 60 " pdb=" C2 NAG Z 1 " pdb=" O5 NAG Z 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.35e+00 chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN H 60 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.29e+00 chirality pdb=" C1 NAG d 1 " pdb=" ND2 ASN P 60 " pdb=" C2 NAG d 1 " pdb=" O5 NAG d 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.28e+00 ... (remaining 4134 not shown) Planarity restraints: 4323 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 476 " 0.020 2.00e-02 2.50e+03 3.98e-02 1.58e+01 pdb=" C ARG A 476 " -0.069 2.00e-02 2.50e+03 pdb=" O ARG A 476 " 0.026 2.00e-02 2.50e+03 pdb=" N ASP A 477 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 476 " -0.020 2.00e-02 2.50e+03 3.98e-02 1.58e+01 pdb=" C ARG E 476 " 0.069 2.00e-02 2.50e+03 pdb=" O ARG E 476 " -0.025 2.00e-02 2.50e+03 pdb=" N ASP E 477 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 476 " -0.020 2.00e-02 2.50e+03 3.97e-02 1.58e+01 pdb=" C ARG F 476 " 0.069 2.00e-02 2.50e+03 pdb=" O ARG F 476 " -0.025 2.00e-02 2.50e+03 pdb=" N ASP F 477 " -0.023 2.00e-02 2.50e+03 ... (remaining 4320 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 210 2.60 - 3.17: 20719 3.17 - 3.75: 37303 3.75 - 4.32: 54597 4.32 - 4.90: 88204 Nonbonded interactions: 201033 Sorted by model distance: nonbonded pdb=" SG CYS F 501 " pdb=" SG CYS I 605 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS E 501 " pdb=" SG CYS G 605 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS I 598 " pdb=" SG CYS I 604 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS G 598 " pdb=" SG CYS G 604 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS Q 23 " pdb=" SG CYS Q 88 " model vdw 2.027 3.760 ... (remaining 201028 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: 0.16 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'H' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'S' selection = chain 'W' selection = chain 'a' } ncs_group { reference = chain 'C' selection = chain 'K' selection = chain 'J' } ncs_group { reference = chain 'V' selection = chain 'Z' selection = chain 'd' } ncs_group { reference = chain 'U' selection = chain 'Y' selection = chain 'c' } ncs_group { reference = chain 'D' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'T' selection = chain 'X' selection = chain 'b' } ncs_group { reference = chain 'L' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.980 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 53.810 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 25452 Z= 0.458 Angle : 1.164 11.163 34554 Z= 0.649 Chirality : 0.066 0.611 4137 Planarity : 0.007 0.074 4260 Dihedral : 14.060 107.487 10641 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.57 % Allowed : 5.25 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.15), residues: 2979 helix: 0.71 (0.24), residues: 420 sheet: 1.18 (0.17), residues: 861 loop : 0.53 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP P 47 HIS 0.006 0.002 HIS E 374 PHE 0.023 0.003 PHE E 383 TYR 0.018 0.003 TYR D 36 ARG 0.020 0.002 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 461 time to evaluate : 3.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.8906 (mtp) cc_final: 0.8621 (mtp) REVERT: L 21 MET cc_start: 0.5719 (mtm) cc_final: 0.5418 (mtm) REVERT: L 24 GLN cc_start: 0.7620 (tt0) cc_final: 0.7208 (tm-30) REVERT: L 58 ILE cc_start: 0.7348 (mm) cc_final: 0.6973 (pt) REVERT: L 75 ILE cc_start: 0.5727 (mt) cc_final: 0.5479 (tt) REVERT: L 85 ASP cc_start: 0.7101 (m-30) cc_final: 0.6445 (m-30) REVERT: L 86 TYR cc_start: 0.8223 (m-80) cc_final: 0.7929 (m-80) REVERT: C 86 ASP cc_start: 0.7786 (m-30) cc_final: 0.7484 (m-30) REVERT: C 94 THR cc_start: 0.8824 (m) cc_final: 0.8466 (p) REVERT: D 69 ASN cc_start: 0.8116 (m-40) cc_final: 0.7690 (m-40) REVERT: E 104 MET cc_start: 0.9467 (ttt) cc_final: 0.9246 (ttt) REVERT: E 426 MET cc_start: 0.8808 (mtp) cc_final: 0.8510 (mmm) REVERT: E 475 MET cc_start: 0.8550 (tpp) cc_final: 0.8342 (mmp) REVERT: O 101 ASP cc_start: 0.7412 (t70) cc_final: 0.7180 (t70) REVERT: Q 21 MET cc_start: 0.5762 (mtm) cc_final: 0.5493 (mtm) REVERT: Q 24 GLN cc_start: 0.7726 (tt0) cc_final: 0.7397 (tm-30) REVERT: Q 75 ILE cc_start: 0.5618 (mt) cc_final: 0.5170 (tt) REVERT: Q 85 ASP cc_start: 0.7311 (m-30) cc_final: 0.6397 (m-30) REVERT: Q 103 ARG cc_start: 0.7744 (mmm160) cc_final: 0.7488 (tpt170) REVERT: J 75 LYS cc_start: 0.9148 (mtpp) cc_final: 0.8942 (mtpt) REVERT: M 6 GLN cc_start: 0.7692 (mt0) cc_final: 0.7341 (mt0) REVERT: M 85 ASP cc_start: 0.8274 (m-30) cc_final: 0.7603 (m-30) REVERT: G 535 MET cc_start: 0.8778 (mtt) cc_final: 0.8404 (mtm) REVERT: G 632 ASP cc_start: 0.8589 (t0) cc_final: 0.8292 (t0) REVERT: F 150 MET cc_start: 0.9018 (mmm) cc_final: 0.8719 (mmt) REVERT: F 426 MET cc_start: 0.8916 (mtp) cc_final: 0.8680 (mtp) REVERT: F 475 MET cc_start: 0.8702 (tpp) cc_final: 0.8241 (mmt) REVERT: R 21 MET cc_start: 0.6214 (mtm) cc_final: 0.5993 (mtt) REVERT: R 24 GLN cc_start: 0.7621 (tt0) cc_final: 0.7332 (tm-30) REVERT: N 74 THR cc_start: 0.7821 (m) cc_final: 0.7429 (p) REVERT: N 85 ASP cc_start: 0.8264 (m-30) cc_final: 0.7835 (m-30) REVERT: I 535 MET cc_start: 0.8654 (mtt) cc_final: 0.8408 (mtp) REVERT: I 657 GLU cc_start: 0.8242 (tt0) cc_final: 0.8007 (tt0) outliers start: 15 outliers final: 3 residues processed: 470 average time/residue: 0.4498 time to fit residues: 313.2623 Evaluate side-chains 336 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 333 time to evaluate : 2.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain R residue 4 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 10.0000 chunk 225 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 232 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 269 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS L 17 HIS L 51 ASN L 52 ASN L 89 ASN C 52 ASN D 95 GLN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS Q 17 HIS Q 52 ASN J 13 GLN J 52 ASN ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 HIS R 17 HIS N 6 GLN ** I 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.106153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.077301 restraints weight = 48225.163| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.72 r_work: 0.2917 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 25452 Z= 0.452 Angle : 0.719 7.128 34554 Z= 0.377 Chirality : 0.051 0.312 4137 Planarity : 0.005 0.047 4260 Dihedral : 10.397 87.419 5238 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.09 % Allowed : 6.74 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.15), residues: 2979 helix: 1.50 (0.26), residues: 423 sheet: 0.86 (0.17), residues: 876 loop : -0.01 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP O 47 HIS 0.008 0.002 HIS F 105 PHE 0.021 0.002 PHE G 522 TYR 0.018 0.002 TYR J 100G ARG 0.006 0.001 ARG Q 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 352 time to evaluate : 2.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.9370 (mmm) cc_final: 0.9157 (mmm) REVERT: A 161 MET cc_start: 0.8738 (tpp) cc_final: 0.8385 (tpp) REVERT: A 241 ASN cc_start: 0.7868 (OUTLIER) cc_final: 0.7644 (m-40) REVERT: A 475 MET cc_start: 0.8540 (tpp) cc_final: 0.8044 (mmt) REVERT: L 24 GLN cc_start: 0.7672 (tt0) cc_final: 0.7472 (tt0) REVERT: D 79 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7020 (mp10) REVERT: B 621 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8380 (mt-10) REVERT: O 3 GLN cc_start: 0.5905 (mp10) cc_final: 0.5647 (mp10) REVERT: Q 4 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6671 (tp) REVERT: Q 24 GLN cc_start: 0.7300 (tt0) cc_final: 0.7016 (tm-30) REVERT: Q 86 TYR cc_start: 0.8366 (m-80) cc_final: 0.7774 (m-80) REVERT: M 78 LEU cc_start: 0.7486 (mt) cc_final: 0.7264 (mt) REVERT: M 79 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7169 (mp10) REVERT: G 632 ASP cc_start: 0.9008 (t0) cc_final: 0.8785 (t0) REVERT: F 241 ASN cc_start: 0.7518 (OUTLIER) cc_final: 0.7295 (m-40) REVERT: F 475 MET cc_start: 0.8602 (tpp) cc_final: 0.8341 (mmt) REVERT: P 46 GLU cc_start: 0.7358 (mp0) cc_final: 0.7138 (mp0) REVERT: P 100 ASP cc_start: 0.7926 (t0) cc_final: 0.7726 (t0) REVERT: R 4 LEU cc_start: 0.6446 (OUTLIER) cc_final: 0.6181 (tp) REVERT: R 24 GLN cc_start: 0.7507 (tt0) cc_final: 0.7207 (tm-30) REVERT: R 61 ARG cc_start: 0.8641 (mtm-85) cc_final: 0.8396 (ttm110) REVERT: K 13 GLN cc_start: 0.7760 (mm-40) cc_final: 0.7525 (mm110) REVERT: N 79 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.6911 (mp10) REVERT: N 85 ASP cc_start: 0.8496 (m-30) cc_final: 0.8230 (m-30) outliers start: 55 outliers final: 29 residues processed: 384 average time/residue: 0.4135 time to fit residues: 240.9686 Evaluate side-chains 337 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 301 time to evaluate : 2.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 79 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 35 optimal weight: 0.8980 chunk 253 optimal weight: 0.0470 chunk 76 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 273 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 236 optimal weight: 0.7980 chunk 191 optimal weight: 0.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 195 ASN D 95 GLN M 17 GLN F 33 ASN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.108172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.078388 restraints weight = 47570.633| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.69 r_work: 0.2989 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25452 Z= 0.195 Angle : 0.569 5.988 34554 Z= 0.299 Chirality : 0.045 0.288 4137 Planarity : 0.004 0.049 4260 Dihedral : 8.913 84.492 5236 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.71 % Allowed : 8.03 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.15), residues: 2979 helix: 1.71 (0.27), residues: 423 sheet: 0.95 (0.17), residues: 852 loop : -0.07 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP O 47 HIS 0.004 0.001 HIS E 105 PHE 0.009 0.001 PHE E 176 TYR 0.016 0.001 TYR O 91 ARG 0.006 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 329 time to evaluate : 3.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8277 (tpp) cc_final: 0.7840 (mmt) REVERT: H 59 TYR cc_start: 0.6782 (m-10) cc_final: 0.6540 (m-10) REVERT: L 24 GLN cc_start: 0.7636 (tt0) cc_final: 0.7412 (tt0) REVERT: C 86 ASP cc_start: 0.7474 (m-30) cc_final: 0.7210 (m-30) REVERT: D 79 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.6989 (mp10) REVERT: E 150 MET cc_start: 0.9046 (mmt) cc_final: 0.8809 (mmt) REVERT: E 328 MET cc_start: 0.8913 (ttm) cc_final: 0.8700 (ttt) REVERT: O 91 TYR cc_start: 0.5329 (m-80) cc_final: 0.5045 (m-80) REVERT: Q 4 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6231 (tp) REVERT: M 79 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7180 (mp10) REVERT: G 648 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8713 (mt-10) REVERT: P 100 ASP cc_start: 0.7792 (t0) cc_final: 0.7530 (t0) REVERT: R 61 ARG cc_start: 0.8651 (mtm-85) cc_final: 0.8403 (ttm110) REVERT: K 13 GLN cc_start: 0.7757 (mm-40) cc_final: 0.7467 (mm110) REVERT: N 85 ASP cc_start: 0.8412 (m-30) cc_final: 0.8153 (m-30) REVERT: I 624 ASP cc_start: 0.8950 (m-30) cc_final: 0.8564 (m-30) outliers start: 45 outliers final: 30 residues processed: 356 average time/residue: 0.4250 time to fit residues: 229.9458 Evaluate side-chains 332 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 299 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 88 CYS Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 88 CYS Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 97 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 186 optimal weight: 4.9990 chunk 239 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 221 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 129 optimal weight: 4.9990 chunk 240 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN H 77 GLN L 89 ASN D 95 GLN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 ASN ** I 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.105208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.073809 restraints weight = 48380.910| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.59 r_work: 0.2910 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 25452 Z= 0.375 Angle : 0.623 6.163 34554 Z= 0.324 Chirality : 0.047 0.300 4137 Planarity : 0.004 0.037 4260 Dihedral : 8.340 84.416 5234 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.97 % Allowed : 7.84 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.15), residues: 2979 helix: 1.80 (0.27), residues: 405 sheet: 0.61 (0.17), residues: 897 loop : -0.24 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 47 HIS 0.007 0.001 HIS F 105 PHE 0.018 0.002 PHE K 29 TYR 0.023 0.002 TYR J 27 ARG 0.007 0.001 ARG K 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 315 time to evaluate : 2.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8401 (tpp) cc_final: 0.7821 (mmt) REVERT: H 24 VAL cc_start: 0.7549 (OUTLIER) cc_final: 0.7173 (t) REVERT: H 51 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8222 (tt) REVERT: H 77 GLN cc_start: 0.8532 (tt0) cc_final: 0.7871 (mm-40) REVERT: L 24 GLN cc_start: 0.7631 (tt0) cc_final: 0.7402 (tt0) REVERT: C 86 ASP cc_start: 0.7288 (m-30) cc_final: 0.6882 (m-30) REVERT: O 51 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8047 (tt) REVERT: O 66 ARG cc_start: 0.5165 (ptt90) cc_final: 0.4891 (ptt90) REVERT: J 72 ASP cc_start: 0.8389 (t0) cc_final: 0.8177 (t0) REVERT: J 86 ASP cc_start: 0.7678 (m-30) cc_final: 0.7286 (m-30) REVERT: G 648 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8703 (mt-10) REVERT: F 241 ASN cc_start: 0.7592 (OUTLIER) cc_final: 0.7357 (m-40) REVERT: R 54 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.8177 (mtp-110) REVERT: R 61 ARG cc_start: 0.8667 (mtm-85) cc_final: 0.8367 (ttm110) REVERT: R 98 PHE cc_start: 0.6431 (OUTLIER) cc_final: 0.4066 (t80) REVERT: K 13 GLN cc_start: 0.7701 (mm-40) cc_final: 0.7314 (mm110) REVERT: K 23 ARG cc_start: 0.8596 (mmm-85) cc_final: 0.8268 (tpp-160) REVERT: N 79 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.6877 (mp10) REVERT: I 624 ASP cc_start: 0.9048 (m-30) cc_final: 0.8630 (m-30) outliers start: 78 outliers final: 47 residues processed: 350 average time/residue: 0.4579 time to fit residues: 247.9864 Evaluate side-chains 353 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 299 time to evaluate : 3.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 88 CYS Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 54 ARG Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 79 GLN Chi-restraints excluded: chain N residue 97 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 129 optimal weight: 6.9990 chunk 267 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 260 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 226 optimal weight: 0.8980 chunk 145 optimal weight: 9.9990 chunk 92 optimal weight: 0.0770 chunk 223 optimal weight: 0.9980 chunk 285 optimal weight: 1.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 195 ASN L 89 ASN D 95 GLN O 39 GLN Q 38 GLN Q 89 ASN F 33 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 3 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.106673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.077842 restraints weight = 47715.798| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.81 r_work: 0.2944 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25452 Z= 0.186 Angle : 0.532 6.114 34554 Z= 0.280 Chirality : 0.044 0.284 4137 Planarity : 0.004 0.037 4260 Dihedral : 7.717 80.642 5232 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.98 % Allowed : 9.67 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.15), residues: 2979 helix: 2.04 (0.27), residues: 405 sheet: 0.60 (0.17), residues: 927 loop : -0.21 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 91 HIS 0.004 0.001 HIS E 105 PHE 0.021 0.001 PHE O 78 TYR 0.016 0.001 TYR K 100G ARG 0.006 0.001 ARG Q 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 324 time to evaluate : 2.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8016 (mm-40) cc_final: 0.7805 (mm-40) REVERT: H 24 VAL cc_start: 0.7489 (OUTLIER) cc_final: 0.7061 (t) REVERT: L 24 GLN cc_start: 0.7570 (tt0) cc_final: 0.7359 (tt0) REVERT: L 79 GLN cc_start: 0.7829 (mm-40) cc_final: 0.7498 (mm110) REVERT: D 79 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.6950 (mp10) REVERT: D 83 GLU cc_start: 0.7669 (pm20) cc_final: 0.7423 (mp0) REVERT: E 328 MET cc_start: 0.9031 (ttm) cc_final: 0.8752 (ttt) REVERT: O 51 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8012 (tt) REVERT: Q 98 PHE cc_start: 0.6163 (OUTLIER) cc_final: 0.3987 (t80) REVERT: J 72 ASP cc_start: 0.8311 (t0) cc_final: 0.8091 (t0) REVERT: J 97 MET cc_start: 0.8674 (ttp) cc_final: 0.8472 (ttp) REVERT: G 648 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8737 (mt-10) REVERT: P 5 GLN cc_start: 0.8358 (mm-40) cc_final: 0.8009 (mm-40) REVERT: P 105 ARG cc_start: 0.6363 (mmm160) cc_final: 0.5725 (mmp80) REVERT: R 61 ARG cc_start: 0.8691 (mtm-85) cc_final: 0.8435 (ttm110) REVERT: R 98 PHE cc_start: 0.6520 (OUTLIER) cc_final: 0.4074 (t80) REVERT: K 13 GLN cc_start: 0.7688 (mm-40) cc_final: 0.7386 (mm110) REVERT: K 23 ARG cc_start: 0.8615 (mmm-85) cc_final: 0.8414 (tpp-160) REVERT: I 624 ASP cc_start: 0.8935 (m-30) cc_final: 0.8526 (m-30) outliers start: 52 outliers final: 33 residues processed: 347 average time/residue: 0.4062 time to fit residues: 215.5020 Evaluate side-chains 341 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 303 time to evaluate : 2.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 77 GLN Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 52 ASN Chi-restraints excluded: chain Q residue 88 CYS Chi-restraints excluded: chain Q residue 98 PHE Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 97 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 78 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 93 optimal weight: 0.0980 chunk 15 optimal weight: 0.7980 chunk 241 optimal weight: 8.9990 chunk 199 optimal weight: 0.9980 chunk 224 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN H 77 GLN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.106474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.077232 restraints weight = 47752.599| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.78 r_work: 0.2941 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25452 Z= 0.201 Angle : 0.528 6.319 34554 Z= 0.277 Chirality : 0.044 0.271 4137 Planarity : 0.004 0.047 4260 Dihedral : 7.514 79.619 5232 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.17 % Allowed : 9.55 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.15), residues: 2979 helix: 2.07 (0.27), residues: 405 sheet: 0.71 (0.17), residues: 912 loop : -0.22 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 479 HIS 0.004 0.001 HIS E 105 PHE 0.019 0.001 PHE O 78 TYR 0.014 0.001 TYR K 100G ARG 0.009 0.001 ARG Q 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 316 time to evaluate : 2.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8219 (mm-40) cc_final: 0.7999 (mm-40) REVERT: L 79 GLN cc_start: 0.7868 (mm-40) cc_final: 0.7544 (mm110) REVERT: C 86 ASP cc_start: 0.7561 (m-30) cc_final: 0.7133 (m-30) REVERT: D 79 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7008 (mp10) REVERT: O 51 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8015 (tt) REVERT: Q 79 GLN cc_start: 0.7827 (mm-40) cc_final: 0.6618 (pm20) REVERT: Q 98 PHE cc_start: 0.6202 (OUTLIER) cc_final: 0.4038 (t80) REVERT: J 72 ASP cc_start: 0.8357 (t0) cc_final: 0.8130 (t0) REVERT: G 648 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8736 (mt-10) REVERT: R 61 ARG cc_start: 0.8685 (mtm-85) cc_final: 0.8401 (ttm110) REVERT: R 98 PHE cc_start: 0.6575 (OUTLIER) cc_final: 0.4112 (t80) REVERT: K 13 GLN cc_start: 0.7686 (mm-40) cc_final: 0.7380 (mm110) REVERT: I 624 ASP cc_start: 0.8960 (m-30) cc_final: 0.8536 (m-30) outliers start: 57 outliers final: 40 residues processed: 344 average time/residue: 0.4119 time to fit residues: 217.1357 Evaluate side-chains 347 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 303 time to evaluate : 2.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 77 GLN Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 52 ASN Chi-restraints excluded: chain Q residue 88 CYS Chi-restraints excluded: chain Q residue 98 PHE Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 97 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 88 optimal weight: 2.9990 chunk 226 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 270 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 243 optimal weight: 3.9990 chunk 259 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 209 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 77 GLN L 38 GLN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 GLN ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 3 GLN ** I 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.104042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.072311 restraints weight = 48106.810| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.67 r_work: 0.2878 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 25452 Z= 0.394 Angle : 0.622 7.111 34554 Z= 0.322 Chirality : 0.047 0.253 4137 Planarity : 0.004 0.054 4260 Dihedral : 7.796 80.738 5232 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.63 % Allowed : 9.93 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.15), residues: 2979 helix: 1.76 (0.27), residues: 405 sheet: 0.51 (0.17), residues: 903 loop : -0.32 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 479 HIS 0.006 0.001 HIS F 105 PHE 0.018 0.002 PHE O 78 TYR 0.015 0.002 TYR C 27 ARG 0.009 0.001 ARG Q 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 302 time to evaluate : 2.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 VAL cc_start: 0.7509 (OUTLIER) cc_final: 0.7171 (t) REVERT: H 27 ASP cc_start: 0.6716 (OUTLIER) cc_final: 0.6298 (m-30) REVERT: L 79 GLN cc_start: 0.7798 (mm-40) cc_final: 0.6549 (pm20) REVERT: L 97 LEU cc_start: 0.7049 (tt) cc_final: 0.6817 (tt) REVERT: C 86 ASP cc_start: 0.7434 (m-30) cc_final: 0.7011 (m-30) REVERT: D 79 GLN cc_start: 0.7386 (OUTLIER) cc_final: 0.6725 (mp10) REVERT: D 83 GLU cc_start: 0.7642 (pm20) cc_final: 0.7430 (pm20) REVERT: O 51 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8013 (tt) REVERT: O 78 PHE cc_start: 0.7384 (OUTLIER) cc_final: 0.6879 (m-80) REVERT: Q 11 LEU cc_start: 0.7469 (tp) cc_final: 0.7259 (mt) REVERT: Q 79 GLN cc_start: 0.7792 (mm-40) cc_final: 0.6705 (pm20) REVERT: J 72 ASP cc_start: 0.8461 (t0) cc_final: 0.8164 (t0) REVERT: G 648 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8704 (mt-10) REVERT: P 5 GLN cc_start: 0.8380 (mm-40) cc_final: 0.8049 (mm-40) REVERT: P 51 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.8047 (tt) REVERT: P 105 ARG cc_start: 0.6417 (mmm160) cc_final: 0.5760 (mmp80) REVERT: R 61 ARG cc_start: 0.8665 (mtm-85) cc_final: 0.8343 (ttm110) REVERT: K 13 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7344 (mm110) REVERT: I 624 ASP cc_start: 0.9077 (m-30) cc_final: 0.8633 (m-30) outliers start: 69 outliers final: 49 residues processed: 337 average time/residue: 0.4034 time to fit residues: 208.3978 Evaluate side-chains 347 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 292 time to evaluate : 2.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 78 PHE Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 52 ASN Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 88 CYS Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain Q residue 98 PHE Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 97 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 224 optimal weight: 0.4980 chunk 227 optimal weight: 0.6980 chunk 66 optimal weight: 20.0000 chunk 167 optimal weight: 0.8980 chunk 189 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 196 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 267 optimal weight: 0.9990 chunk 235 optimal weight: 0.7980 chunk 283 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.106109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.077147 restraints weight = 47772.206| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.75 r_work: 0.2909 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25452 Z= 0.199 Angle : 0.543 6.932 34554 Z= 0.283 Chirality : 0.044 0.262 4137 Planarity : 0.004 0.054 4260 Dihedral : 7.462 77.226 5232 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.98 % Allowed : 10.88 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 2979 helix: 2.01 (0.27), residues: 405 sheet: 0.49 (0.17), residues: 918 loop : -0.29 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 91 HIS 0.005 0.001 HIS Q 95B PHE 0.021 0.001 PHE P 78 TYR 0.015 0.001 TYR C 27 ARG 0.013 0.001 ARG Q 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 313 time to evaluate : 2.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 ARG cc_start: 0.7118 (mpt180) cc_final: 0.6902 (mmt-90) REVERT: H 24 VAL cc_start: 0.7430 (OUTLIER) cc_final: 0.7132 (t) REVERT: H 27 ASP cc_start: 0.6956 (OUTLIER) cc_final: 0.6481 (m-30) REVERT: H 77 GLN cc_start: 0.8424 (tt0) cc_final: 0.7820 (mm-40) REVERT: H 91 TYR cc_start: 0.5765 (m-80) cc_final: 0.5214 (m-80) REVERT: L 24 GLN cc_start: 0.7908 (tt0) cc_final: 0.7660 (tm-30) REVERT: L 79 GLN cc_start: 0.7920 (mm-40) cc_final: 0.6602 (pm20) REVERT: C 86 ASP cc_start: 0.7548 (m-30) cc_final: 0.7239 (m-30) REVERT: D 78 LEU cc_start: 0.7926 (mt) cc_final: 0.7717 (mp) REVERT: D 79 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.6966 (mp10) REVERT: D 103 ARG cc_start: 0.8632 (tpp80) cc_final: 0.8365 (tpp80) REVERT: O 27 ASP cc_start: 0.7130 (OUTLIER) cc_final: 0.6691 (m-30) REVERT: O 51 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8033 (tt) REVERT: O 105 ARG cc_start: 0.7229 (tpp80) cc_final: 0.6857 (mmp80) REVERT: Q 11 LEU cc_start: 0.7528 (tp) cc_final: 0.7251 (mt) REVERT: Q 79 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7642 (mm110) REVERT: J 72 ASP cc_start: 0.8467 (t0) cc_final: 0.8242 (t0) REVERT: G 648 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8778 (mt-10) REVERT: P 5 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8123 (mm-40) REVERT: P 24 VAL cc_start: 0.7542 (OUTLIER) cc_final: 0.7339 (t) REVERT: P 51 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.8047 (tt) REVERT: P 105 ARG cc_start: 0.6571 (mmm160) cc_final: 0.5887 (mmp80) REVERT: R 61 ARG cc_start: 0.8652 (mtm-85) cc_final: 0.8352 (ttm110) REVERT: R 98 PHE cc_start: 0.6472 (OUTLIER) cc_final: 0.4393 (t80) REVERT: K 13 GLN cc_start: 0.7593 (mm-40) cc_final: 0.7372 (mm110) REVERT: K 23 ARG cc_start: 0.8624 (tpp-160) cc_final: 0.8368 (tpp-160) REVERT: I 624 ASP cc_start: 0.9011 (m-30) cc_final: 0.8575 (m-30) outliers start: 52 outliers final: 41 residues processed: 333 average time/residue: 0.4114 time to fit residues: 208.8797 Evaluate side-chains 350 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 301 time to evaluate : 2.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 78 PHE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 52 ASN Chi-restraints excluded: chain Q residue 98 PHE Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 78 PHE Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 97 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 278 optimal weight: 0.9990 chunk 167 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 217 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 264 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 240 optimal weight: 0.9980 chunk 226 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.104587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.072635 restraints weight = 48304.658| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.37 r_work: 0.2909 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 25452 Z= 0.338 Angle : 0.591 6.916 34554 Z= 0.306 Chirality : 0.046 0.253 4137 Planarity : 0.004 0.039 4260 Dihedral : 7.560 77.675 5232 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.44 % Allowed : 10.54 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.15), residues: 2979 helix: 1.86 (0.27), residues: 405 sheet: 0.46 (0.18), residues: 903 loop : -0.35 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 479 HIS 0.006 0.001 HIS F 105 PHE 0.020 0.002 PHE P 78 TYR 0.013 0.001 TYR J 100G ARG 0.011 0.001 ARG Q 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 299 time to evaluate : 3.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 VAL cc_start: 0.7519 (OUTLIER) cc_final: 0.7251 (t) REVERT: H 27 ASP cc_start: 0.7009 (OUTLIER) cc_final: 0.6527 (m-30) REVERT: H 77 GLN cc_start: 0.8437 (tt0) cc_final: 0.7838 (mm-40) REVERT: L 61 ARG cc_start: 0.8461 (mtm-85) cc_final: 0.8218 (ttm110) REVERT: L 79 GLN cc_start: 0.7937 (mm-40) cc_final: 0.6655 (pm20) REVERT: L 97 LEU cc_start: 0.7047 (tt) cc_final: 0.6820 (tt) REVERT: C 86 ASP cc_start: 0.7551 (m-30) cc_final: 0.7254 (m-30) REVERT: D 78 LEU cc_start: 0.7942 (mt) cc_final: 0.7529 (mt) REVERT: D 79 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.6903 (mp10) REVERT: D 103 ARG cc_start: 0.8689 (tpp80) cc_final: 0.8406 (tpp80) REVERT: O 24 VAL cc_start: 0.7757 (OUTLIER) cc_final: 0.7542 (t) REVERT: O 27 ASP cc_start: 0.7154 (OUTLIER) cc_final: 0.6620 (m-30) REVERT: O 51 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8060 (tt) REVERT: O 105 ARG cc_start: 0.7247 (tpp80) cc_final: 0.6852 (mmp80) REVERT: Q 11 LEU cc_start: 0.7419 (tp) cc_final: 0.7204 (mt) REVERT: Q 79 GLN cc_start: 0.7890 (mm-40) cc_final: 0.6810 (pm20) REVERT: J 72 ASP cc_start: 0.8454 (t0) cc_final: 0.8166 (t0) REVERT: G 648 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8638 (mt-10) REVERT: P 24 VAL cc_start: 0.7666 (OUTLIER) cc_final: 0.7458 (t) REVERT: P 51 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8102 (tt) REVERT: P 66 ARG cc_start: 0.5480 (ptt90) cc_final: 0.5236 (ptt90) REVERT: P 105 ARG cc_start: 0.6443 (mmm160) cc_final: 0.6137 (mmm160) REVERT: R 61 ARG cc_start: 0.8616 (mtm-85) cc_final: 0.8257 (ttm110) REVERT: R 98 PHE cc_start: 0.6399 (OUTLIER) cc_final: 0.4403 (t80) REVERT: K 13 GLN cc_start: 0.7645 (mm-40) cc_final: 0.7368 (mm110) REVERT: K 23 ARG cc_start: 0.8572 (tpp-160) cc_final: 0.8261 (tpp-160) REVERT: I 624 ASP cc_start: 0.9046 (m-30) cc_final: 0.8603 (m-30) outliers start: 64 outliers final: 46 residues processed: 326 average time/residue: 0.3902 time to fit residues: 194.1935 Evaluate side-chains 347 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 292 time to evaluate : 2.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 52 ASN Chi-restraints excluded: chain Q residue 88 CYS Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain Q residue 98 PHE Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain N residue 5 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 246 optimal weight: 10.0000 chunk 61 optimal weight: 0.0050 chunk 24 optimal weight: 1.9990 chunk 205 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 181 optimal weight: 0.6980 chunk 170 optimal weight: 0.9980 chunk 226 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: