Starting phenix.real_space_refine on Fri Sep 19 08:09:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mia_48286/09_2025/9mia_48286.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mia_48286/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9mia_48286/09_2025/9mia_48286.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mia_48286/09_2025/9mia_48286.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mia_48286/09_2025/9mia_48286.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mia_48286/09_2025/9mia_48286.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: J, O, K, P, M, Q, N, R, C, E, D, F, U, W, V, X Time building chain proxies: 5.81, per 1000 atoms: 0.24 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: 2.29 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.95 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: 4.87 Time building geometry restraints manager: 3.08 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: 0.07 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'P' } ncs_group { reference = chain 'I' selection = chain 'M' selection = chain 'Q' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'T' selection = chain 'V' selection = chain 'X' } 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: 5.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 23.840 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.740 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (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 ARG 0.036 0.002 ARG O 71 TYR 0.028 0.002 TYR R 36 PHE 0.027 0.003 PHE O 102 TRP 0.032 0.002 TRP E 427 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00537 (25191) covalent geometry : angle 0.98657 (34212) SS BOND : bond 0.00336 ( 45) SS BOND : angle 1.28378 ( 90) hydrogen bonds : bond 0.12382 ( 645) hydrogen bonds : angle 7.02773 ( 1683) link_ALPHA1-3 : bond 0.00269 ( 3) link_ALPHA1-3 : angle 1.53807 ( 9) link_BETA1-4 : bond 0.00353 ( 9) link_BETA1-4 : angle 1.66098 ( 27) link_NAG-ASN : bond 0.00456 ( 48) link_NAG-ASN : angle 3.81828 ( 144) *********************** 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 : 0.993 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: 0.6392 time to fit residues: 332.9978 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 : 1.011 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 53 GLN A 130 GLN B 653 GLN B 658 GLN K 61 GLN K 62 ASN M 53 GLN M 79 GLN N 37 GLN C 130 GLN D 658 GLN O 100BGLN Q 53 GLN E 130 GLN E 197 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 653 GLN F 658 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.168600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.135968 restraints weight = 26148.686| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.67 r_work: 0.3382 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 25296 Z= 0.202 Angle : 0.674 7.269 34482 Z= 0.339 Chirality : 0.048 0.197 3951 Planarity : 0.004 0.055 4305 Dihedral : 6.972 62.539 4562 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.24 % Allowed : 14.73 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.15), residues: 3015 helix: -0.13 (0.25), residues: 453 sheet: 0.16 (0.15), residues: 1026 loop : -0.09 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 83 TYR 0.016 0.002 TYR I 96 PHE 0.020 0.002 PHE J 100H TRP 0.031 0.002 TRP E 427 HIS 0.005 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00477 (25191) covalent geometry : angle 0.64794 (34212) SS BOND : bond 0.00428 ( 45) SS BOND : angle 0.90621 ( 90) hydrogen bonds : bond 0.04451 ( 645) hydrogen bonds : angle 5.40270 ( 1683) link_ALPHA1-3 : bond 0.00855 ( 3) link_ALPHA1-3 : angle 1.61441 ( 9) link_BETA1-4 : bond 0.00334 ( 9) link_BETA1-4 : angle 1.92257 ( 27) link_NAG-ASN : bond 0.00383 ( 48) link_NAG-ASN : angle 2.75527 ( 144) *********************** 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 471 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 412 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 12 LYS cc_start: 0.8206 (mmmt) cc_final: 0.7787 (mmmt) REVERT: I 47 MET cc_start: 0.8731 (mmm) cc_final: 0.8497 (mmm) REVERT: A 151 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.6682 (ttp-170) REVERT: A 479 TRP cc_start: 0.7831 (m-10) cc_final: 0.7608 (m-10) REVERT: J 12 VAL cc_start: 0.8988 (m) cc_final: 0.8706 (p) REVERT: C 117 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7375 (mttp) REVERT: C 164 GLU cc_start: 0.8101 (pm20) cc_final: 0.7824 (pm20) REVERT: C 166 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.6686 (ttp80) REVERT: D 634 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7695 (mt-10) REVERT: O 23 ARG cc_start: 0.8239 (mmm160) cc_final: 0.7958 (mmm160) REVERT: O 46 GLU cc_start: 0.8824 (tt0) cc_final: 0.8487 (tt0) REVERT: O 100 TYR cc_start: 0.9179 (m-80) cc_final: 0.8928 (m-80) REVERT: P 12 LYS cc_start: 0.8374 (mmmt) cc_final: 0.8034 (mmmt) REVERT: P 23 LYS cc_start: 0.9009 (tptm) cc_final: 0.8700 (tptt) REVERT: P 46 GLU cc_start: 0.8598 (tt0) cc_final: 0.8356 (tt0) REVERT: E 95 MET cc_start: 0.8991 (ptm) cc_final: 0.8784 (ptm) REVERT: E 166 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7377 (mmp-170) REVERT: E 479 TRP cc_start: 0.7809 (m-10) cc_final: 0.7355 (m-10) REVERT: F 634 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7812 (mt-10) REVERT: F 647 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7463 (tm-30) REVERT: F 652 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7894 (mp10) outliers start: 59 outliers final: 28 residues processed: 446 average time/residue: 0.6244 time to fit residues: 321.2598 Evaluate side-chains 420 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 387 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 46 LYS Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 151 ARG 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 A residue 396 ILE Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain K residue 89 VAL 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 D residue 639 THR 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 Q residue 45 LYS Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 652 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 90 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 268 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 212 optimal weight: 5.9990 chunk 257 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 221 optimal weight: 1.9990 chunk 172 optimal weight: 0.0000 chunk 254 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 100BGLN I 69 ASN L 79 GLN B 653 GLN B 658 GLN K 61 GLN M 53 GLN M 69 ASN C 136 ASN D 653 GLN E 82 GLN F 577 GLN F 658 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.150680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.112536 restraints weight = 26334.103| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.88 r_work: 0.3101 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 25296 Z= 0.180 Angle : 0.620 8.446 34482 Z= 0.310 Chirality : 0.046 0.266 3951 Planarity : 0.004 0.035 4305 Dihedral : 5.976 43.628 4557 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.47 % Allowed : 15.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.15), residues: 3015 helix: -0.00 (0.25), residues: 459 sheet: 0.07 (0.15), residues: 1029 loop : 0.02 (0.16), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 83 TYR 0.016 0.001 TYR M 96 PHE 0.014 0.002 PHE E 353 TRP 0.022 0.002 TRP E 427 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00425 (25191) covalent geometry : angle 0.59316 (34212) SS BOND : bond 0.00432 ( 45) SS BOND : angle 0.98256 ( 90) hydrogen bonds : bond 0.04212 ( 645) hydrogen bonds : angle 5.15227 ( 1683) link_ALPHA1-3 : bond 0.00909 ( 3) link_ALPHA1-3 : angle 1.19718 ( 9) link_BETA1-4 : bond 0.00394 ( 9) link_BETA1-4 : angle 1.60314 ( 27) link_NAG-ASN : bond 0.00337 ( 48) link_NAG-ASN : angle 2.68792 ( 144) *********************** 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 477 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 412 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 12 LYS cc_start: 0.8042 (mmmt) cc_final: 0.7498 (mmmt) REVERT: H 23 LYS cc_start: 0.8850 (tptp) cc_final: 0.8529 (tptp) REVERT: A 91 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.6935 (tm-30) REVERT: A 479 TRP cc_start: 0.7783 (m-10) cc_final: 0.7536 (m-10) REVERT: B 538 THR cc_start: 0.9099 (m) cc_final: 0.8876 (p) REVERT: B 652 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7707 (mt0) REVERT: K 12 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7731 (mmtp) REVERT: K 21 SER cc_start: 0.8491 (p) cc_final: 0.8266 (t) REVERT: K 81 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7827 (tm-30) REVERT: C 117 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.7179 (mttp) REVERT: C 164 GLU cc_start: 0.7884 (pm20) cc_final: 0.7355 (pm20) REVERT: C 166 ARG cc_start: 0.7853 (mmp-170) cc_final: 0.6548 (ttp80) REVERT: C 440 GLN cc_start: 0.7619 (mp10) cc_final: 0.7360 (mp10) REVERT: C 479 TRP cc_start: 0.7624 (m-10) cc_final: 0.6927 (m-10) REVERT: D 647 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7791 (tm-30) REVERT: D 652 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7369 (mt0) REVERT: R 61 ARG cc_start: 0.5967 (mtp180) cc_final: 0.5152 (ttp-170) REVERT: E 95 MET cc_start: 0.9052 (ptm) cc_final: 0.8834 (ptm) REVERT: E 151 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.6773 (ttp-170) REVERT: E 232 LYS cc_start: 0.8377 (mtmt) cc_final: 0.8070 (mtmm) REVERT: E 479 TRP cc_start: 0.7753 (m-10) cc_final: 0.7226 (m-10) outliers start: 65 outliers final: 32 residues processed: 448 average time/residue: 0.6997 time to fit residues: 359.6596 Evaluate side-chains 437 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 398 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 L residue 105 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 434 MET 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 K residue 12 LYS Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 89 VAL 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 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 82 GLN Chi-restraints excluded: chain E residue 151 ARG 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 639 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 10 optimal weight: 0.3980 chunk 156 optimal weight: 3.9990 chunk 245 optimal weight: 0.1980 chunk 37 optimal weight: 4.9990 chunk 157 optimal weight: 0.9980 chunk 254 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 193 optimal weight: 0.9980 chunk 185 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 ASN I 69 ASN L 79 GLN A 315 GLN B 653 GLN B 658 GLN K 61 GLN ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 ASN D 653 GLN O 76 ASN E 67 ASN E 82 GLN F 577 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.151689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.114321 restraints weight = 26393.756| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.82 r_work: 0.3120 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1898 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= 0.134 Angle : 0.579 10.440 34482 Z= 0.291 Chirality : 0.044 0.210 3951 Planarity : 0.004 0.031 4305 Dihedral : 5.413 42.715 4557 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.92 % Favored : 98.01 % Rotamer: Outliers : 2.47 % Allowed : 17.31 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.15), residues: 3015 helix: 0.28 (0.26), residues: 435 sheet: 0.08 (0.15), residues: 1014 loop : 0.16 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 83 TYR 0.014 0.001 TYR M 96 PHE 0.012 0.001 PHE E 353 TRP 0.018 0.001 TRP A 427 HIS 0.003 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00311 (25191) covalent geometry : angle 0.55073 (34212) SS BOND : bond 0.00317 ( 45) SS BOND : angle 1.65320 ( 90) hydrogen bonds : bond 0.03887 ( 645) hydrogen bonds : angle 4.96269 ( 1683) link_ALPHA1-3 : bond 0.01129 ( 3) link_ALPHA1-3 : angle 1.06241 ( 9) link_BETA1-4 : bond 0.00393 ( 9) link_BETA1-4 : angle 1.50053 ( 27) link_NAG-ASN : bond 0.00340 ( 48) link_NAG-ASN : angle 2.46530 ( 144) *********************** 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 473 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 408 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.6957 (tm-30) REVERT: A 479 TRP cc_start: 0.7734 (m-10) cc_final: 0.7502 (m-10) REVERT: B 647 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7847 (tm-30) REVERT: B 652 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7665 (mt0) REVERT: K 21 SER cc_start: 0.8474 (p) cc_final: 0.8274 (t) REVERT: C 117 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.7035 (tppt) REVERT: C 164 GLU cc_start: 0.7834 (pm20) cc_final: 0.7479 (pm20) REVERT: C 166 ARG cc_start: 0.7869 (mmp-170) cc_final: 0.6575 (ttp80) REVERT: C 479 TRP cc_start: 0.7638 (m-10) cc_final: 0.6936 (m-10) REVERT: D 647 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7590 (tm-30) REVERT: D 652 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7254 (mt0) REVERT: O 34 MET cc_start: 0.8951 (mmm) cc_final: 0.8421 (mmt) REVERT: P 81 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7777 (tm-30) REVERT: Q 53 GLN cc_start: 0.8364 (mm110) cc_final: 0.7869 (mp10) REVERT: R 61 ARG cc_start: 0.5981 (mtp180) cc_final: 0.5132 (ttp-170) REVERT: E 91 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.7240 (tm-30) REVERT: E 95 MET cc_start: 0.9031 (ptm) cc_final: 0.8736 (ptm) REVERT: E 232 LYS cc_start: 0.8358 (mtmt) cc_final: 0.8055 (mtmm) REVERT: E 479 TRP cc_start: 0.7679 (m-10) cc_final: 0.7187 (m-10) outliers start: 65 outliers final: 35 residues processed: 446 average time/residue: 0.6931 time to fit residues: 354.4774 Evaluate side-chains 436 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 395 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 100 GLN Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain A residue 54 CYS 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 434 MET 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 82 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 C residue 117 LYS Chi-restraints excluded: chain C residue 158 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 28 THR Chi-restraints excluded: chain O residue 108 LEU 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 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 381 GLU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 639 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 40 optimal weight: 10.0000 chunk 177 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 278 optimal weight: 0.9980 chunk 161 optimal weight: 0.0040 chunk 218 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 ASN ** I 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN A 67 ASN B 658 GLN K 61 GLN ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 HIS D 653 GLN O 100BGLN E 173 HIS F 577 GLN F 652 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.149373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.111160 restraints weight = 26349.093| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.89 r_work: 0.3090 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 25296 Z= 0.188 Angle : 0.620 9.681 34482 Z= 0.310 Chirality : 0.045 0.192 3951 Planarity : 0.004 0.031 4305 Dihedral : 5.253 41.881 4557 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.16 % Favored : 97.78 % Rotamer: Outliers : 3.34 % Allowed : 16.67 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.15), residues: 3015 helix: 0.03 (0.25), residues: 465 sheet: 0.02 (0.15), residues: 987 loop : 0.05 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 83 TYR 0.018 0.001 TYR M 96 PHE 0.014 0.002 PHE E 353 TRP 0.018 0.002 TRP A 427 HIS 0.005 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00445 (25191) covalent geometry : angle 0.59014 (34212) SS BOND : bond 0.00400 ( 45) SS BOND : angle 1.71249 ( 90) hydrogen bonds : bond 0.04154 ( 645) hydrogen bonds : angle 4.97861 ( 1683) link_ALPHA1-3 : bond 0.01106 ( 3) link_ALPHA1-3 : angle 1.12706 ( 9) link_BETA1-4 : bond 0.00410 ( 9) link_BETA1-4 : angle 1.57806 ( 27) link_NAG-ASN : bond 0.00455 ( 48) link_NAG-ASN : angle 2.62679 ( 144) *********************** 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 492 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 404 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.6922 (tm-30) REVERT: A 95 MET cc_start: 0.9124 (ptm) cc_final: 0.8777 (ptm) REVERT: A 479 TRP cc_start: 0.7790 (m-10) cc_final: 0.7460 (m-10) REVERT: B 652 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7682 (mt0) REVERT: K 12 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7750 (mmtp) REVERT: K 81 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7864 (tm-30) REVERT: C 95 MET cc_start: 0.9159 (ptm) cc_final: 0.8861 (ptm) REVERT: C 102 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7826 (mm-30) REVERT: C 117 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.7078 (tppt) REVERT: C 166 ARG cc_start: 0.7816 (mmp-170) cc_final: 0.6510 (ttp80) REVERT: C 479 TRP cc_start: 0.7624 (m-10) cc_final: 0.6751 (m-10) REVERT: D 652 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7166 (mt0) REVERT: P 81 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7853 (tt0) REVERT: E 91 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7234 (tm-30) REVERT: E 95 MET cc_start: 0.9076 (ptm) cc_final: 0.8801 (ptm) REVERT: E 117 LYS cc_start: 0.7400 (ttmm) cc_final: 0.6998 (tppt) REVERT: E 232 LYS cc_start: 0.8383 (mtmt) cc_final: 0.8121 (mtmm) REVERT: E 479 TRP cc_start: 0.7769 (m-10) cc_final: 0.7129 (m-10) REVERT: F 652 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.8055 (mp10) outliers start: 88 outliers final: 46 residues processed: 460 average time/residue: 0.6950 time to fit residues: 366.5706 Evaluate side-chains 442 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 386 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 89 VAL Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 104 LEU 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 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 434 MET 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 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 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 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 108 LEU 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 48 ILE Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain R residue 5 THR 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 303 THR Chi-restraints excluded: chain E residue 321 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 193 optimal weight: 0.9980 chunk 227 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 201 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN ** I 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN B 653 GLN B 658 GLN K 61 GLN C 173 HIS 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 = 0.3637 r_free = 0.3637 target = 0.149453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.111315 restraints weight = 26448.487| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.89 r_work: 0.3087 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2242 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= 0.181 Angle : 0.605 8.257 34482 Z= 0.304 Chirality : 0.045 0.178 3951 Planarity : 0.004 0.035 4305 Dihedral : 5.161 42.647 4557 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.16 % Favored : 97.74 % Rotamer: Outliers : 3.23 % Allowed : 17.08 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.15), residues: 3015 helix: 0.13 (0.26), residues: 450 sheet: -0.01 (0.15), residues: 987 loop : 0.04 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 83 TYR 0.017 0.001 TYR M 96 PHE 0.014 0.002 PHE E 353 TRP 0.019 0.002 TRP A 427 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00429 (25191) covalent geometry : angle 0.57582 (34212) SS BOND : bond 0.00381 ( 45) SS BOND : angle 1.48302 ( 90) hydrogen bonds : bond 0.04083 ( 645) hydrogen bonds : angle 4.98680 ( 1683) link_ALPHA1-3 : bond 0.01059 ( 3) link_ALPHA1-3 : angle 1.09431 ( 9) link_BETA1-4 : bond 0.00395 ( 9) link_BETA1-4 : angle 1.52863 ( 27) link_NAG-ASN : bond 0.00435 ( 48) link_NAG-ASN : angle 2.66776 ( 144) *********************** 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 486 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 401 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.6929 (tm-30) REVERT: A 95 MET cc_start: 0.9127 (ptm) cc_final: 0.8788 (ptm) REVERT: A 211 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7076 (tp30) REVERT: A 479 TRP cc_start: 0.7761 (m-10) cc_final: 0.7394 (m-10) REVERT: B 652 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7704 (mt0) REVERT: K 81 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7919 (tm-30) REVERT: M 27 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7629 (p0) REVERT: C 95 MET cc_start: 0.9172 (ptm) cc_final: 0.8871 (ptm) REVERT: C 102 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7835 (mm-30) REVERT: C 117 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.6996 (tppt) REVERT: C 166 ARG cc_start: 0.7808 (mmp-170) cc_final: 0.6517 (ttp80) REVERT: C 269 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8156 (mt-10) REVERT: C 479 TRP cc_start: 0.7574 (m-10) cc_final: 0.6662 (m-10) REVERT: D 652 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7249 (mt0) REVERT: O 34 MET cc_start: 0.8971 (mmm) cc_final: 0.8524 (mmt) REVERT: P 81 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7864 (tt0) REVERT: Q 27 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7478 (p0) REVERT: E 91 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.7261 (tm-30) REVERT: E 95 MET cc_start: 0.9072 (ptm) cc_final: 0.8746 (ptm) REVERT: E 117 LYS cc_start: 0.7394 (ttmm) cc_final: 0.6986 (tppt) REVERT: E 191 TYR cc_start: 0.8773 (m-80) cc_final: 0.8545 (m-80) REVERT: E 232 LYS cc_start: 0.8381 (mtmt) cc_final: 0.8109 (mtmm) REVERT: E 236 THR cc_start: 0.8896 (m) cc_final: 0.8667 (p) REVERT: E 479 TRP cc_start: 0.7763 (m-10) cc_final: 0.7067 (m-10) outliers start: 85 outliers final: 56 residues processed: 459 average time/residue: 0.6335 time to fit residues: 334.9939 Evaluate side-chains 455 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 388 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 89 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 104 LEU 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 117 LYS 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 A residue 434 MET 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 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 27 ASP 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 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 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 77 THR Chi-restraints excluded: chain O residue 108 LEU 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 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 264 SER Chi-restraints excluded: chain E residue 269 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 260 optimal weight: 0.0270 chunk 279 optimal weight: 0.1980 chunk 98 optimal weight: 0.9990 chunk 265 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 202 optimal weight: 0.0070 chunk 127 optimal weight: 4.9990 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 79 GLN A 72 HIS A 283 ASN B 658 GLN K 61 GLN C 72 HIS P 39 GLN E 72 HIS F 577 GLN F 652 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.153455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.116344 restraints weight = 26344.530| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.84 r_work: 0.3150 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25296 Z= 0.095 Angle : 0.522 7.559 34482 Z= 0.263 Chirality : 0.042 0.167 3951 Planarity : 0.003 0.033 4305 Dihedral : 4.754 42.713 4557 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.92 % Favored : 97.94 % Rotamer: Outliers : 2.01 % Allowed : 18.94 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.15), residues: 3015 helix: 0.39 (0.26), residues: 456 sheet: 0.21 (0.15), residues: 972 loop : 0.19 (0.16), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 83 TYR 0.013 0.001 TYR M 96 PHE 0.011 0.001 PHE A 53 TRP 0.016 0.001 TRP A 427 HIS 0.002 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00210 (25191) covalent geometry : angle 0.49427 (34212) SS BOND : bond 0.00205 ( 45) SS BOND : angle 1.24127 ( 90) hydrogen bonds : bond 0.03399 ( 645) hydrogen bonds : angle 4.70948 ( 1683) link_ALPHA1-3 : bond 0.01108 ( 3) link_ALPHA1-3 : angle 1.10690 ( 9) link_BETA1-4 : bond 0.00476 ( 9) link_BETA1-4 : angle 1.33148 ( 27) link_NAG-ASN : bond 0.00313 ( 48) link_NAG-ASN : angle 2.42487 ( 144) *********************** 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 464 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 411 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 34 MET cc_start: 0.8941 (mmm) cc_final: 0.8722 (mmt) REVERT: A 91 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7002 (tm-30) REVERT: A 95 MET cc_start: 0.9165 (ptm) cc_final: 0.8845 (ptm) REVERT: A 211 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.6941 (tp30) REVERT: A 232 LYS cc_start: 0.8232 (mtmt) cc_final: 0.7556 (mmmm) REVERT: B 652 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7731 (mp10) REVERT: C 102 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7710 (mm-30) REVERT: C 117 LYS cc_start: 0.7270 (OUTLIER) cc_final: 0.6909 (tppt) REVERT: C 166 ARG cc_start: 0.7831 (mmp-170) cc_final: 0.6508 (ttp80) REVERT: C 479 TRP cc_start: 0.7529 (m-10) cc_final: 0.7104 (m-10) REVERT: D 647 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7185 (pp20) REVERT: D 652 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7110 (mt0) REVERT: O 34 MET cc_start: 0.8976 (mmm) cc_final: 0.8370 (mmt) REVERT: Q 27 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7462 (p0) REVERT: E 91 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.7238 (tm-30) REVERT: E 95 MET cc_start: 0.9034 (ptm) cc_final: 0.8750 (ptm) REVERT: E 117 LYS cc_start: 0.7351 (ttmm) cc_final: 0.6996 (tppt) REVERT: E 232 LYS cc_start: 0.8338 (mtmt) cc_final: 0.8088 (mtmm) REVERT: E 236 THR cc_start: 0.8826 (m) cc_final: 0.8594 (p) REVERT: E 479 TRP cc_start: 0.7657 (m-10) cc_final: 0.7188 (m-10) REVERT: F 647 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7613 (pp20) outliers start: 53 outliers final: 28 residues processed: 445 average time/residue: 0.6622 time to fit residues: 339.6060 Evaluate side-chains 428 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 392 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 110 THR 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 637 ASN Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain J residue 70 SER 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 381 GLU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain P residue 69 MET Chi-restraints excluded: chain Q residue 27 ASP Chi-restraints excluded: chain Q residue 48 ILE 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 11 optimal weight: 0.1980 chunk 210 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 124 optimal weight: 0.0010 chunk 288 optimal weight: 2.9990 chunk 284 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 242 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 79 GLN ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN B 658 GLN J 76 ASN K 32 HIS K 62 ASN P 39 GLN F 577 GLN ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.151174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.113792 restraints weight = 26385.295| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.83 r_work: 0.3118 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25296 Z= 0.141 Angle : 0.563 9.707 34482 Z= 0.282 Chirality : 0.044 0.159 3951 Planarity : 0.004 0.030 4305 Dihedral : 4.759 42.565 4557 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.92 % Favored : 97.91 % Rotamer: Outliers : 1.97 % Allowed : 19.29 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.15), residues: 3015 helix: 0.34 (0.26), residues: 456 sheet: 0.13 (0.15), residues: 993 loop : 0.25 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 83 TYR 0.014 0.001 TYR M 96 PHE 0.012 0.002 PHE E 353 TRP 0.014 0.001 TRP E 427 HIS 0.004 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00334 (25191) covalent geometry : angle 0.53519 (34212) SS BOND : bond 0.00320 ( 45) SS BOND : angle 1.35513 ( 90) hydrogen bonds : bond 0.03719 ( 645) hydrogen bonds : angle 4.77555 ( 1683) link_ALPHA1-3 : bond 0.01010 ( 3) link_ALPHA1-3 : angle 1.18257 ( 9) link_BETA1-4 : bond 0.00381 ( 9) link_BETA1-4 : angle 1.42573 ( 27) link_NAG-ASN : bond 0.00344 ( 48) link_NAG-ASN : angle 2.48435 ( 144) *********************** 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 451 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 399 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 27 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7713 (p0) REVERT: A 91 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.6973 (tm-30) REVERT: A 95 MET cc_start: 0.9176 (ptm) cc_final: 0.8848 (ptm) REVERT: A 211 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7026 (tp30) REVERT: A 479 TRP cc_start: 0.7645 (m-10) cc_final: 0.7094 (m-10) REVERT: B 647 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7827 (tm-30) REVERT: B 652 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7653 (mt0) REVERT: J 4 LEU cc_start: 0.8138 (mt) cc_final: 0.7930 (mt) REVERT: K 81 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7930 (tm-30) REVERT: C 102 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7725 (mm-30) REVERT: C 117 LYS cc_start: 0.7326 (mtmm) cc_final: 0.6935 (tppt) REVERT: C 166 ARG cc_start: 0.7821 (mmp-170) cc_final: 0.6511 (ttp80) REVERT: C 426 MET cc_start: 0.8180 (tpp) cc_final: 0.7719 (ttt) REVERT: C 479 TRP cc_start: 0.7609 (m-10) cc_final: 0.6795 (m-10) REVERT: D 652 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7228 (mt0) REVERT: O 23 ARG cc_start: 0.8012 (mmm160) cc_final: 0.7587 (mmm160) REVERT: O 34 MET cc_start: 0.8966 (mmm) cc_final: 0.8417 (mmt) REVERT: P 39 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.8802 (tt0) REVERT: P 80 MET cc_start: 0.8839 (tmm) cc_final: 0.8620 (ttp) REVERT: Q 27 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7465 (p0) REVERT: E 91 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7265 (tm-30) REVERT: E 95 MET cc_start: 0.9067 (ptm) cc_final: 0.8789 (ptm) REVERT: E 117 LYS cc_start: 0.7395 (ttmm) cc_final: 0.7004 (tppt) REVERT: E 168 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7326 (mptt) REVERT: E 232 LYS cc_start: 0.8347 (mtmt) cc_final: 0.8082 (mtmm) REVERT: E 236 THR cc_start: 0.8793 (m) cc_final: 0.8590 (p) REVERT: E 479 TRP cc_start: 0.7707 (m-10) cc_final: 0.7133 (m-10) outliers start: 52 outliers final: 31 residues processed: 436 average time/residue: 0.6670 time to fit residues: 334.7674 Evaluate side-chains 435 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 393 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain I residue 27 ASP 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 269 GLU Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain K residue 81 GLU 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 158 SER Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain P residue 39 GLN Chi-restraints excluded: chain Q residue 27 ASP 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 168 LYS 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 88 optimal weight: 0.0970 chunk 290 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 175 optimal weight: 0.6980 chunk 220 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 292 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 79 GLN ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN C 173 HIS C 283 ASN P 39 GLN F 577 GLN ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.149803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.111691 restraints weight = 26359.092| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.89 r_work: 0.3092 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 25296 Z= 0.175 Angle : 0.592 10.628 34482 Z= 0.297 Chirality : 0.045 0.161 3951 Planarity : 0.004 0.040 4305 Dihedral : 4.867 42.839 4557 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.09 % Favored : 97.71 % Rotamer: Outliers : 2.13 % Allowed : 19.29 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.15), residues: 3015 helix: 0.17 (0.26), residues: 462 sheet: 0.11 (0.15), residues: 981 loop : 0.24 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 83 TYR 0.016 0.001 TYR O 100F PHE 0.013 0.002 PHE A 353 TRP 0.016 0.002 TRP A 427 HIS 0.004 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00414 (25191) covalent geometry : angle 0.56401 (34212) SS BOND : bond 0.00380 ( 45) SS BOND : angle 1.42108 ( 90) hydrogen bonds : bond 0.03960 ( 645) hydrogen bonds : angle 4.88148 ( 1683) link_ALPHA1-3 : bond 0.00953 ( 3) link_ALPHA1-3 : angle 1.21098 ( 9) link_BETA1-4 : bond 0.00366 ( 9) link_BETA1-4 : angle 1.49338 ( 27) link_NAG-ASN : bond 0.00385 ( 48) link_NAG-ASN : angle 2.55824 ( 144) *********************** 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 450 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 394 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.6944 (tm-30) REVERT: A 211 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7118 (tp30) REVERT: A 232 LYS cc_start: 0.8233 (mtmt) cc_final: 0.7592 (mmtm) REVERT: A 479 TRP cc_start: 0.7755 (m-10) cc_final: 0.7153 (m-10) REVERT: B 652 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7827 (mp10) REVERT: J 4 LEU cc_start: 0.8162 (mt) cc_final: 0.7959 (mt) REVERT: K 81 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7953 (tm-30) REVERT: C 102 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7821 (mm-30) REVERT: C 117 LYS cc_start: 0.7354 (mtmm) cc_final: 0.6971 (tppt) REVERT: C 166 ARG cc_start: 0.7856 (mmp-170) cc_final: 0.6564 (ttp80) REVERT: C 232 LYS cc_start: 0.8066 (mtmm) cc_final: 0.7859 (mttp) REVERT: C 426 MET cc_start: 0.8211 (tpp) cc_final: 0.7796 (ttt) REVERT: C 479 TRP cc_start: 0.7591 (m-10) cc_final: 0.6788 (m-10) REVERT: D 652 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7287 (mt0) REVERT: O 23 ARG cc_start: 0.7981 (mmm160) cc_final: 0.7548 (mmm160) REVERT: Q 27 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7486 (p0) REVERT: E 91 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.7307 (tm-30) REVERT: E 95 MET cc_start: 0.9096 (ptm) cc_final: 0.8815 (ptm) REVERT: E 117 LYS cc_start: 0.7434 (ttmm) cc_final: 0.7041 (tppt) REVERT: E 479 TRP cc_start: 0.7766 (m-10) cc_final: 0.7118 (m-10) outliers start: 56 outliers final: 37 residues processed: 432 average time/residue: 0.6715 time to fit residues: 333.3227 Evaluate side-chains 435 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 390 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 110 THR 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 269 GLU Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain B residue 637 ASN 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 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 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 158 SER Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain Q residue 27 ASP 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 212 optimal weight: 5.9990 chunk 276 optimal weight: 0.5980 chunk 257 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 279 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN B 653 GLN B 658 GLN C 173 HIS D 652 GLN F 577 GLN ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.147150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.109454 restraints weight = 26493.101| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.87 r_work: 0.3043 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 25296 Z= 0.242 Angle : 0.666 11.711 34482 Z= 0.335 Chirality : 0.047 0.166 3951 Planarity : 0.005 0.044 4305 Dihedral : 5.235 43.448 4557 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.32 % Favored : 97.48 % Rotamer: Outliers : 2.09 % Allowed : 19.67 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.15), residues: 3015 helix: -0.05 (0.25), residues: 459 sheet: 0.07 (0.15), residues: 969 loop : 0.05 (0.16), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 83 TYR 0.020 0.002 TYR O 100F PHE 0.017 0.002 PHE C 383 TRP 0.019 0.002 TRP A 427 HIS 0.006 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00581 (25191) covalent geometry : angle 0.63703 (34212) SS BOND : bond 0.00506 ( 45) SS BOND : angle 1.62915 ( 90) hydrogen bonds : bond 0.04491 ( 645) hydrogen bonds : angle 5.16443 ( 1683) link_ALPHA1-3 : bond 0.00855 ( 3) link_ALPHA1-3 : angle 1.26997 ( 9) link_BETA1-4 : bond 0.00398 ( 9) link_BETA1-4 : angle 1.67759 ( 27) link_NAG-ASN : bond 0.00507 ( 48) link_NAG-ASN : angle 2.74875 ( 144) ********************** 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 451 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 396 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7032 (tm-30) REVERT: A 211 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7167 (tp30) REVERT: A 269 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8088 (mm-30) REVERT: A 479 TRP cc_start: 0.7771 (m-10) cc_final: 0.6679 (m-10) REVERT: B 652 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7834 (mp10) REVERT: J 4 LEU cc_start: 0.8163 (mt) cc_final: 0.7941 (mt) REVERT: K 81 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7897 (tm-30) REVERT: C 92 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8108 (tp30) REVERT: C 102 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7857 (mm-30) REVERT: C 117 LYS cc_start: 0.7360 (mtmm) cc_final: 0.6972 (tppt) REVERT: C 232 LYS cc_start: 0.8081 (mtmm) cc_final: 0.7612 (mmtp) REVERT: C 269 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8252 (mt-10) REVERT: C 426 MET cc_start: 0.8216 (tpp) cc_final: 0.7812 (ttt) REVERT: C 479 TRP cc_start: 0.7607 (m-10) cc_final: 0.6446 (m-10) REVERT: D 647 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7436 (pp20) REVERT: D 652 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7449 (mt0) REVERT: O 23 ARG cc_start: 0.7970 (mmm160) cc_final: 0.7533 (mmm160) REVERT: P 81 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7877 (tt0) REVERT: Q 27 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7427 (p0) REVERT: E 91 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.7147 (tm-30) REVERT: E 95 MET cc_start: 0.9086 (ptm) cc_final: 0.8828 (ptm) REVERT: E 117 LYS cc_start: 0.7442 (ttmm) cc_final: 0.7011 (tppt) REVERT: E 232 LYS cc_start: 0.8392 (mtmt) cc_final: 0.8118 (mtmm) REVERT: E 269 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8037 (mm-30) REVERT: E 479 TRP cc_start: 0.7880 (m-10) cc_final: 0.6866 (m-10) REVERT: F 647 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7944 (pp20) outliers start: 55 outliers final: 36 residues processed: 434 average time/residue: 0.6839 time to fit residues: 341.3079 Evaluate side-chains 425 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 378 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 77 THR 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 269 GLU Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 637 ASN 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 M residue 48 ILE 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 158 SER Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain P residue 81 GLU Chi-restraints excluded: chain Q residue 27 ASP 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 264 SER Chi-restraints excluded: chain E residue 269 GLU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 296 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 237 optimal weight: 2.9990 chunk 188 optimal weight: 0.7980 chunk 287 optimal weight: 0.9990 chunk 271 optimal weight: 0.9990 chunk 217 optimal weight: 0.0060 chunk 222 optimal weight: 1.9990 chunk 268 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- 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 652 GLN B 653 GLN B 658 GLN C 173 HIS D 652 GLN F 577 GLN ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.149802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.113099 restraints weight = 26437.648| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.79 r_work: 0.3106 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25296 Z= 0.135 Angle : 0.574 11.080 34482 Z= 0.289 Chirality : 0.044 0.166 3951 Planarity : 0.004 0.045 4305 Dihedral : 4.964 43.450 4557 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.06 % Favored : 97.74 % Rotamer: Outliers : 1.71 % Allowed : 20.05 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.15), residues: 3015 helix: 0.14 (0.26), residues: 453 sheet: 0.06 (0.15), residues: 987 loop : 0.19 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 83 TYR 0.012 0.001 TYR E 40 PHE 0.012 0.001 PHE E 353 TRP 0.020 0.001 TRP A 427 HIS 0.004 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00316 (25191) covalent geometry : angle 0.54529 (34212) SS BOND : bond 0.00311 ( 45) SS BOND : angle 1.35130 ( 90) hydrogen bonds : bond 0.03888 ( 645) hydrogen bonds : angle 4.96261 ( 1683) link_ALPHA1-3 : bond 0.00939 ( 3) link_ALPHA1-3 : angle 1.19906 ( 9) link_BETA1-4 : bond 0.00348 ( 9) link_BETA1-4 : angle 1.42922 ( 27) link_NAG-ASN : bond 0.00346 ( 48) link_NAG-ASN : angle 2.57564 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9959.85 seconds wall clock time: 170 minutes 27.99 seconds (10227.99 seconds total)