Starting phenix.real_space_refine on Sat Jun 21 03:15:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mia_48286/06_2025/9mia_48286.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mia_48286/06_2025/9mia_48286.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mia_48286/06_2025/9mia_48286.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mia_48286/06_2025/9mia_48286.map" model { file = "/net/cci-nas-00/data/ceres_data/9mia_48286/06_2025/9mia_48286.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mia_48286/06_2025/9mia_48286.cif" } resolution = 2.8 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 150 5.16 5 C 15435 2.51 5 N 4185 2.21 5 O 4887 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-5710/modules/chem_data/mon_lib" Total number of atoms: 24657 Number of models: 1 Model: "" Number of chains: 10 Chain: "G" 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: "H" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 957 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "I" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "L" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 755 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "A" Number of atoms: 3496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3496 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 23, 'TRANS': 419} Chain breaks: 2 Chain: "B" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 997 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "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: C, E, M, Q, J, O, D, F, V, X, N, R, U, W, K, P Time building chain proxies: 12.63, per 1000 atoms: 0.51 Number of scatterers: 24657 At special positions: 0 Unit cell: (142.678, 145.78, 146.814, 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 150 16.00 O 4887 8.00 N 4185 7.00 C 15435 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA T 3 " - " MAN T 4 " " BMA V 3 " - " MAN V 4 " " BMA X 3 " - " MAN X 4 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG A 601 " - " ASN A 160 " " NAG A 602 " - " ASN A 295 " " NAG A 603 " - " ASN A 88 " " NAG A 604 " - " ASN A 133 " " NAG A 605 " - " ASN A 392 " " NAG A 606 " - " ASN A 448 " " NAG A 607 " - " ASN A 234 " " NAG A 608 " - " ASN A 301 " " NAG A 609 " - " ASN A 332 " " NAG A 610 " - " ASN A 339 " " NAG A 611 " - " ASN A 363 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 611 " " NAG B 703 " - " ASN B 618 " " NAG C 601 " - " ASN C 160 " " NAG C 602 " - " ASN C 295 " " NAG C 603 " - " ASN C 88 " " NAG C 604 " - " ASN C 133 " " NAG C 605 " - " ASN C 392 " " NAG C 606 " - " ASN C 448 " " NAG C 607 " - " ASN C 234 " " NAG C 608 " - " ASN C 301 " " NAG C 609 " - " ASN C 332 " " NAG C 610 " - " ASN C 339 " " NAG C 611 " - " ASN C 363 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 611 " " NAG D 703 " - " ASN D 618 " " NAG E 601 " - " ASN E 160 " " NAG E 602 " - " ASN E 295 " " NAG E 603 " - " ASN E 88 " " NAG E 604 " - " ASN E 133 " " NAG E 605 " - " ASN E 392 " " NAG E 606 " - " ASN E 448 " " NAG E 607 " - " ASN E 234 " " NAG E 608 " - " ASN E 301 " " NAG E 609 " - " ASN E 332 " " NAG E 610 " - " ASN E 339 " " NAG E 611 " - " ASN E 363 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 611 " " NAG F 703 " - " ASN F 618 " " NAG S 1 " - " ASN A 156 " " NAG T 1 " - " ASN A 262 " " NAG U 1 " - " ASN C 156 " " NAG V 1 " - " ASN C 262 " " NAG W 1 " - " ASN E 156 " " NAG X 1 " - " ASN E 262 " Time building additional restraints: 5.78 Conformation dependent library (CDL) restraints added in 2.7 seconds 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5610 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 48 sheets defined 17.5% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.551A pdb=" N THR G 87 " --> pdb=" O ASP G 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.668A pdb=" N HIS H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.652A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.591A pdb=" N GLU I 83 " --> pdb=" O ALA I 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.979A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.848A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.080A 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 475 through 480 Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.338A 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 542 removed outlier: 3.657A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.599A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 648 Processing helix chain 'B' and resid 648 through 662 removed outlier: 3.691A pdb=" N GLN B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) 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 removed outlier: 3.551A pdb=" N THR J 87 " --> pdb=" O ASP J 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.668A pdb=" N HIS K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.651A pdb=" N THR K 87 " --> pdb=" O SER K 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.591A pdb=" N GLU M 83 " --> pdb=" O ALA M 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.980A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.849A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 480 Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.337A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 removed outlier: 3.657A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 596 removed outlier: 3.598A pdb=" N GLN D 575 " --> pdb=" O TRP D 571 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 638 through 648 Processing helix chain 'D' and resid 648 through 662 removed outlier: 3.690A pdb=" N GLN D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 61 through 64 Processing helix chain 'O' and resid 83 through 87 removed outlier: 3.551A pdb=" N THR O 87 " --> pdb=" O ASP O 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 32 removed outlier: 3.668A pdb=" N HIS P 32 " --> pdb=" O PHE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 87 removed outlier: 3.651A pdb=" N THR P 87 " --> pdb=" O SER P 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 83 removed outlier: 3.591A pdb=" N GLU Q 83 " --> pdb=" O ALA Q 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 removed outlier: 3.980A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 139 through 151 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.848A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.080A 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 475 through 480 Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.337A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.657A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.598A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 648 Processing helix chain 'F' and resid 648 through 662 removed outlier: 3.690A pdb=" N GLN F 652 " --> pdb=" O GLU F 648 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'G' and resid 34 through 39 removed outlier: 6.957A pdb=" N MET G 34 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LEU G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 57 through 59 current: chain 'G' and resid 100H through 103 Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 12 current: chain 'H' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 102 through 103 Processing sheet with id=AA5, first strand: chain 'I' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 9 through 12 current: chain 'I' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 45 through 48 current: chain 'I' and resid 96 through 98 No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'I' and resid 19 through 24 Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA8, first strand: chain 'L' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 13 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=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.265A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.866A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AB3, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AB4, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AB5, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.335A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB6, 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 302 removed outlier: 4.270A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 322 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 470 Processing sheet with id=AB7, first strand: chain 'A' and resid 305 through 308 Processing sheet with id=AB8, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AB9, first strand: chain 'J' and resid 34 through 39 removed outlier: 6.958A pdb=" N MET J 34 " --> pdb=" O LEU J 50 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LEU J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 100H through 103 Processing sheet with id=AC1, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AC2, first strand: chain 'K' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 10 through 12 current: chain 'K' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 57 through 59 current: chain 'K' and resid 102 through 103 Processing sheet with id=AC3, first strand: chain 'M' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 9 through 12 current: chain 'M' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 45 through 48 current: chain 'M' and resid 96 through 98 No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=AC5, first strand: chain 'N' and resid 4 through 5 Processing sheet with id=AC6, first strand: chain 'N' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 9 through 13 current: chain 'N' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 45 through 48 current: chain 'N' and resid 97 through 98 No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.265A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.866A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AD1, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AD2, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AD3, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.335A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 302 removed outlier: 4.270A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 322 through 323 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AD5, first strand: chain 'C' and resid 305 through 308 Processing sheet with id=AD6, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AD7, first strand: chain 'O' and resid 34 through 39 removed outlier: 6.958A pdb=" N MET O 34 " --> pdb=" O LEU O 50 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP O 36 " --> pdb=" O VAL 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=AD8, first strand: chain 'P' and resid 3 through 6 Processing sheet with id=AD9, first strand: chain 'P' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 10 through 12 current: chain 'P' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 57 through 59 current: chain 'P' and resid 102 through 103 Processing sheet with id=AE1, 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 96 through 98 No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'Q' and resid 19 through 24 Processing sheet with id=AE3, first strand: chain 'R' and resid 4 through 5 Processing sheet with id=AE4, first strand: chain 'R' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 9 through 13 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=AE4 Processing sheet with id=AE5, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.264A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.866A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AE8, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AE9, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AF1, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.335A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AF2, 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 302 removed outlier: 4.270A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 322 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 470 Processing sheet with id=AF3, first strand: chain 'E' and resid 305 through 308 645 hydrogen bonds defined for protein. 1683 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: 7.61 Time building geometry restraints manager: 6.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7553 1.34 - 1.46: 5375 1.46 - 1.58: 12053 1.58 - 1.70: 0 1.70 - 1.82: 210 Bond restraints: 25191 Sorted by residual: bond pdb=" C HIS R 39 " pdb=" N PRO R 40 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.69e+00 bond pdb=" C HIS N 39 " pdb=" N PRO N 40 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.68e+00 bond pdb=" C HIS L 39 " pdb=" N PRO L 40 " ideal model delta sigma weight residual 1.334 1.378 -0.045 2.34e-02 1.83e+03 3.63e+00 bond pdb=" N GLU G 1 " pdb=" CA GLU G 1 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.54e+00 bond pdb=" N GLU J 1 " pdb=" CA GLU J 1 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.54e+00 ... (remaining 25186 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 32298 1.91 - 3.82: 1493 3.82 - 5.73: 340 5.73 - 7.63: 69 7.63 - 9.54: 12 Bond angle restraints: 34212 Sorted by residual: angle pdb=" CB ARG P 83 " pdb=" CG ARG P 83 " pdb=" CD ARG P 83 " ideal model delta sigma weight residual 111.30 120.46 -9.16 2.30e+00 1.89e-01 1.59e+01 angle pdb=" CB ARG H 83 " pdb=" CG ARG H 83 " pdb=" CD ARG H 83 " ideal model delta sigma weight residual 111.30 120.45 -9.15 2.30e+00 1.89e-01 1.58e+01 angle pdb=" CB ARG K 83 " pdb=" CG ARG K 83 " pdb=" CD ARG K 83 " ideal model delta sigma weight residual 111.30 120.43 -9.13 2.30e+00 1.89e-01 1.58e+01 angle pdb=" CG1 VAL L 106 " pdb=" CB VAL L 106 " pdb=" CG2 VAL L 106 " ideal model delta sigma weight residual 110.80 102.10 8.70 2.20e+00 2.07e-01 1.56e+01 angle pdb=" CG1 VAL N 106 " pdb=" CB VAL N 106 " pdb=" CG2 VAL N 106 " ideal model delta sigma weight residual 110.80 102.12 8.68 2.20e+00 2.07e-01 1.56e+01 ... (remaining 34207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.79: 14426 20.79 - 41.58: 958 41.58 - 62.37: 282 62.37 - 83.16: 42 83.16 - 103.95: 33 Dihedral angle restraints: 15741 sinusoidal: 6960 harmonic: 8781 Sorted by residual: dihedral pdb=" CB CYS Q 23 " pdb=" SG CYS Q 23 " pdb=" SG CYS Q 88 " pdb=" CB CYS Q 88 " ideal model delta sinusoidal sigma weight residual 93.00 163.94 -70.94 1 1.00e+01 1.00e-02 6.46e+01 dihedral pdb=" CB CYS I 23 " pdb=" SG CYS I 23 " pdb=" SG CYS I 88 " pdb=" CB CYS I 88 " ideal model delta sinusoidal sigma weight residual 93.00 163.94 -70.94 1 1.00e+01 1.00e-02 6.46e+01 dihedral pdb=" CB CYS M 23 " pdb=" SG CYS M 23 " pdb=" SG CYS M 88 " pdb=" CB CYS M 88 " ideal model delta sinusoidal sigma weight residual 93.00 163.92 -70.92 1 1.00e+01 1.00e-02 6.46e+01 ... (remaining 15738 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3232 0.066 - 0.133: 591 0.133 - 0.199: 119 0.199 - 0.265: 3 0.265 - 0.331: 6 Chirality restraints: 3951 Sorted by residual: chirality pdb=" C1 NAG F 701 " pdb=" ND2 ASN F 637 " pdb=" C2 NAG F 701 " pdb=" O5 NAG F 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" C1 NAG D 701 " pdb=" ND2 ASN D 637 " pdb=" C2 NAG D 701 " pdb=" O5 NAG D 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" C1 NAG B 701 " pdb=" ND2 ASN B 637 " pdb=" C2 NAG B 701 " pdb=" O5 NAG B 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 3948 not shown) Planarity restraints: 4353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 71 " 0.414 9.50e-02 1.11e+02 1.87e-01 2.55e+01 pdb=" NE ARG J 71 " -0.037 2.00e-02 2.50e+03 pdb=" CZ ARG J 71 " 0.031 2.00e-02 2.50e+03 pdb=" NH1 ARG J 71 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG J 71 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG O 71 " 0.414 9.50e-02 1.11e+02 1.87e-01 2.55e+01 pdb=" NE ARG O 71 " -0.037 2.00e-02 2.50e+03 pdb=" CZ ARG O 71 " 0.031 2.00e-02 2.50e+03 pdb=" NH1 ARG O 71 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG O 71 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 71 " 0.414 9.50e-02 1.11e+02 1.86e-01 2.54e+01 pdb=" NE ARG G 71 " -0.037 2.00e-02 2.50e+03 pdb=" CZ ARG G 71 " 0.031 2.00e-02 2.50e+03 pdb=" NH1 ARG G 71 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG G 71 " 0.002 2.00e-02 2.50e+03 ... (remaining 4350 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 183 2.59 - 3.17: 19837 3.17 - 3.75: 37094 3.75 - 4.32: 56986 4.32 - 4.90: 92626 Nonbonded interactions: 206726 Sorted by model distance: nonbonded pdb=" CA ALA G 100 " pdb=" CD2 LEU F 663 " model vdw 2.017 3.890 nonbonded pdb=" CD2 LEU D 663 " pdb=" CA ALA O 100 " model vdw 2.017 3.890 nonbonded pdb=" CD2 LEU B 663 " pdb=" CA ALA J 100 " model vdw 2.017 3.890 nonbonded pdb=" NH1 ARG A 350 " pdb=" O THR A 357 " model vdw 2.205 3.120 nonbonded pdb=" NH1 ARG E 350 " pdb=" O THR E 357 " model vdw 2.205 3.120 ... (remaining 206721 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'I' selection = chain 'M' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'T' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'P' } 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: 4.600 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: 0.870 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 49.620 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 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 : 0.005 0.051 25296 Z= 0.227 Angle : 1.017 11.390 34482 Z= 0.515 Chirality : 0.056 0.331 3951 Planarity : 0.008 0.187 4305 Dihedral : 15.367 103.949 9996 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.15 % Allowed : 15.45 % Favored : 84.40 % 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: -0.45 (0.15), residues: 3015 helix: -0.53 (0.24), residues: 438 sheet: 0.20 (0.16), residues: 1017 loop : -0.49 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 427 HIS 0.006 0.001 HIS A 374 PHE 0.027 0.003 PHE O 102 TYR 0.028 0.002 TYR R 36 ARG 0.036 0.002 ARG O 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00456 ( 48) link_NAG-ASN : angle 3.81828 ( 144) link_BETA1-4 : bond 0.00353 ( 9) link_BETA1-4 : angle 1.66098 ( 27) link_ALPHA1-3 : bond 0.00269 ( 3) link_ALPHA1-3 : angle 1.53807 ( 9) hydrogen bonds : bond 0.12382 ( 645) hydrogen bonds : angle 7.02773 ( 1683) SS BOND : bond 0.00336 ( 45) SS BOND : angle 1.28378 ( 90) covalent geometry : bond 0.00537 (25191) covalent geometry : angle 0.98657 (34212) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 446 time to evaluate : 2.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 23 LYS cc_start: 0.8743 (tptp) cc_final: 0.8464 (tptt) REVERT: L 61 ARG cc_start: 0.6710 (mtp180) cc_final: 0.6108 (ttp-170) REVERT: A 95 MET cc_start: 0.8804 (ptm) cc_final: 0.8552 (ptm) REVERT: K 46 GLU cc_start: 0.8050 (tt0) cc_final: 0.7706 (tt0) REVERT: K 52 ASN cc_start: 0.9040 (t0) cc_final: 0.8674 (t0) REVERT: N 36 TYR cc_start: 0.8501 (m-80) cc_final: 0.8260 (m-80) REVERT: C 108 ILE cc_start: 0.8325 (mm) cc_final: 0.8121 (mm) REVERT: C 117 LYS cc_start: 0.7576 (mtmm) cc_final: 0.7227 (mttp) REVERT: C 164 GLU cc_start: 0.7819 (pm20) cc_final: 0.7550 (pm20) REVERT: O 23 ARG cc_start: 0.8117 (mmm160) cc_final: 0.7612 (tpt90) REVERT: P 82 SER cc_start: 0.8415 (m) cc_final: 0.7790 (p) REVERT: R 87 TYR cc_start: 0.8594 (m-80) cc_final: 0.8388 (m-80) REVERT: F 634 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7289 (mt-10) outliers start: 4 outliers final: 2 residues processed: 450 average time/residue: 1.2954 time to fit residues: 677.0321 Evaluate side-chains 404 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 402 time to evaluate : 2.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain E residue 381 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 0.5980 chunk 227 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 77 optimal weight: 0.1980 chunk 153 optimal weight: 0.4980 chunk 121 optimal weight: 5.9990 chunk 235 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 272 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN B 658 GLN K 61 GLN K 62 ASN M 53 GLN M 79 GLN C 130 GLN D 658 GLN O 100BGLN E 130 GLN E 197 ASN F 658 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.172896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.140542 restraints weight = 26125.553| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.65 r_work: 0.3444 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 25296 Z= 0.137 Angle : 0.608 7.117 34482 Z= 0.305 Chirality : 0.045 0.155 3951 Planarity : 0.004 0.053 4305 Dihedral : 7.039 65.813 4562 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.90 % Allowed : 14.88 % Favored : 83.22 % 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: 0.00 (0.15), residues: 3015 helix: 0.04 (0.25), residues: 453 sheet: 0.27 (0.16), residues: 990 loop : -0.06 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 427 HIS 0.004 0.001 HIS E 105 PHE 0.014 0.002 PHE E 53 TYR 0.012 0.001 TYR I 96 ARG 0.009 0.001 ARG P 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 48) link_NAG-ASN : angle 2.62599 ( 144) link_BETA1-4 : bond 0.00429 ( 9) link_BETA1-4 : angle 1.79683 ( 27) link_ALPHA1-3 : bond 0.00994 ( 3) link_ALPHA1-3 : angle 1.64719 ( 9) hydrogen bonds : bond 0.04043 ( 645) hydrogen bonds : angle 5.32961 ( 1683) SS BOND : bond 0.00288 ( 45) SS BOND : angle 0.75179 ( 90) covalent geometry : bond 0.00315 (25191) covalent geometry : angle 0.58254 (34212) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 407 time to evaluate : 2.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 12 LYS cc_start: 0.8120 (mmmt) cc_final: 0.7716 (mmmt) REVERT: A 69 TRP cc_start: 0.6435 (OUTLIER) cc_final: 0.4759 (m100) REVERT: A 151 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.6650 (ttp-170) REVERT: C 95 MET cc_start: 0.9080 (ptm) cc_final: 0.8804 (ptm) REVERT: C 117 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7360 (mttp) REVERT: C 164 GLU cc_start: 0.8067 (pm20) cc_final: 0.7788 (pm20) REVERT: C 166 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.6691 (ttp80) REVERT: D 634 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7711 (mt-10) REVERT: O 23 ARG cc_start: 0.8282 (mmm160) cc_final: 0.7892 (mmm160) REVERT: P 82 SER cc_start: 0.8444 (m) cc_final: 0.7750 (p) REVERT: E 121 LYS cc_start: 0.8637 (mttt) cc_final: 0.8065 (mttp) REVERT: F 634 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7690 (mt-10) outliers start: 50 outliers final: 22 residues processed: 437 average time/residue: 1.3211 time to fit residues: 669.6158 Evaluate side-chains 407 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 381 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain K residue 94 ARG Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 73 THR Chi-restraints excluded: chain P residue 89 VAL Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain F residue 639 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 201 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.0070 chunk 2 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 236 optimal weight: 2.9990 chunk 281 optimal weight: 2.9990 chunk 270 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 81 GLN G 100BGLN H 32 HIS ** I 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN A 67 ASN B 653 GLN B 658 GLN K 32 HIS K 61 GLN M 53 GLN M 69 ASN N 37 GLN C 67 ASN C 136 ASN D 653 GLN E 67 ASN E 82 GLN F 577 GLN F 653 GLN F 658 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.147422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.109506 restraints weight = 26236.011| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.85 r_work: 0.3032 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.125 25296 Z= 0.287 Angle : 0.740 10.645 34482 Z= 0.369 Chirality : 0.051 0.301 3951 Planarity : 0.005 0.050 4305 Dihedral : 6.317 44.359 4557 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.43 % Allowed : 16.02 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 3015 helix: -0.13 (0.25), residues: 441 sheet: -0.02 (0.15), residues: 1002 loop : -0.02 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP E 427 HIS 0.006 0.001 HIS P 35 PHE 0.022 0.003 PHE G 100H TYR 0.019 0.002 TYR M 96 ARG 0.007 0.001 ARG P 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00566 ( 48) link_NAG-ASN : angle 3.04060 ( 144) link_BETA1-4 : bond 0.00389 ( 9) link_BETA1-4 : angle 1.88056 ( 27) link_ALPHA1-3 : bond 0.00814 ( 3) link_ALPHA1-3 : angle 1.22954 ( 9) hydrogen bonds : bond 0.04987 ( 645) hydrogen bonds : angle 5.41844 ( 1683) SS BOND : bond 0.00573 ( 45) SS BOND : angle 1.01784 ( 90) covalent geometry : bond 0.00684 (25191) covalent geometry : angle 0.71214 (34212) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 417 time to evaluate : 2.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 18 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7150 (tt) REVERT: G 34 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.8516 (mmp) REVERT: I 47 MET cc_start: 0.8673 (mmm) cc_final: 0.8466 (mmm) REVERT: A 91 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.6847 (tm-30) REVERT: A 479 TRP cc_start: 0.7856 (m-10) cc_final: 0.7152 (m-10) REVERT: B 647 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8169 (tm-30) REVERT: B 652 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7779 (mt0) REVERT: K 81 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7756 (tm-30) REVERT: C 117 LYS cc_start: 0.7424 (OUTLIER) cc_final: 0.7048 (mttp) REVERT: C 164 GLU cc_start: 0.7894 (pm20) cc_final: 0.7362 (pm20) REVERT: C 166 ARG cc_start: 0.7659 (mmp-170) cc_final: 0.6383 (ttp80) REVERT: C 232 LYS cc_start: 0.8195 (mtmt) cc_final: 0.7953 (mtmm) REVERT: C 440 GLN cc_start: 0.7603 (mp10) cc_final: 0.7286 (mp10) REVERT: C 479 TRP cc_start: 0.7597 (m-10) cc_final: 0.6749 (m-10) REVERT: D 647 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8251 (tm-30) REVERT: D 652 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7427 (mt0) REVERT: R 61 ARG cc_start: 0.5967 (mtp180) cc_final: 0.5063 (ttp-170) REVERT: E 95 MET cc_start: 0.9059 (ptm) cc_final: 0.8823 (ptm) REVERT: E 151 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.6775 (ttp-170) REVERT: E 191 TYR cc_start: 0.8809 (m-80) cc_final: 0.8413 (m-80) REVERT: E 232 LYS cc_start: 0.8360 (mtmt) cc_final: 0.8053 (mtmm) REVERT: E 479 TRP cc_start: 0.7786 (m-10) cc_final: 0.7047 (m-10) REVERT: F 652 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7901 (mp10) outliers start: 64 outliers final: 39 residues processed: 451 average time/residue: 1.3450 time to fit residues: 701.6826 Evaluate side-chains 443 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 395 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 94 ARG Chi-restraints excluded: chain M residue 59 SER Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 169 ARG Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 70 SER Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain P residue 89 VAL Chi-restraints excluded: chain Q residue 45 LYS Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 381 GLU Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 652 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 131 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 299 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN B 653 GLN B 658 GLN K 61 GLN M 53 GLN M 69 ASN C 173 HIS D 653 GLN O 76 ASN E 173 HIS F 577 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.150108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.111993 restraints weight = 26376.194| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.90 r_work: 0.3070 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 25296 Z= 0.157 Angle : 0.618 10.783 34482 Z= 0.310 Chirality : 0.045 0.222 3951 Planarity : 0.004 0.032 4305 Dihedral : 5.680 43.145 4557 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.02 % Favored : 97.88 % Rotamer: Outliers : 2.66 % Allowed : 16.97 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 3015 helix: -0.02 (0.25), residues: 453 sheet: -0.02 (0.15), residues: 999 loop : 0.01 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 427 HIS 0.003 0.001 HIS A 105 PHE 0.013 0.002 PHE E 353 TYR 0.015 0.001 TYR M 96 ARG 0.007 0.001 ARG H 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00392 ( 48) link_NAG-ASN : angle 2.66126 ( 144) link_BETA1-4 : bond 0.00399 ( 9) link_BETA1-4 : angle 1.57966 ( 27) link_ALPHA1-3 : bond 0.01081 ( 3) link_ALPHA1-3 : angle 1.08126 ( 9) hydrogen bonds : bond 0.04148 ( 645) hydrogen bonds : angle 5.13891 ( 1683) SS BOND : bond 0.00379 ( 45) SS BOND : angle 1.85007 ( 90) covalent geometry : bond 0.00366 (25191) covalent geometry : angle 0.58665 (34212) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 404 time to evaluate : 2.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 34 MET cc_start: 0.9085 (mmt) cc_final: 0.8431 (mmt) REVERT: A 91 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.6964 (tm-30) REVERT: A 95 MET cc_start: 0.9112 (ptm) cc_final: 0.8817 (ptm) REVERT: A 191 TYR cc_start: 0.8549 (m-80) cc_final: 0.8209 (m-80) REVERT: A 479 TRP cc_start: 0.7771 (m-10) cc_final: 0.7390 (m-10) REVERT: B 647 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7943 (tm-30) REVERT: B 652 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7673 (mt0) REVERT: K 21 SER cc_start: 0.8475 (p) cc_final: 0.8250 (t) REVERT: N 53 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7390 (mttm) REVERT: C 102 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7819 (mm-30) REVERT: C 117 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.7006 (tppt) REVERT: C 164 GLU cc_start: 0.7853 (pm20) cc_final: 0.7327 (pm20) REVERT: C 166 ARG cc_start: 0.7781 (mmp-170) cc_final: 0.6468 (ttp80) REVERT: C 232 LYS cc_start: 0.8192 (mtmt) cc_final: 0.7915 (mtmm) REVERT: C 269 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8282 (mt-10) REVERT: C 479 TRP cc_start: 0.7607 (m-10) cc_final: 0.6834 (m-10) REVERT: D 647 GLU cc_start: 0.8287 (tm-30) cc_final: 0.8019 (tm-30) REVERT: D 652 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7350 (mt0) REVERT: O 100 TYR cc_start: 0.9199 (m-80) cc_final: 0.8950 (m-80) REVERT: R 61 ARG cc_start: 0.5943 (mtp180) cc_final: 0.5124 (ttp-170) REVERT: E 91 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.7229 (tm-30) REVERT: E 95 MET cc_start: 0.9067 (ptm) cc_final: 0.8840 (ptm) REVERT: E 232 LYS cc_start: 0.8353 (mtmt) cc_final: 0.8071 (mtmm) REVERT: E 236 THR cc_start: 0.8798 (m) cc_final: 0.8542 (p) REVERT: E 479 TRP cc_start: 0.7798 (m-10) cc_final: 0.7033 (m-10) REVERT: F 652 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7911 (mp10) outliers start: 70 outliers final: 33 residues processed: 448 average time/residue: 1.5365 time to fit residues: 793.0108 Evaluate side-chains 437 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 395 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain N residue 53 LYS Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 70 SER Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 89 VAL Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 381 GLU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 652 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 157 optimal weight: 0.6980 chunk 30 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 265 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 236 optimal weight: 0.0040 chunk 219 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 187 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN B 653 GLN B 658 GLN K 61 GLN F 577 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.151026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.113600 restraints weight = 26459.681| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.83 r_work: 0.3117 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25296 Z= 0.131 Angle : 0.564 8.028 34482 Z= 0.283 Chirality : 0.044 0.202 3951 Planarity : 0.004 0.032 4305 Dihedral : 5.145 41.715 4557 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.06 % Favored : 97.84 % Rotamer: Outliers : 2.73 % Allowed : 17.16 % Favored : 80.11 % 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: 0.00 (0.15), residues: 3015 helix: 0.14 (0.26), residues: 453 sheet: 0.08 (0.15), residues: 972 loop : 0.06 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 427 HIS 0.002 0.001 HIS A 105 PHE 0.011 0.001 PHE E 353 TYR 0.015 0.001 TYR M 96 ARG 0.010 0.000 ARG H 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 48) link_NAG-ASN : angle 2.49479 ( 144) link_BETA1-4 : bond 0.00384 ( 9) link_BETA1-4 : angle 1.42755 ( 27) link_ALPHA1-3 : bond 0.01134 ( 3) link_ALPHA1-3 : angle 1.04876 ( 9) hydrogen bonds : bond 0.03783 ( 645) hydrogen bonds : angle 4.91028 ( 1683) SS BOND : bond 0.00285 ( 45) SS BOND : angle 1.46617 ( 90) covalent geometry : bond 0.00304 (25191) covalent geometry : angle 0.53536 (34212) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 409 time to evaluate : 2.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 34 MET cc_start: 0.9056 (mmt) cc_final: 0.8453 (mmt) REVERT: I 27 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7795 (p0) REVERT: A 91 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.6956 (tm-30) REVERT: A 95 MET cc_start: 0.9134 (ptm) cc_final: 0.8811 (ptm) REVERT: A 191 TYR cc_start: 0.8450 (m-80) cc_final: 0.8175 (m-80) REVERT: A 211 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6843 (tp30) REVERT: A 479 TRP cc_start: 0.7764 (m-10) cc_final: 0.7448 (m-10) REVERT: B 647 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7911 (tm-30) REVERT: B 652 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7669 (mt0) REVERT: K 21 SER cc_start: 0.8493 (p) cc_final: 0.8267 (t) REVERT: C 102 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7773 (mm-30) REVERT: C 117 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.7052 (tppt) REVERT: C 232 LYS cc_start: 0.8193 (mtmt) cc_final: 0.7931 (mtmm) REVERT: C 479 TRP cc_start: 0.7595 (m-10) cc_final: 0.6955 (m-10) REVERT: D 647 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7778 (tm-30) REVERT: D 652 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7178 (mt0) REVERT: O 34 MET cc_start: 0.8977 (mmm) cc_final: 0.8413 (mmt) REVERT: O 100 TYR cc_start: 0.9180 (m-80) cc_final: 0.8876 (m-80) REVERT: P 80 MET cc_start: 0.8832 (tmm) cc_final: 0.8630 (ttp) REVERT: Q 27 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7405 (p0) REVERT: R 61 ARG cc_start: 0.5943 (mtp180) cc_final: 0.5115 (ttp-170) REVERT: E 91 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.7234 (tm-30) REVERT: E 95 MET cc_start: 0.9056 (ptm) cc_final: 0.8806 (ptm) REVERT: E 117 LYS cc_start: 0.7565 (ttmm) cc_final: 0.7086 (tppt) REVERT: E 232 LYS cc_start: 0.8367 (mtmt) cc_final: 0.8106 (mtmm) REVERT: E 236 THR cc_start: 0.8818 (m) cc_final: 0.8586 (p) REVERT: E 479 TRP cc_start: 0.7756 (m-10) cc_final: 0.7130 (m-10) outliers start: 72 outliers final: 43 residues processed: 456 average time/residue: 1.4900 time to fit residues: 784.9753 Evaluate side-chains 441 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 389 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain I residue 27 ASP Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 70 SER Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 89 VAL Chi-restraints excluded: chain Q residue 27 ASP Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 381 GLU Chi-restraints excluded: chain F residue 639 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 65 optimal weight: 0.6980 chunk 124 optimal weight: 0.0770 chunk 208 optimal weight: 5.9990 chunk 107 optimal weight: 0.5980 chunk 192 optimal weight: 1.9990 chunk 225 optimal weight: 7.9990 chunk 141 optimal weight: 8.9990 chunk 185 optimal weight: 1.9990 chunk 77 optimal weight: 0.0010 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 overall best weight: 0.4544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN ** I 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN A 72 HIS A 283 ASN B 658 GLN K 61 GLN C 72 HIS P 39 GLN E 72 HIS E 82 GLN E 283 ASN F 577 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.152483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.115290 restraints weight = 26266.465| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.82 r_work: 0.3137 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 25296 Z= 0.106 Angle : 0.533 7.493 34482 Z= 0.268 Chirality : 0.043 0.167 3951 Planarity : 0.003 0.038 4305 Dihedral : 4.825 42.016 4557 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.02 % Favored : 97.91 % Rotamer: Outliers : 2.47 % Allowed : 17.88 % Favored : 79.65 % 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: 0.21 (0.15), residues: 3015 helix: 0.38 (0.26), residues: 456 sheet: 0.22 (0.15), residues: 969 loop : 0.15 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 427 HIS 0.002 0.001 HIS E 72 PHE 0.010 0.001 PHE E 353 TYR 0.012 0.001 TYR M 96 ARG 0.010 0.000 ARG H 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 48) link_NAG-ASN : angle 2.37612 ( 144) link_BETA1-4 : bond 0.00373 ( 9) link_BETA1-4 : angle 1.34212 ( 27) link_ALPHA1-3 : bond 0.01178 ( 3) link_ALPHA1-3 : angle 1.09401 ( 9) hydrogen bonds : bond 0.03506 ( 645) hydrogen bonds : angle 4.74597 ( 1683) SS BOND : bond 0.00236 ( 45) SS BOND : angle 1.25408 ( 90) covalent geometry : bond 0.00241 (25191) covalent geometry : angle 0.50640 (34212) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 403 time to evaluate : 3.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 34 MET cc_start: 0.9034 (mmt) cc_final: 0.8467 (mmt) REVERT: A 91 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.6992 (tm-30) REVERT: A 95 MET cc_start: 0.9150 (ptm) cc_final: 0.8826 (ptm) REVERT: A 211 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.6827 (tp30) REVERT: A 479 TRP cc_start: 0.7710 (m-10) cc_final: 0.7475 (m-10) REVERT: B 647 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7982 (tm-30) REVERT: B 652 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7647 (mt0) REVERT: N 53 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7444 (mttm) REVERT: C 102 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7743 (mm-30) REVERT: C 117 LYS cc_start: 0.7434 (mtmm) cc_final: 0.7044 (tppt) REVERT: C 166 ARG cc_start: 0.7824 (mmp-170) cc_final: 0.6508 (ttp80) REVERT: C 232 LYS cc_start: 0.8181 (mtmt) cc_final: 0.7944 (mtmm) REVERT: C 479 TRP cc_start: 0.7511 (m-10) cc_final: 0.6906 (m-10) REVERT: D 652 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7266 (mt0) REVERT: O 34 MET cc_start: 0.8985 (mmm) cc_final: 0.8361 (mmt) REVERT: O 100 TYR cc_start: 0.9181 (m-80) cc_final: 0.8933 (m-80) REVERT: P 80 MET cc_start: 0.8844 (tmm) cc_final: 0.8634 (tmm) REVERT: P 81 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7846 (tm-30) REVERT: Q 27 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7471 (p0) REVERT: E 91 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.7240 (tm-30) REVERT: E 95 MET cc_start: 0.9029 (ptm) cc_final: 0.8735 (ptm) REVERT: E 117 LYS cc_start: 0.7584 (ttmm) cc_final: 0.7110 (tppt) REVERT: E 161 MET cc_start: 0.9023 (tpt) cc_final: 0.8791 (tpt) REVERT: E 232 LYS cc_start: 0.8351 (mtmt) cc_final: 0.8103 (mtmm) REVERT: E 236 THR cc_start: 0.8813 (m) cc_final: 0.8536 (p) REVERT: E 479 TRP cc_start: 0.7726 (m-10) cc_final: 0.7243 (m-10) outliers start: 65 outliers final: 34 residues processed: 446 average time/residue: 1.3802 time to fit residues: 711.5025 Evaluate side-chains 428 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 385 time to evaluate : 3.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 53 LYS Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain O residue 70 SER Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain P residue 81 GLU Chi-restraints excluded: chain P residue 89 VAL Chi-restraints excluded: chain Q residue 27 ASP Chi-restraints excluded: chain Q residue 45 LYS Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 381 GLU Chi-restraints excluded: chain E residue 412 ASP Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 655 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 206 optimal weight: 0.0050 chunk 213 optimal weight: 5.9990 chunk 228 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 223 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 225 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 161 optimal weight: 1.9990 chunk 292 optimal weight: 4.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN B 653 GLN B 658 GLN J 76 ASN C 283 ASN D 653 GLN O 100BGLN P 39 GLN E 82 GLN F 577 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.149285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.111238 restraints weight = 26521.409| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.88 r_work: 0.3090 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 25296 Z= 0.183 Angle : 0.605 8.503 34482 Z= 0.303 Chirality : 0.045 0.183 3951 Planarity : 0.004 0.034 4305 Dihedral : 4.989 42.817 4557 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.16 % Favored : 97.68 % Rotamer: Outliers : 3.15 % Allowed : 17.73 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.15), residues: 3015 helix: 0.20 (0.26), residues: 453 sheet: 0.08 (0.15), residues: 981 loop : 0.19 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 427 HIS 0.004 0.001 HIS A 105 PHE 0.014 0.002 PHE E 353 TYR 0.016 0.001 TYR M 96 ARG 0.011 0.000 ARG H 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 48) link_NAG-ASN : angle 2.64727 ( 144) link_BETA1-4 : bond 0.00405 ( 9) link_BETA1-4 : angle 1.54701 ( 27) link_ALPHA1-3 : bond 0.01082 ( 3) link_ALPHA1-3 : angle 1.22680 ( 9) hydrogen bonds : bond 0.04074 ( 645) hydrogen bonds : angle 4.93924 ( 1683) SS BOND : bond 0.00381 ( 45) SS BOND : angle 1.39555 ( 90) covalent geometry : bond 0.00436 (25191) covalent geometry : angle 0.57603 (34212) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 395 time to evaluate : 3.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 34 MET cc_start: 0.9092 (mmt) cc_final: 0.8566 (mmt) REVERT: H 81 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: A 91 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.6948 (tm-30) REVERT: A 95 MET cc_start: 0.9173 (ptm) cc_final: 0.8881 (ptm) REVERT: A 211 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7040 (tp30) REVERT: A 269 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8048 (mm-30) REVERT: A 479 TRP cc_start: 0.7771 (m-10) cc_final: 0.7399 (m-10) REVERT: B 647 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7899 (tm-30) REVERT: B 652 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7747 (mt0) REVERT: K 81 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7972 (tm-30) REVERT: N 85 ASP cc_start: 0.8091 (m-30) cc_final: 0.7870 (m-30) REVERT: C 117 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.7046 (tppt) REVERT: C 166 ARG cc_start: 0.7844 (mmp-170) cc_final: 0.6564 (ttp80) REVERT: C 232 LYS cc_start: 0.8247 (mtmt) cc_final: 0.7977 (mtmm) REVERT: C 269 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8290 (mt-10) REVERT: C 479 TRP cc_start: 0.7585 (m-10) cc_final: 0.6668 (m-10) REVERT: D 652 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7331 (mt0) REVERT: O 100 TYR cc_start: 0.9197 (m-80) cc_final: 0.8917 (m-80) REVERT: P 69 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8731 (mtt) REVERT: P 80 MET cc_start: 0.8864 (tmm) cc_final: 0.8647 (tmm) REVERT: P 81 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7866 (tt0) REVERT: Q 27 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7448 (p0) REVERT: E 91 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.7300 (tm-30) REVERT: E 95 MET cc_start: 0.9107 (ptm) cc_final: 0.8859 (ptm) REVERT: E 117 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.7116 (tppt) REVERT: E 232 LYS cc_start: 0.8382 (mtmt) cc_final: 0.8157 (mtmm) REVERT: E 479 TRP cc_start: 0.7807 (m-10) cc_final: 0.7114 (m-10) outliers start: 83 outliers final: 56 residues processed: 449 average time/residue: 1.9917 time to fit residues: 1042.6392 Evaluate side-chains 456 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 387 time to evaluate : 4.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 70 SER Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain P residue 69 MET Chi-restraints excluded: chain P residue 81 GLU Chi-restraints excluded: chain P residue 89 VAL Chi-restraints excluded: chain Q residue 27 ASP Chi-restraints excluded: chain Q residue 45 LYS Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 381 GLU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 655 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 51 optimal weight: 0.2980 chunk 117 optimal weight: 0.6980 chunk 246 optimal weight: 0.7980 chunk 233 optimal weight: 2.9990 chunk 266 optimal weight: 3.9990 chunk 253 optimal weight: 5.9990 chunk 203 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN B 653 GLN B 658 GLN C 173 HIS P 39 GLN F 577 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.149177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.111092 restraints weight = 26396.808| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.88 r_work: 0.3088 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 25296 Z= 0.179 Angle : 0.596 9.297 34482 Z= 0.300 Chirality : 0.045 0.178 3951 Planarity : 0.004 0.036 4305 Dihedral : 5.010 43.214 4557 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.19 % Favored : 97.61 % Rotamer: Outliers : 3.08 % Allowed : 18.03 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.15), residues: 3015 helix: 0.18 (0.26), residues: 453 sheet: 0.07 (0.15), residues: 972 loop : 0.13 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 427 HIS 0.004 0.001 HIS E 72 PHE 0.014 0.002 PHE E 353 TYR 0.017 0.001 TYR M 96 ARG 0.011 0.000 ARG H 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 48) link_NAG-ASN : angle 2.68286 ( 144) link_BETA1-4 : bond 0.00379 ( 9) link_BETA1-4 : angle 1.49756 ( 27) link_ALPHA1-3 : bond 0.00968 ( 3) link_ALPHA1-3 : angle 1.19003 ( 9) hydrogen bonds : bond 0.04026 ( 645) hydrogen bonds : angle 4.98418 ( 1683) SS BOND : bond 0.00397 ( 45) SS BOND : angle 1.37531 ( 90) covalent geometry : bond 0.00425 (25191) covalent geometry : angle 0.56651 (34212) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 395 time to evaluate : 2.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 34 MET cc_start: 0.9089 (mmt) cc_final: 0.8541 (mmt) REVERT: H 81 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8137 (tt0) REVERT: A 91 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7013 (tm-30) REVERT: A 95 MET cc_start: 0.9180 (ptm) cc_final: 0.8892 (ptm) REVERT: A 211 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7116 (tp30) REVERT: A 269 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8065 (mm-30) REVERT: A 479 TRP cc_start: 0.7775 (m-10) cc_final: 0.7375 (m-10) REVERT: B 647 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7800 (pp20) REVERT: B 652 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7754 (mt0) REVERT: K 12 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7766 (mmtp) REVERT: K 81 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7950 (tm-30) REVERT: N 53 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7363 (mttm) REVERT: N 85 ASP cc_start: 0.8087 (m-30) cc_final: 0.7863 (m-30) REVERT: C 102 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7836 (mm-30) REVERT: C 117 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.6961 (tppt) REVERT: C 161 MET cc_start: 0.8760 (tpp) cc_final: 0.7969 (tpp) REVERT: C 166 ARG cc_start: 0.7852 (mmp-170) cc_final: 0.6590 (ttp80) REVERT: C 232 LYS cc_start: 0.8241 (mtmt) cc_final: 0.7951 (mtmm) REVERT: C 269 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8295 (mt-10) REVERT: C 479 TRP cc_start: 0.7612 (m-10) cc_final: 0.6699 (m-10) REVERT: D 647 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7381 (pp20) REVERT: D 652 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7352 (mt0) REVERT: O 34 MET cc_start: 0.8936 (mmm) cc_final: 0.8511 (mmt) REVERT: O 100 TYR cc_start: 0.9183 (m-80) cc_final: 0.8872 (m-80) REVERT: P 39 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8752 (tt0) REVERT: P 69 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8698 (mtt) REVERT: P 80 MET cc_start: 0.8866 (tmm) cc_final: 0.8626 (tmm) REVERT: P 81 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7880 (tt0) REVERT: P 82 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7732 (mm) REVERT: Q 27 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7479 (p0) REVERT: E 91 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.7249 (tm-30) REVERT: E 117 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.7011 (tppt) REVERT: E 161 MET cc_start: 0.9091 (tpt) cc_final: 0.8890 (tpt) REVERT: E 232 LYS cc_start: 0.8426 (mtmt) cc_final: 0.8135 (mtmm) REVERT: E 479 TRP cc_start: 0.7812 (m-10) cc_final: 0.7047 (m-10) REVERT: F 652 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.8006 (mp10) outliers start: 81 outliers final: 53 residues processed: 449 average time/residue: 1.4542 time to fit residues: 764.3119 Evaluate side-chains 463 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 391 time to evaluate : 2.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain K residue 12 LYS Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 53 LYS Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 70 SER Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain P residue 39 GLN Chi-restraints excluded: chain P residue 69 MET Chi-restraints excluded: chain P residue 81 GLU Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 89 VAL Chi-restraints excluded: chain Q residue 27 ASP Chi-restraints excluded: chain Q residue 45 LYS Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 381 GLU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 652 GLN Chi-restraints excluded: chain F residue 655 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 94 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 chunk 255 optimal weight: 1.9990 chunk 253 optimal weight: 5.9990 chunk 200 optimal weight: 8.9990 chunk 133 optimal weight: 2.9990 chunk 274 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 134 optimal weight: 0.0570 chunk 176 optimal weight: 2.9990 chunk 220 optimal weight: 0.4980 overall best weight: 0.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN B 658 GLN K 61 GLN O 100BGLN P 39 GLN F 577 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.149714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.112132 restraints weight = 26531.964| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.84 r_work: 0.3100 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25296 Z= 0.147 Angle : 0.576 10.207 34482 Z= 0.289 Chirality : 0.044 0.167 3951 Planarity : 0.004 0.045 4305 Dihedral : 4.931 43.362 4557 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.22 % Favored : 97.58 % Rotamer: Outliers : 2.77 % Allowed : 18.45 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.15), residues: 3015 helix: 0.25 (0.26), residues: 453 sheet: 0.08 (0.15), residues: 990 loop : 0.21 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 427 HIS 0.004 0.001 HIS A 72 PHE 0.013 0.002 PHE E 353 TYR 0.014 0.001 TYR M 96 ARG 0.012 0.000 ARG H 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 48) link_NAG-ASN : angle 2.64275 ( 144) link_BETA1-4 : bond 0.00375 ( 9) link_BETA1-4 : angle 1.45200 ( 27) link_ALPHA1-3 : bond 0.00982 ( 3) link_ALPHA1-3 : angle 1.19354 ( 9) hydrogen bonds : bond 0.03870 ( 645) hydrogen bonds : angle 4.91789 ( 1683) SS BOND : bond 0.00340 ( 45) SS BOND : angle 1.31340 ( 90) covalent geometry : bond 0.00347 (25191) covalent geometry : angle 0.54675 (34212) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 386 time to evaluate : 2.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 34 MET cc_start: 0.9063 (mmt) cc_final: 0.8557 (mmt) REVERT: H 81 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8125 (tt0) REVERT: A 91 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.6964 (tm-30) REVERT: A 95 MET cc_start: 0.9166 (ptm) cc_final: 0.8874 (ptm) REVERT: A 211 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7035 (tp30) REVERT: A 269 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8051 (mm-30) REVERT: A 479 TRP cc_start: 0.7722 (m-10) cc_final: 0.7276 (m-10) REVERT: B 647 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7773 (pp20) REVERT: B 652 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7676 (mt0) REVERT: K 81 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: N 53 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7332 (mttm) REVERT: N 85 ASP cc_start: 0.8045 (m-30) cc_final: 0.7829 (m-30) REVERT: C 102 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7789 (mm-30) REVERT: C 117 LYS cc_start: 0.7283 (OUTLIER) cc_final: 0.6904 (tppt) REVERT: C 166 ARG cc_start: 0.7827 (mmp-170) cc_final: 0.6535 (ttp80) REVERT: C 232 LYS cc_start: 0.8205 (mtmt) cc_final: 0.7925 (mtmm) REVERT: C 269 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8203 (mt-10) REVERT: C 479 TRP cc_start: 0.7553 (m-10) cc_final: 0.6698 (m-10) REVERT: D 647 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7327 (pp20) REVERT: D 652 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7235 (mt0) REVERT: O 34 MET cc_start: 0.8945 (mmm) cc_final: 0.8511 (mmt) REVERT: O 100 TYR cc_start: 0.9180 (m-80) cc_final: 0.8957 (m-80) REVERT: P 69 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8675 (mtt) REVERT: P 80 MET cc_start: 0.8863 (tmm) cc_final: 0.8628 (tmm) REVERT: P 81 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7840 (tt0) REVERT: Q 27 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7437 (p0) REVERT: E 91 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.7208 (tm-30) REVERT: E 117 LYS cc_start: 0.7382 (ttmm) cc_final: 0.6956 (tppt) REVERT: E 191 TYR cc_start: 0.8739 (m-80) cc_final: 0.8508 (m-80) REVERT: E 211 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7056 (tp30) REVERT: E 232 LYS cc_start: 0.8378 (mtmt) cc_final: 0.8063 (mtmm) REVERT: E 479 TRP cc_start: 0.7748 (m-10) cc_final: 0.7050 (m-10) outliers start: 73 outliers final: 49 residues processed: 441 average time/residue: 1.4172 time to fit residues: 722.4055 Evaluate side-chains 443 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 379 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 53 LYS Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain P residue 69 MET Chi-restraints excluded: chain P residue 81 GLU Chi-restraints excluded: chain P residue 89 VAL Chi-restraints excluded: chain Q residue 27 ASP Chi-restraints excluded: chain Q residue 45 LYS Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 381 GLU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 655 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 69 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 276 optimal weight: 0.5980 chunk 31 optimal weight: 9.9990 chunk 52 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN B 653 GLN B 658 GLN K 61 GLN O 100BGLN F 577 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.150109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.112761 restraints weight = 26398.237| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.83 r_work: 0.3110 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25296 Z= 0.139 Angle : 0.568 10.504 34482 Z= 0.285 Chirality : 0.044 0.161 3951 Planarity : 0.004 0.046 4305 Dihedral : 4.854 43.207 4557 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.06 % Favored : 97.74 % Rotamer: Outliers : 2.47 % Allowed : 18.83 % Favored : 78.70 % 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: 0.20 (0.15), residues: 3015 helix: 0.29 (0.26), residues: 453 sheet: 0.14 (0.15), residues: 990 loop : 0.24 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 427 HIS 0.004 0.001 HIS E 72 PHE 0.012 0.001 PHE E 353 TYR 0.014 0.001 TYR E 40 ARG 0.012 0.000 ARG H 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00343 ( 48) link_NAG-ASN : angle 2.59886 ( 144) link_BETA1-4 : bond 0.00374 ( 9) link_BETA1-4 : angle 1.42031 ( 27) link_ALPHA1-3 : bond 0.00948 ( 3) link_ALPHA1-3 : angle 1.21006 ( 9) hydrogen bonds : bond 0.03774 ( 645) hydrogen bonds : angle 4.87871 ( 1683) SS BOND : bond 0.00322 ( 45) SS BOND : angle 1.27779 ( 90) covalent geometry : bond 0.00327 (25191) covalent geometry : angle 0.53919 (34212) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 392 time to evaluate : 2.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 34 MET cc_start: 0.8990 (mmt) cc_final: 0.8595 (mmt) REVERT: H 81 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8124 (tt0) REVERT: A 91 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7001 (tm-30) REVERT: A 95 MET cc_start: 0.9174 (ptm) cc_final: 0.8817 (ptm) REVERT: A 211 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7066 (tp30) REVERT: A 232 LYS cc_start: 0.8280 (mtmt) cc_final: 0.7632 (mmmm) REVERT: A 269 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8085 (mm-30) REVERT: A 396 ILE cc_start: 0.8511 (pt) cc_final: 0.8304 (mt) REVERT: A 479 TRP cc_start: 0.7730 (m-10) cc_final: 0.7401 (m-10) REVERT: B 647 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7642 (pp20) REVERT: B 652 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7716 (mt0) REVERT: K 81 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7957 (tm-30) REVERT: N 85 ASP cc_start: 0.8067 (m-30) cc_final: 0.7852 (m-30) REVERT: C 102 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7807 (mm-30) REVERT: C 117 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.6935 (tppt) REVERT: C 166 ARG cc_start: 0.7863 (mmp-170) cc_final: 0.6577 (ttp80) REVERT: C 232 LYS cc_start: 0.8234 (mtmt) cc_final: 0.7972 (mtmm) REVERT: C 269 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8217 (mt-10) REVERT: C 479 TRP cc_start: 0.7592 (m-10) cc_final: 0.6771 (m-10) REVERT: D 647 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7308 (pp20) REVERT: D 652 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7346 (mt0) REVERT: O 34 MET cc_start: 0.8960 (mmm) cc_final: 0.8497 (mmt) REVERT: O 100 TYR cc_start: 0.9184 (m-80) cc_final: 0.8956 (m-80) REVERT: P 69 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8682 (mtt) REVERT: P 80 MET cc_start: 0.8873 (tmm) cc_final: 0.8636 (tmm) REVERT: P 81 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7876 (tt0) REVERT: Q 27 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7475 (p0) REVERT: E 91 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.7223 (tm-30) REVERT: E 117 LYS cc_start: 0.7425 (ttmm) cc_final: 0.7007 (tppt) REVERT: E 211 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7139 (tp30) REVERT: E 232 LYS cc_start: 0.8412 (mtmt) cc_final: 0.8104 (mtmm) REVERT: E 479 TRP cc_start: 0.7736 (m-10) cc_final: 0.7170 (m-10) outliers start: 65 outliers final: 47 residues processed: 437 average time/residue: 1.3777 time to fit residues: 699.0654 Evaluate side-chains 438 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 377 time to evaluate : 2.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain P residue 69 MET Chi-restraints excluded: chain P residue 81 GLU Chi-restraints excluded: chain P residue 89 VAL Chi-restraints excluded: chain Q residue 27 ASP Chi-restraints excluded: chain Q residue 45 LYS Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 381 GLU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 655 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 185 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 200 optimal weight: 8.9990 chunk 146 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 236 optimal weight: 8.9990 chunk 247 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 225 optimal weight: 0.6980 chunk 262 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN B 658 GLN O 100BGLN P 39 GLN F 577 GLN F 652 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.149227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.110974 restraints weight = 26491.624| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.90 r_work: 0.3084 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 25296 Z= 0.193 Angle : 0.617 11.752 34482 Z= 0.309 Chirality : 0.045 0.219 3951 Planarity : 0.004 0.043 4305 Dihedral : 4.999 43.527 4557 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.12 % Favored : 97.68 % Rotamer: Outliers : 3.00 % Allowed : 18.49 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 3015 helix: 0.09 (0.26), residues: 453 sheet: 0.15 (0.16), residues: 975 loop : 0.21 (0.16), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 427 HIS 0.005 0.001 HIS E 72 PHE 0.014 0.002 PHE E 353 TYR 0.018 0.001 TYR E 191 ARG 0.012 0.001 ARG H 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 48) link_NAG-ASN : angle 2.67553 ( 144) link_BETA1-4 : bond 0.00376 ( 9) link_BETA1-4 : angle 1.53933 ( 27) link_ALPHA1-3 : bond 0.00792 ( 3) link_ALPHA1-3 : angle 1.22438 ( 9) hydrogen bonds : bond 0.04162 ( 645) hydrogen bonds : angle 4.98775 ( 1683) SS BOND : bond 0.00416 ( 45) SS BOND : angle 1.40008 ( 90) covalent geometry : bond 0.00462 (25191) covalent geometry : angle 0.58784 (34212) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20475.28 seconds wall clock time: 360 minutes 23.39 seconds (21623.39 seconds total)