Starting phenix.real_space_refine on Fri May 23 22:47:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t49_41024/05_2025/8t49_41024.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t49_41024/05_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_41024/05_2025/8t49_41024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t49_41024/05_2025/8t49_41024.map" model { file = "/net/cci-nas-00/data/ceres_data/8t49_41024/05_2025/8t49_41024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t49_41024/05_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-5687/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: 13.55, per 1000 atoms: 0.54 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=45, 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 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.05 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.05 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS G 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS I 605 " distance=2.02 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " 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: 7.56 Conformation dependent library (CDL) restraints added in 3.1 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: 3.56 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: 8.79 Time building geometry restraints manager: 8.56 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: 15536 21.50 - 42.99: 541 42.99 - 64.49: 141 64.49 - 85.99: 81 85.99 - 107.49: 39 Dihedral angle restraints: 16338 sinusoidal: 7644 harmonic: 8694 Sorted by residual: dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -136.38 50.38 1 1.00e+01 1.00e-02 3.48e+01 dihedral pdb=" CB CYS F 378 " pdb=" SG CYS F 378 " pdb=" SG CYS F 445 " pdb=" CB CYS F 445 " ideal model delta sinusoidal sigma weight residual -86.00 -136.37 50.37 1 1.00e+01 1.00e-02 3.48e+01 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 ... (remaining 16335 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: 2.19 - 2.73: 1542 2.73 - 3.27: 23524 3.27 - 3.81: 40256 3.81 - 4.36: 50950 4.36 - 4.90: 84671 Nonbonded interactions: 200943 Sorted by model distance: nonbonded pdb=" OD1 ASP F 477 " pdb=" NH1 ARG F 480 " model vdw 2.187 3.120 nonbonded pdb=" OD1 ASP E 477 " pdb=" NH1 ARG E 480 " model vdw 2.187 3.120 nonbonded pdb=" OD1 ASP A 477 " pdb=" NH1 ARG A 480 " model vdw 2.187 3.120 nonbonded pdb=" O SER C 99 " pdb=" OG SER C 99 " model vdw 2.267 3.040 nonbonded pdb=" O SER J 99 " pdb=" OG SER J 99 " model vdw 2.267 3.040 ... (remaining 200938 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: 0.17 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: 4.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.050 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 55.510 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.470 ------------------------------------------------------------------------------- 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 25593 Z= 0.318 Angle : 1.196 11.163 34932 Z= 0.654 Chirality : 0.066 0.611 4137 Planarity : 0.007 0.074 4260 Dihedral : 14.060 107.487 10641 Min Nonbonded Distance : 2.187 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00777 ( 63) link_NAG-ASN : angle 2.94063 ( 189) link_ALPHA1-6 : bond 0.00746 ( 3) link_ALPHA1-6 : angle 0.79566 ( 9) link_BETA1-4 : bond 0.00576 ( 21) link_BETA1-4 : angle 2.89638 ( 63) link_ALPHA1-2 : bond 0.00599 ( 3) link_ALPHA1-2 : angle 5.93316 ( 9) link_ALPHA1-3 : bond 0.00195 ( 6) link_ALPHA1-3 : angle 2.75980 ( 18) hydrogen bonds : bond 0.15447 ( 720) hydrogen bonds : angle 6.54430 ( 1782) SS BOND : bond 0.00823 ( 45) SS BOND : angle 2.36853 ( 90) covalent geometry : bond 0.00714 (25452) covalent geometry : angle 1.16423 (34554) *********************** 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 : 2.600 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: 0.4175 time to fit residues: 290.4641 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 : 2.893 ------------------------------------------------------------------------------- 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: 0.9980 chunk 76 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 232 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 269 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.106909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.077081 restraints weight = 47829.129| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.85 r_work: 0.2929 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 25593 Z= 0.267 Angle : 0.742 8.934 34932 Z= 0.378 Chirality : 0.051 0.332 4137 Planarity : 0.005 0.046 4260 Dihedral : 10.263 87.375 5238 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.09 % Allowed : 6.89 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.62 (0.15), residues: 2979 helix: 1.49 (0.26), residues: 423 sheet: 0.82 (0.17), residues: 876 loop : -0.03 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP O 47 HIS 0.010 0.002 HIS L 95B PHE 0.020 0.002 PHE G 522 TYR 0.019 0.002 TYR J 100G ARG 0.006 0.001 ARG Q 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00603 ( 63) link_NAG-ASN : angle 2.72167 ( 189) link_ALPHA1-6 : bond 0.00038 ( 3) link_ALPHA1-6 : angle 1.53329 ( 9) link_BETA1-4 : bond 0.00591 ( 21) link_BETA1-4 : angle 2.22976 ( 63) link_ALPHA1-2 : bond 0.00870 ( 3) link_ALPHA1-2 : angle 4.06623 ( 9) link_ALPHA1-3 : bond 0.00702 ( 6) link_ALPHA1-3 : angle 1.88564 ( 18) hydrogen bonds : bond 0.05874 ( 720) hydrogen bonds : angle 5.07640 ( 1782) SS BOND : bond 0.00432 ( 45) SS BOND : angle 1.17388 ( 90) covalent geometry : bond 0.00634 (25452) covalent geometry : angle 0.70484 (34554) *********************** 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 416 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 361 time to evaluate : 3.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.9373 (mmm) cc_final: 0.9151 (mmm) REVERT: A 161 MET cc_start: 0.8696 (tpp) cc_final: 0.8343 (tpp) REVERT: A 241 ASN cc_start: 0.7866 (OUTLIER) cc_final: 0.7665 (m-40) REVERT: H 59 TYR cc_start: 0.6951 (m-10) cc_final: 0.6718 (m-10) REVERT: L 24 GLN cc_start: 0.7592 (tt0) cc_final: 0.7373 (tt0) REVERT: D 79 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7202 (mp10) REVERT: O 3 GLN cc_start: 0.5884 (mp10) cc_final: 0.5626 (mp10) REVERT: O 66 ARG cc_start: 0.5126 (ptt90) cc_final: 0.4843 (ptt90) REVERT: Q 24 GLN cc_start: 0.7556 (tt0) cc_final: 0.7195 (tm-30) REVERT: Q 86 TYR cc_start: 0.8418 (m-80) cc_final: 0.7867 (m-80) REVERT: M 78 LEU cc_start: 0.7482 (mt) cc_final: 0.7266 (mt) REVERT: M 79 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7193 (mp10) REVERT: G 632 ASP cc_start: 0.8982 (t0) cc_final: 0.8777 (t0) REVERT: F 475 MET cc_start: 0.8552 (tpp) cc_final: 0.8334 (mmt) REVERT: P 5 GLN cc_start: 0.8257 (mm-40) cc_final: 0.7878 (mm-40) REVERT: P 105 ARG cc_start: 0.6170 (mmm160) cc_final: 0.5696 (mmp80) REVERT: R 24 GLN cc_start: 0.7565 (tt0) cc_final: 0.7221 (tm-30) REVERT: R 61 ARG cc_start: 0.8629 (mtm-85) cc_final: 0.8412 (ttm110) REVERT: R 86 TYR cc_start: 0.8200 (m-80) cc_final: 0.7617 (m-10) REVERT: K 13 GLN cc_start: 0.7757 (mm-40) cc_final: 0.7525 (mm110) REVERT: N 79 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.6890 (mp10) REVERT: N 85 ASP cc_start: 0.8450 (m-30) cc_final: 0.8184 (m-30) outliers start: 55 outliers final: 30 residues processed: 392 average time/residue: 0.3936 time to fit residues: 236.0012 Evaluate side-chains 338 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 304 time to evaluate : 2.610 ------------------------------------------------------------------------------- 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 C residue 12 VAL 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 D residue 97 ILE 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 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 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: 0.6980 chunk 253 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 273 optimal weight: 0.9990 chunk 66 optimal weight: 0.2980 chunk 180 optimal weight: 4.9990 chunk 236 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** D 95 GLN Q 89 ASN M 17 GLN F 33 ASN F 103 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 ASN N 17 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.108020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.079421 restraints weight = 47350.359| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.80 r_work: 0.2984 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25593 Z= 0.140 Angle : 0.612 9.601 34932 Z= 0.310 Chirality : 0.045 0.276 4137 Planarity : 0.004 0.041 4260 Dihedral : 8.872 84.711 5232 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.75 % Allowed : 8.07 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.15), residues: 2979 helix: 1.71 (0.27), residues: 423 sheet: 0.91 (0.17), residues: 852 loop : -0.10 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP P 47 HIS 0.005 0.001 HIS Q 95B PHE 0.010 0.001 PHE C 29 TYR 0.015 0.001 TYR C 100G ARG 0.006 0.001 ARG Q 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00533 ( 63) link_NAG-ASN : angle 2.47995 ( 189) link_ALPHA1-6 : bond 0.00161 ( 3) link_ALPHA1-6 : angle 1.62543 ( 9) link_BETA1-4 : bond 0.00591 ( 21) link_BETA1-4 : angle 1.86542 ( 63) link_ALPHA1-2 : bond 0.00823 ( 3) link_ALPHA1-2 : angle 3.84387 ( 9) link_ALPHA1-3 : bond 0.00759 ( 6) link_ALPHA1-3 : angle 1.60307 ( 18) hydrogen bonds : bond 0.04618 ( 720) hydrogen bonds : angle 4.69956 ( 1782) SS BOND : bond 0.00519 ( 45) SS BOND : angle 0.78421 ( 90) covalent geometry : bond 0.00314 (25452) covalent geometry : angle 0.57555 (34554) *********************** 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 375 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 329 time to evaluate : 2.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 59 TYR cc_start: 0.7145 (m-10) cc_final: 0.6926 (m-10) REVERT: L 24 GLN cc_start: 0.7629 (tt0) cc_final: 0.7409 (tt0) REVERT: C 43 LYS cc_start: 0.7158 (mppt) cc_final: 0.6955 (mttp) REVERT: C 86 ASP cc_start: 0.7404 (m-30) cc_final: 0.7149 (m-30) REVERT: D 79 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.6889 (mp10) REVERT: Q 24 GLN cc_start: 0.7539 (tt0) cc_final: 0.7202 (tm-30) REVERT: Q 86 TYR cc_start: 0.8053 (m-80) cc_final: 0.7731 (m-80) REVERT: M 79 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7065 (mp10) REVERT: G 648 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8656 (mt-10) REVERT: R 24 GLN cc_start: 0.7566 (tt0) cc_final: 0.7217 (tm-30) REVERT: R 61 ARG cc_start: 0.8648 (mtm-85) cc_final: 0.8402 (ttm110) REVERT: K 13 GLN cc_start: 0.7725 (mm-40) cc_final: 0.7426 (mm110) REVERT: N 85 ASP cc_start: 0.8427 (m-30) cc_final: 0.8132 (m-30) REVERT: I 624 ASP cc_start: 0.8987 (m-30) cc_final: 0.8589 (m-30) outliers start: 46 outliers final: 26 residues processed: 349 average time/residue: 0.4151 time to fit residues: 218.2825 Evaluate side-chains 326 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 298 time to evaluate : 2.795 ------------------------------------------------------------------------------- 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 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 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 244 THR Chi-restraints excluded: chain E residue 434 MET 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 J residue 28 THR Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 75 ILE 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 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: 0.9990 chunk 108 optimal weight: 1.9990 chunk 221 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 240 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN L 89 ASN D 95 GLN B 607 ASN B 653 GLN ** O 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 89 ASN ** Q 95BHIS ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.103919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.074630 restraints weight = 48130.411| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.85 r_work: 0.2848 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 25593 Z= 0.288 Angle : 0.703 9.462 34932 Z= 0.353 Chirality : 0.049 0.295 4137 Planarity : 0.005 0.041 4260 Dihedral : 8.522 84.863 5232 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.12 % Allowed : 7.69 % 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: 0.14 (0.15), residues: 2979 helix: 1.33 (0.26), residues: 423 sheet: 0.44 (0.17), residues: 876 loop : -0.38 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 479 HIS 0.008 0.002 HIS F 105 PHE 0.021 0.002 PHE K 29 TYR 0.025 0.002 TYR J 27 ARG 0.009 0.001 ARG R 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00619 ( 63) link_NAG-ASN : angle 2.60231 ( 189) link_ALPHA1-6 : bond 0.00190 ( 3) link_ALPHA1-6 : angle 1.85272 ( 9) link_BETA1-4 : bond 0.00571 ( 21) link_BETA1-4 : angle 2.00744 ( 63) link_ALPHA1-2 : bond 0.00604 ( 3) link_ALPHA1-2 : angle 3.66889 ( 9) link_ALPHA1-3 : bond 0.00586 ( 6) link_ALPHA1-3 : angle 1.53083 ( 18) hydrogen bonds : bond 0.05527 ( 720) hydrogen bonds : angle 4.81199 ( 1782) SS BOND : bond 0.00446 ( 45) SS BOND : angle 1.14551 ( 90) covalent geometry : bond 0.00695 (25452) covalent geometry : angle 0.66813 (34554) *********************** 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 392 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 310 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 24 VAL cc_start: 0.7466 (OUTLIER) cc_final: 0.7048 (t) REVERT: H 51 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8255 (tt) REVERT: L 24 GLN cc_start: 0.7646 (tt0) cc_final: 0.7422 (tt0) REVERT: L 97 LEU cc_start: 0.7223 (tt) cc_final: 0.6983 (tt) REVERT: O 51 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8139 (tt) REVERT: Q 61 ARG cc_start: 0.8467 (mtm-85) cc_final: 0.7991 (ttm110) REVERT: P 5 GLN cc_start: 0.8334 (mm-40) cc_final: 0.8122 (mm-40) REVERT: R 24 GLN cc_start: 0.7630 (tt0) cc_final: 0.7425 (tt0) REVERT: R 61 ARG cc_start: 0.8656 (mtm-85) cc_final: 0.8366 (ttm110) REVERT: R 98 PHE cc_start: 0.6476 (OUTLIER) cc_final: 0.4003 (t80) REVERT: K 13 GLN cc_start: 0.7737 (mm-40) cc_final: 0.7402 (mm110) REVERT: N 79 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.6990 (mp10) REVERT: I 624 ASP cc_start: 0.9049 (m-30) cc_final: 0.8638 (m-30) outliers start: 82 outliers final: 48 residues processed: 345 average time/residue: 0.3922 time to fit residues: 206.2766 Evaluate side-chains 350 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 297 time to evaluate : 2.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 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 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 92 ASP 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 92 ASP Chi-restraints excluded: chain Q residue 98 PHE 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 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 100 MET Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 48 VAL 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 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 Chi-restraints excluded: chain I residue 612 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 129 optimal weight: 0.9990 chunk 267 optimal weight: 0.7980 chunk 127 optimal weight: 0.7980 chunk 260 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 226 optimal weight: 0.6980 chunk 145 optimal weight: 10.0000 chunk 92 optimal weight: 0.4980 chunk 223 optimal weight: 2.9990 chunk 285 optimal weight: 0.9990 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 188 ASN L 89 ASN D 95 GLN F 33 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.106333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.077630 restraints weight = 47379.877| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.81 r_work: 0.2929 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25593 Z= 0.129 Angle : 0.580 9.539 34932 Z= 0.292 Chirality : 0.044 0.279 4137 Planarity : 0.004 0.038 4260 Dihedral : 7.853 80.761 5232 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.44 % Allowed : 8.79 % Favored : 88.77 % 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: 0.37 (0.15), residues: 2979 helix: 1.95 (0.27), residues: 405 sheet: 0.55 (0.17), residues: 918 loop : -0.33 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 479 HIS 0.004 0.001 HIS F 105 PHE 0.020 0.001 PHE O 78 TYR 0.016 0.001 TYR K 100G ARG 0.007 0.001 ARG K 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00503 ( 63) link_NAG-ASN : angle 2.41087 ( 189) link_ALPHA1-6 : bond 0.00045 ( 3) link_ALPHA1-6 : angle 1.66402 ( 9) link_BETA1-4 : bond 0.00551 ( 21) link_BETA1-4 : angle 1.68547 ( 63) link_ALPHA1-2 : bond 0.00697 ( 3) link_ALPHA1-2 : angle 3.18953 ( 9) link_ALPHA1-3 : bond 0.00745 ( 6) link_ALPHA1-3 : angle 1.50003 ( 18) hydrogen bonds : bond 0.04231 ( 720) hydrogen bonds : angle 4.50418 ( 1782) SS BOND : bond 0.00350 ( 45) SS BOND : angle 0.71600 ( 90) covalent geometry : bond 0.00295 (25452) covalent geometry : angle 0.54528 (34554) *********************** 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 388 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 324 time to evaluate : 2.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 24 GLN cc_start: 0.7585 (tt0) cc_final: 0.7366 (tt0) REVERT: D 79 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.6970 (mp10) REVERT: O 51 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8050 (tt) REVERT: Q 24 GLN cc_start: 0.7579 (tt0) cc_final: 0.7096 (tm-30) REVERT: J 97 MET cc_start: 0.8682 (ttp) cc_final: 0.8450 (ttp) REVERT: G 648 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8708 (mt-10) REVERT: P 105 ARG cc_start: 0.6397 (mmm160) cc_final: 0.5812 (mmp80) REVERT: R 24 GLN cc_start: 0.7566 (tt0) cc_final: 0.7158 (tm-30) REVERT: R 61 ARG cc_start: 0.8659 (mtm-85) cc_final: 0.8351 (ttm110) REVERT: K 13 GLN cc_start: 0.7736 (mm-40) cc_final: 0.7419 (mm110) REVERT: K 23 ARG cc_start: 0.8596 (mmm-85) cc_final: 0.8372 (tpp-160) REVERT: I 624 ASP cc_start: 0.8951 (m-30) cc_final: 0.8567 (m-30) outliers start: 64 outliers final: 42 residues processed: 353 average time/residue: 0.4042 time to fit residues: 219.3652 Evaluate side-chains 349 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 305 time to evaluate : 2.840 ------------------------------------------------------------------------------- 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 69 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 108 LEU 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 426 MET Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 52 ASN Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 92 ASP 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 M residue 27 ASP Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 28 LEU 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 Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain I residue 612 SER 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: 1.9990 chunk 89 optimal weight: 0.2980 chunk 8 optimal weight: 2.9990 chunk 93 optimal weight: 0.0870 chunk 15 optimal weight: 3.9990 chunk 241 optimal weight: 10.0000 chunk 199 optimal weight: 2.9990 chunk 224 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 overall best weight: 1.4764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN H 39 GLN L 38 GLN L 79 GLN O 39 GLN Q 38 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** ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.105134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.075745 restraints weight = 47512.327| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.81 r_work: 0.2881 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 25593 Z= 0.200 Angle : 0.612 9.295 34932 Z= 0.307 Chirality : 0.045 0.268 4137 Planarity : 0.004 0.040 4260 Dihedral : 7.793 80.715 5232 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.59 % Allowed : 9.21 % Favored : 88.20 % 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: 1.88 (0.27), residues: 405 sheet: 0.48 (0.17), residues: 954 loop : -0.36 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP O 47 HIS 0.005 0.001 HIS F 105 PHE 0.017 0.002 PHE O 78 TYR 0.013 0.001 TYR O 91 ARG 0.009 0.001 ARG R 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00528 ( 63) link_NAG-ASN : angle 2.40501 ( 189) link_ALPHA1-6 : bond 0.00102 ( 3) link_ALPHA1-6 : angle 1.77214 ( 9) link_BETA1-4 : bond 0.00530 ( 21) link_BETA1-4 : angle 1.77691 ( 63) link_ALPHA1-2 : bond 0.00594 ( 3) link_ALPHA1-2 : angle 3.22686 ( 9) link_ALPHA1-3 : bond 0.00650 ( 6) link_ALPHA1-3 : angle 1.44752 ( 18) hydrogen bonds : bond 0.04630 ( 720) hydrogen bonds : angle 4.50278 ( 1782) SS BOND : bond 0.00357 ( 45) SS BOND : angle 0.91934 ( 90) covalent geometry : bond 0.00481 (25452) covalent geometry : angle 0.57816 (34554) *********************** 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 379 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 311 time to evaluate : 2.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 VAL cc_start: 0.7385 (OUTLIER) cc_final: 0.7048 (t) REVERT: H 27 ASP cc_start: 0.6553 (OUTLIER) cc_final: 0.6147 (m-30) REVERT: L 79 GLN cc_start: 0.7880 (mm-40) cc_final: 0.6843 (pm20) REVERT: D 79 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.6844 (mp10) REVERT: D 103 ARG cc_start: 0.8617 (tpp80) cc_final: 0.8319 (tpp80) REVERT: O 51 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8053 (tt) REVERT: Q 4 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7279 (tp) REVERT: Q 24 GLN cc_start: 0.7733 (tt0) cc_final: 0.7133 (tm-30) REVERT: Q 79 GLN cc_start: 0.7853 (mm-40) cc_final: 0.6610 (pm20) REVERT: G 648 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8748 (mt-10) REVERT: P 24 VAL cc_start: 0.7493 (OUTLIER) cc_final: 0.7277 (t) REVERT: P 105 ARG cc_start: 0.6511 (mmm160) cc_final: 0.5889 (mmp80) REVERT: R 24 GLN cc_start: 0.7578 (tt0) cc_final: 0.7142 (tm-30) REVERT: R 61 ARG cc_start: 0.8685 (mtm-85) cc_final: 0.8346 (ttm110) REVERT: K 13 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7430 (mm110) REVERT: K 23 ARG cc_start: 0.8619 (mmm-85) cc_final: 0.8387 (tpp-160) REVERT: I 624 ASP cc_start: 0.9000 (m-30) cc_final: 0.8573 (m-30) outliers start: 68 outliers final: 52 residues processed: 343 average time/residue: 0.4182 time to fit residues: 219.9495 Evaluate side-chains 357 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 299 time to evaluate : 2.955 ------------------------------------------------------------------------------- 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 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 12 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 Q residue 4 LEU Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 52 ASN Chi-restraints excluded: chain Q residue 58 ILE 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 M residue 27 ASP Chi-restraints excluded: chain F residue 42 VAL 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 R residue 13 VAL Chi-restraints excluded: chain R residue 28 LEU 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 Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain I residue 612 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 88 optimal weight: 1.9990 chunk 226 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 270 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 243 optimal weight: 0.9980 chunk 259 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 209 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN H 77 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.105764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.076270 restraints weight = 47352.602| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.83 r_work: 0.2890 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25593 Z= 0.163 Angle : 0.590 9.363 34932 Z= 0.296 Chirality : 0.044 0.263 4137 Planarity : 0.004 0.043 4260 Dihedral : 7.644 78.873 5232 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.55 % Allowed : 9.70 % Favored : 87.75 % 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: 0.28 (0.15), residues: 2979 helix: 1.93 (0.27), residues: 405 sheet: 0.47 (0.17), residues: 945 loop : -0.39 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Q 91 HIS 0.004 0.001 HIS A 105 PHE 0.018 0.001 PHE H 78 TYR 0.018 0.001 TYR O 91 ARG 0.009 0.001 ARG Q 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00494 ( 63) link_NAG-ASN : angle 2.36610 ( 189) link_ALPHA1-6 : bond 0.00090 ( 3) link_ALPHA1-6 : angle 1.72271 ( 9) link_BETA1-4 : bond 0.00504 ( 21) link_BETA1-4 : angle 1.69499 ( 63) link_ALPHA1-2 : bond 0.00606 ( 3) link_ALPHA1-2 : angle 2.99295 ( 9) link_ALPHA1-3 : bond 0.00636 ( 6) link_ALPHA1-3 : angle 1.41706 ( 18) hydrogen bonds : bond 0.04345 ( 720) hydrogen bonds : angle 4.42735 ( 1782) SS BOND : bond 0.00549 ( 45) SS BOND : angle 1.05951 ( 90) covalent geometry : bond 0.00388 (25452) covalent geometry : angle 0.55592 (34554) *********************** 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 375 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 308 time to evaluate : 2.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 VAL cc_start: 0.7357 (OUTLIER) cc_final: 0.7031 (t) REVERT: H 27 ASP cc_start: 0.6895 (OUTLIER) cc_final: 0.6409 (m-30) REVERT: L 79 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7654 (mm110) REVERT: C 86 ASP cc_start: 0.7532 (m-30) cc_final: 0.7127 (m-30) REVERT: D 79 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.6893 (mp10) REVERT: O 24 VAL cc_start: 0.7502 (OUTLIER) cc_final: 0.7286 (t) REVERT: O 27 ASP cc_start: 0.6726 (OUTLIER) cc_final: 0.6254 (m-30) REVERT: O 51 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.8035 (tt) REVERT: Q 24 GLN cc_start: 0.7706 (tt0) cc_final: 0.7110 (tm-30) REVERT: Q 79 GLN cc_start: 0.7860 (mm-40) cc_final: 0.6628 (pm20) REVERT: G 648 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8747 (mt-10) REVERT: F 141 MET cc_start: 0.9225 (mtp) cc_final: 0.8880 (ttm) REVERT: P 27 ASP cc_start: 0.6998 (OUTLIER) cc_final: 0.6732 (m-30) REVERT: P 105 ARG cc_start: 0.6577 (mmm160) cc_final: 0.6049 (mmp80) REVERT: R 24 GLN cc_start: 0.7602 (tt0) cc_final: 0.7142 (tm-30) REVERT: K 13 GLN cc_start: 0.7690 (mm-40) cc_final: 0.7430 (mm110) REVERT: I 624 ASP cc_start: 0.9032 (m-30) cc_final: 0.8592 (m-30) outliers start: 67 outliers final: 50 residues processed: 338 average time/residue: 0.3989 time to fit residues: 206.8951 Evaluate side-chains 352 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 295 time to evaluate : 2.597 ------------------------------------------------------------------------------- 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 H residue 101 ASP 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 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 426 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 O residue 77 GLN Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 52 ASN 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 M residue 27 ASP Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 28 LEU 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 Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain I residue 612 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 224 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 167 optimal weight: 4.9990 chunk 189 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 267 optimal weight: 0.4980 chunk 235 optimal weight: 0.2980 chunk 283 optimal weight: 9.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 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** P 39 GLN R 38 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.105726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.076677 restraints weight = 47492.058| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.80 r_work: 0.2906 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25593 Z= 0.167 Angle : 0.596 9.333 34932 Z= 0.300 Chirality : 0.045 0.257 4137 Planarity : 0.004 0.040 4260 Dihedral : 7.552 77.753 5232 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.55 % Allowed : 10.08 % Favored : 87.37 % 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: 0.29 (0.15), residues: 2979 helix: 1.94 (0.27), residues: 405 sheet: 0.48 (0.17), residues: 939 loop : -0.39 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 479 HIS 0.005 0.001 HIS A 105 PHE 0.016 0.001 PHE H 78 TYR 0.014 0.001 TYR K 100G ARG 0.012 0.001 ARG Q 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 63) link_NAG-ASN : angle 2.33362 ( 189) link_ALPHA1-6 : bond 0.00051 ( 3) link_ALPHA1-6 : angle 1.78563 ( 9) link_BETA1-4 : bond 0.00489 ( 21) link_BETA1-4 : angle 1.69211 ( 63) link_ALPHA1-2 : bond 0.00567 ( 3) link_ALPHA1-2 : angle 2.89263 ( 9) link_ALPHA1-3 : bond 0.00583 ( 6) link_ALPHA1-3 : angle 1.39290 ( 18) hydrogen bonds : bond 0.04351 ( 720) hydrogen bonds : angle 4.40139 ( 1782) SS BOND : bond 0.00376 ( 45) SS BOND : angle 1.29152 ( 90) covalent geometry : bond 0.00399 (25452) covalent geometry : angle 0.56137 (34554) *********************** 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 370 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 303 time to evaluate : 2.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 VAL cc_start: 0.7384 (OUTLIER) cc_final: 0.7130 (t) REVERT: H 27 ASP cc_start: 0.6964 (OUTLIER) cc_final: 0.6480 (m-30) REVERT: L 24 GLN cc_start: 0.8011 (tt0) cc_final: 0.7733 (tm-30) REVERT: L 61 ARG cc_start: 0.8283 (mtm-85) cc_final: 0.8034 (mtm-85) REVERT: L 79 GLN cc_start: 0.7851 (mm-40) cc_final: 0.6846 (pm20) REVERT: C 86 ASP cc_start: 0.7564 (m-30) cc_final: 0.7246 (m-30) REVERT: D 79 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.6882 (mp10) REVERT: D 103 ARG cc_start: 0.8649 (tpp80) cc_final: 0.8386 (tpp80) REVERT: O 27 ASP cc_start: 0.7048 (OUTLIER) cc_final: 0.6552 (m-30) REVERT: O 51 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8053 (tt) REVERT: O 105 ARG cc_start: 0.7230 (tpp80) cc_final: 0.6823 (mmp80) REVERT: Q 4 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7156 (tp) REVERT: Q 11 LEU cc_start: 0.7957 (mt) cc_final: 0.7716 (tp) REVERT: Q 24 GLN cc_start: 0.7801 (tt0) cc_final: 0.7154 (tm-30) REVERT: Q 79 GLN cc_start: 0.7866 (mm-40) cc_final: 0.6735 (pm20) REVERT: G 648 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8710 (mt-10) REVERT: P 27 ASP cc_start: 0.7137 (OUTLIER) cc_final: 0.6755 (m-30) REVERT: P 105 ARG cc_start: 0.6585 (mmm160) cc_final: 0.6053 (mmp80) REVERT: R 61 ARG cc_start: 0.8687 (mtm-85) cc_final: 0.8451 (ttm110) REVERT: K 13 GLN cc_start: 0.7663 (mm-40) cc_final: 0.7414 (mm110) REVERT: I 624 ASP cc_start: 0.8998 (m-30) cc_final: 0.8567 (m-30) outliers start: 67 outliers final: 49 residues processed: 335 average time/residue: 0.3804 time to fit residues: 195.7181 Evaluate side-chains 349 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 293 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 188 ASN 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 H residue 101 ASP 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 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 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 O residue 27 ASP Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 52 ASN Chi-restraints excluded: chain Q residue 75 ILE 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 M residue 27 ASP Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 28 LEU 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 70 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain I residue 612 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 278 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 264 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 240 optimal weight: 0.7980 chunk 226 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN H 77 GLN ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN F 188 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.104907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.073168 restraints weight = 47832.933| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.75 r_work: 0.2895 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 25593 Z= 0.206 Angle : 0.625 9.270 34932 Z= 0.313 Chirality : 0.045 0.257 4137 Planarity : 0.004 0.038 4260 Dihedral : 7.596 77.485 5232 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.70 % Allowed : 10.05 % Favored : 87.25 % 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: 0.21 (0.15), residues: 2979 helix: 1.84 (0.27), residues: 405 sheet: 0.42 (0.17), residues: 939 loop : -0.43 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 479 HIS 0.005 0.001 HIS F 105 PHE 0.021 0.002 PHE H 78 TYR 0.017 0.002 TYR C 27 ARG 0.012 0.001 ARG Q 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00526 ( 63) link_NAG-ASN : angle 2.38072 ( 189) link_ALPHA1-6 : bond 0.00174 ( 3) link_ALPHA1-6 : angle 1.84277 ( 9) link_BETA1-4 : bond 0.00489 ( 21) link_BETA1-4 : angle 1.73487 ( 63) link_ALPHA1-2 : bond 0.00511 ( 3) link_ALPHA1-2 : angle 2.86577 ( 9) link_ALPHA1-3 : bond 0.00545 ( 6) link_ALPHA1-3 : angle 1.39214 ( 18) hydrogen bonds : bond 0.04643 ( 720) hydrogen bonds : angle 4.46716 ( 1782) SS BOND : bond 0.00411 ( 45) SS BOND : angle 1.08965 ( 90) covalent geometry : bond 0.00497 (25452) covalent geometry : angle 0.59317 (34554) *********************** 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 365 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 294 time to evaluate : 2.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 VAL cc_start: 0.7538 (OUTLIER) cc_final: 0.7332 (t) REVERT: H 27 ASP cc_start: 0.7027 (OUTLIER) cc_final: 0.6469 (m-30) REVERT: H 77 GLN cc_start: 0.8443 (tt0) cc_final: 0.7811 (mm-40) REVERT: L 61 ARG cc_start: 0.8225 (mtm-85) cc_final: 0.7961 (mtm-85) REVERT: L 79 GLN cc_start: 0.7820 (mm-40) cc_final: 0.6869 (pm20) REVERT: C 86 ASP cc_start: 0.7394 (m-30) cc_final: 0.7088 (m-30) REVERT: D 79 GLN cc_start: 0.7292 (OUTLIER) cc_final: 0.6666 (mp10) REVERT: D 103 ARG cc_start: 0.8688 (tpp80) cc_final: 0.8389 (tpp80) REVERT: O 27 ASP cc_start: 0.7042 (OUTLIER) cc_final: 0.6532 (m-30) REVERT: O 51 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8064 (tt) REVERT: O 105 ARG cc_start: 0.7308 (tpp80) cc_final: 0.6763 (mmp80) REVERT: Q 11 LEU cc_start: 0.7929 (mt) cc_final: 0.7673 (tp) REVERT: Q 24 GLN cc_start: 0.7799 (tt0) cc_final: 0.7108 (tm-30) REVERT: Q 79 GLN cc_start: 0.7802 (mm-40) cc_final: 0.6702 (pm20) REVERT: G 648 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8589 (mt-10) REVERT: P 27 ASP cc_start: 0.6953 (OUTLIER) cc_final: 0.6629 (m-30) REVERT: P 66 ARG cc_start: 0.5394 (ptt90) cc_final: 0.5169 (ptt90) REVERT: P 105 ARG cc_start: 0.6476 (mmm160) cc_final: 0.5854 (mmp80) REVERT: R 24 GLN cc_start: 0.7623 (tt0) cc_final: 0.7017 (tm-30) REVERT: R 61 ARG cc_start: 0.8657 (mtm-85) cc_final: 0.8304 (ttm110) REVERT: R 98 PHE cc_start: 0.6636 (OUTLIER) cc_final: 0.5518 (m-80) REVERT: K 13 GLN cc_start: 0.7673 (mm-40) cc_final: 0.7352 (mm110) REVERT: I 624 ASP cc_start: 0.9091 (m-30) cc_final: 0.8637 (m-30) outliers start: 71 outliers final: 52 residues processed: 326 average time/residue: 0.3891 time to fit residues: 195.6187 Evaluate side-chains 347 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 288 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 328 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 H residue 101 ASP 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 92 ASP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 28 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 426 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 58 ILE Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 92 ASP 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 M residue 27 ASP 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 188 ASN Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 28 LEU 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 Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain I residue 612 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 246 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 205 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 181 optimal weight: 0.7980 chunk 170 optimal weight: 0.9990 chunk 226 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 184 optimal weight: 7.9990 chunk 56 optimal weight: 20.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 188 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** ** 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 = 0.3614 r_free = 0.3614 target = 0.105922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.074015 restraints weight = 47265.564| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.40 r_work: 0.2933 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25593 Z= 0.143 Angle : 0.587 9.273 34932 Z= 0.295 Chirality : 0.044 0.270 4137 Planarity : 0.004 0.048 4260 Dihedral : 7.415 75.568 5232 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.25 % Allowed : 10.62 % 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: 0.28 (0.15), residues: 2979 helix: 1.99 (0.27), residues: 405 sheet: 0.43 (0.17), residues: 939 loop : -0.39 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 35 HIS 0.004 0.001 HIS A 105 PHE 0.025 0.001 PHE H 78 TYR 0.019 0.001 TYR O 91 ARG 0.011 0.001 ARG L 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00498 ( 63) link_NAG-ASN : angle 2.30871 ( 189) link_ALPHA1-6 : bond 0.00056 ( 3) link_ALPHA1-6 : angle 1.72798 ( 9) link_BETA1-4 : bond 0.00466 ( 21) link_BETA1-4 : angle 1.62915 ( 63) link_ALPHA1-2 : bond 0.00560 ( 3) link_ALPHA1-2 : angle 2.67278 ( 9) link_ALPHA1-3 : bond 0.00585 ( 6) link_ALPHA1-3 : angle 1.38835 ( 18) hydrogen bonds : bond 0.04218 ( 720) hydrogen bonds : angle 4.38169 ( 1782) SS BOND : bond 0.00362 ( 45) SS BOND : angle 0.89212 ( 90) covalent geometry : bond 0.00337 (25452) covalent geometry : angle 0.55515 (34554) ********************** REFINEMENT MACRO_CYCLE 10 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 359 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 300 time to evaluate : 3.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 27 ASP cc_start: 0.7004 (OUTLIER) cc_final: 0.6461 (m-30) REVERT: H 77 GLN cc_start: 0.8556 (tt0) cc_final: 0.7930 (mm-40) REVERT: H 91 TYR cc_start: 0.5630 (m-80) cc_final: 0.5075 (m-80) REVERT: L 61 ARG cc_start: 0.8247 (mtm-85) cc_final: 0.7942 (ttm110) REVERT: L 79 GLN cc_start: 0.7830 (mm-40) cc_final: 0.6887 (pm20) REVERT: C 86 ASP cc_start: 0.7540 (m-30) cc_final: 0.7233 (m-30) REVERT: D 78 LEU cc_start: 0.7850 (mt) cc_final: 0.7426 (mt) REVERT: D 79 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.6649 (mp10) REVERT: D 103 ARG cc_start: 0.8693 (tpp80) cc_final: 0.8400 (tpp80) REVERT: O 27 ASP cc_start: 0.7031 (OUTLIER) cc_final: 0.6518 (m-30) REVERT: O 51 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.8060 (tt) REVERT: O 105 ARG cc_start: 0.7278 (tpp80) cc_final: 0.6785 (mmp80) REVERT: Q 11 LEU cc_start: 0.7948 (mt) cc_final: 0.7689 (tp) REVERT: Q 24 GLN cc_start: 0.7785 (tt0) cc_final: 0.7421 (tt0) REVERT: Q 79 GLN cc_start: 0.7849 (mm-40) cc_final: 0.7574 (mp10) REVERT: G 648 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8551 (mt-10) REVERT: F 141 MET cc_start: 0.9210 (mtp) cc_final: 0.8863 (ttm) REVERT: P 27 ASP cc_start: 0.6950 (OUTLIER) cc_final: 0.6625 (m-30) REVERT: P 66 ARG cc_start: 0.5387 (ptt90) cc_final: 0.5165 (ptt90) REVERT: P 105 ARG cc_start: 0.6483 (mmm160) cc_final: 0.6078 (mmm160) REVERT: R 24 GLN cc_start: 0.7542 (tt0) cc_final: 0.7251 (tm-30) REVERT: R 61 ARG cc_start: 0.8673 (mtm-85) cc_final: 0.8360 (ttm110) REVERT: R 79 GLN cc_start: 0.8053 (mm-40) cc_final: 0.6865 (pm20) REVERT: K 13 GLN cc_start: 0.7638 (mm-40) cc_final: 0.7275 (mm-40) REVERT: I 601 LYS cc_start: 0.9226 (mttm) cc_final: 0.8874 (mtpt) REVERT: I 624 ASP cc_start: 0.9055 (m-30) cc_final: 0.8596 (m-30) outliers start: 59 outliers final: 48 residues processed: 325 average time/residue: 0.3817 time to fit residues: 191.0889 Evaluate side-chains 343 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 290 time to evaluate : 2.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 101 ASP 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 92 ASP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 28 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 188 ASN Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 426 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 92 ASP 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 M residue 27 ASP 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 27 ASP Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 19 VAL Chi-restraints excluded: chain R residue 28 LEU 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 70 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain I residue 612 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 190 optimal weight: 1.9990 chunk 258 optimal weight: 0.0870 chunk 22 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 92 optimal weight: 0.0370 chunk 182 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 overall best weight: 1.0240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 188 ASN ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN F 188 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.105884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.074272 restraints weight = 47326.500| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.57 r_work: 0.2926 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.168 25593 Z= 0.176 Angle : 0.712 59.183 34932 Z= 0.382 Chirality : 0.047 0.932 4137 Planarity : 0.004 0.041 4260 Dihedral : 7.412 75.555 5232 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.13 % Allowed : 10.73 % Favored : 87.14 % Cbeta Deviations : 0.04 % 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: 2.00 (0.27), residues: 405 sheet: 0.43 (0.17), residues: 939 loop : -0.39 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP Q 91 HIS 0.007 0.001 HIS Q 95B PHE 0.022 0.001 PHE H 78 TYR 0.018 0.001 TYR O 91 ARG 0.010 0.000 ARG L 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00495 ( 63) link_NAG-ASN : angle 2.30844 ( 189) link_ALPHA1-6 : bond 0.00350 ( 3) link_ALPHA1-6 : angle 1.68070 ( 9) link_BETA1-4 : bond 0.00458 ( 21) link_BETA1-4 : angle 1.63458 ( 63) link_ALPHA1-2 : bond 0.00566 ( 3) link_ALPHA1-2 : angle 2.67330 ( 9) link_ALPHA1-3 : bond 0.00551 ( 6) link_ALPHA1-3 : angle 1.36874 ( 18) hydrogen bonds : bond 0.04232 ( 720) hydrogen bonds : angle 4.38140 ( 1782) SS BOND : bond 0.00340 ( 45) SS BOND : angle 0.84517 ( 90) covalent geometry : bond 0.00400 (25452) covalent geometry : angle 0.68795 (34554) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14343.55 seconds wall clock time: 248 minutes 52.41 seconds (14932.41 seconds total)