Starting phenix.real_space_refine on Sat Jun 21 01:46:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t4b_41026/06_2025/8t4b_41026.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t4b_41026/06_2025/8t4b_41026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t4b_41026/06_2025/8t4b_41026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t4b_41026/06_2025/8t4b_41026.map" model { file = "/net/cci-nas-00/data/ceres_data/8t4b_41026/06_2025/8t4b_41026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t4b_41026/06_2025/8t4b_41026.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.032 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 147 5.16 5 C 15429 2.51 5 N 4074 2.21 5 O 4875 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24525 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3445 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 21, 'TRANS': 412} Chain breaks: 4 Chain: "C" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "D" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 789 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "B" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 950 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "H" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 942 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 8, 'TRANS': 116} Chain: "L" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 96} Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: G, I, Q, R, K, J, E, F, O, P, V, X, M, N, U, W Time building chain proxies: 15.00, per 1000 atoms: 0.61 Number of scatterers: 24525 At special positions: 0 Unit cell: (142.6, 151.8, 174.8, 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 147 16.00 O 4875 8.00 N 4074 7.00 C 15429 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.05 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 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 C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.05 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.05 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.04 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS G 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS I 605 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 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 S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " ALPHA1-6 " BMA S 3 " - " MAN S 5 " " BMA U 3 " - " MAN U 5 " " BMA W 3 " - " MAN W 5 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG A 601 " - " ASN A 289 " " NAG A 602 " - " ASN A 301 " " NAG A 603 " - " ASN A 88 " " NAG A 604 " - " ASN A 156 " " NAG A 605 " - " ASN A 160 " " NAG A 606 " - " ASN A 197 " " NAG A 607 " - " ASN A 234 " " NAG A 608 " - " ASN A 276 " " NAG A 609 " - " ASN A 295 " " NAG A 610 " - " ASN A 339 " " NAG A 611 " - " ASN A 386 " " NAG A 612 " - " ASN A 448 " " NAG A 613 " - " ASN A 241 " " NAG B 701 " - " ASN B 611 " " NAG E 601 " - " ASN E 289 " " NAG E 602 " - " ASN E 301 " " NAG E 603 " - " ASN E 88 " " NAG E 604 " - " ASN E 156 " " NAG E 605 " - " ASN E 160 " " NAG E 606 " - " ASN E 197 " " NAG E 607 " - " ASN E 234 " " NAG E 608 " - " ASN E 276 " " NAG E 609 " - " ASN E 295 " " NAG E 610 " - " ASN E 339 " " NAG E 611 " - " ASN E 386 " " NAG E 612 " - " ASN E 448 " " NAG E 613 " - " ASN E 241 " " NAG F 601 " - " ASN F 289 " " NAG F 602 " - " ASN F 301 " " NAG F 603 " - " ASN F 88 " " NAG F 604 " - " ASN F 156 " " NAG F 605 " - " ASN F 160 " " NAG F 606 " - " ASN F 197 " " NAG F 607 " - " ASN F 234 " " NAG F 608 " - " ASN F 276 " " NAG F 609 " - " ASN F 295 " " NAG F 610 " - " ASN F 339 " " NAG F 611 " - " ASN F 386 " " NAG F 612 " - " ASN F 448 " " NAG F 613 " - " ASN F 241 " " NAG G 701 " - " ASN G 611 " " NAG I 701 " - " ASN I 611 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 262 " " NAG U 1 " - " ASN E 332 " " NAG V 1 " - " ASN E 262 " " NAG W 1 " - " ASN F 332 " " NAG X 1 " - " ASN F 262 " Time building additional restraints: 7.03 Conformation dependent library (CDL) restraints added in 3.4 seconds 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5562 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 48 sheets defined 19.6% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 194 through 199 removed outlier: 4.184A pdb=" N THR A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.681A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 391 removed outlier: 3.531A pdb=" N PHE A 391 " --> pdb=" O SER A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.157A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 484 removed outlier: 4.080A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 removed outlier: 4.058A pdb=" N GLU D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.423A 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: 3.665A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 595 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.582A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100B through 100F Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 194 through 199 removed outlier: 4.184A pdb=" N THR E 198 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.681A pdb=" N THR E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 391 removed outlier: 3.531A pdb=" N PHE E 391 " --> pdb=" O SER E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.157A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 484 removed outlier: 4.080A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 removed outlier: 4.057A pdb=" N GLU M 83 " --> pdb=" O ALA M 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 523 through 528 removed outlier: 4.423A pdb=" N GLY G 527 " --> pdb=" O GLY G 524 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 536 through 542 removed outlier: 3.665A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 595 Processing helix chain 'G' and resid 618 through 625 Processing helix chain 'G' and resid 627 through 635 removed outlier: 3.582A pdb=" N LYS G 633 " --> pdb=" O LEU G 629 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 661 Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'O' and resid 100B through 100F Processing helix chain 'Q' and resid 79 through 83 Processing helix chain 'F' and resid 96 through 98 No H-bonds generated for 'chain 'F' and resid 96 through 98' Processing helix chain 'F' and resid 99 through 117 Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 194 through 199 removed outlier: 4.184A pdb=" N THR F 198 " --> pdb=" O ILE F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 350 Processing helix chain 'F' and resid 351 through 353 No H-bonds generated for 'chain 'F' and resid 351 through 353' Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.681A pdb=" N THR F 373 " --> pdb=" O LEU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 391 removed outlier: 3.531A pdb=" N PHE F 391 " --> pdb=" O SER F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 429 removed outlier: 4.157A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 484 removed outlier: 4.080A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 4.057A pdb=" N GLU N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 523 through 528 removed outlier: 4.423A pdb=" N GLY I 527 " --> pdb=" O GLY I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 542 removed outlier: 3.665A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 573 through 595 Processing helix chain 'I' and resid 618 through 625 Processing helix chain 'I' and resid 627 through 635 removed outlier: 3.582A pdb=" N LYS I 633 " --> pdb=" O LEU I 629 " (cutoff:3.500A) Processing helix chain 'I' and resid 638 through 661 Processing helix chain 'P' and resid 28 through 32 Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'P' and resid 100B through 100F Processing helix chain 'R' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.185A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.813A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.725A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.381A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 7.077A pdb=" N ASN A 301 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 469 Processing sheet with id=AA8, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.842A pdb=" N GLY C 16 " --> pdb=" O SER C 82B" (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 34 through 39 removed outlier: 5.751A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 57 through 59 current: chain 'C' and resid 100H through 103 Processing sheet with id=AB1, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AB2, first strand: chain 'D' and resid 33 through 38 removed outlier: 6.468A pdb=" N TRP D 35 " --> pdb=" O MET D 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 45 through 48 current: chain 'D' and resid 95A through 98 Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'H' and resid 33 through 39 removed outlier: 6.580A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 102 through 103 Processing sheet with id=AB5, first strand: chain 'H' and resid 98 through 99 Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 10 through 12 current: chain 'L' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 53 through 54 current: chain 'L' and resid 97 through 98 Processing sheet with id=AB8, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.185A pdb=" N VAL G 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL E 38 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N THR G 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N TYR E 40 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N CYS G 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.812A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC2, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.725A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 172 through 177 Processing sheet with id=AC4, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.382A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 7.077A pdb=" N ASN E 301 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N VAL E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323 current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 465 through 469 Processing sheet with id=AC6, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.843A pdb=" N GLY J 16 " --> pdb=" O SER J 82B" (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 34 through 39 removed outlier: 5.750A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 100H through 103 Processing sheet with id=AC8, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=AC9, first strand: chain 'M' and resid 33 through 38 removed outlier: 6.469A pdb=" N TRP M 35 " --> pdb=" O MET M 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 45 through 48 current: chain 'M' and resid 95A through 98 Processing sheet with id=AD1, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'O' and resid 33 through 39 removed outlier: 6.580A pdb=" N TRP O 34 " --> pdb=" O TYR O 50 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TYR O 50 " --> pdb=" O TRP O 34 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 57 through 59 current: chain 'O' and resid 102 through 103 Processing sheet with id=AD3, first strand: chain 'O' and resid 98 through 99 Processing sheet with id=AD4, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'Q' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 10 through 12 current: chain 'Q' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 53 through 54 current: chain 'Q' and resid 97 through 98 Processing sheet with id=AD6, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.186A pdb=" N VAL I 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL F 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N THR I 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N TYR F 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N CYS I 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.813A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AD9, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.725A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 172 through 177 Processing sheet with id=AE2, first strand: chain 'F' and resid 201 through 203 removed outlier: 6.382A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 259 through 261 current: chain 'F' and resid 284 through 312 removed outlier: 7.077A pdb=" N ASN F 301 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N VAL F 323 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 315 through 323 current: chain 'F' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 381 through 385 current: chain 'F' and resid 465 through 469 Processing sheet with id=AE4, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.842A pdb=" N GLY K 16 " --> pdb=" O SER K 82B" (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 34 through 39 removed outlier: 5.751A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 57 through 59 current: chain 'K' and resid 100H through 103 Processing sheet with id=AE6, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AE7, first strand: chain 'N' and resid 33 through 38 removed outlier: 6.468A pdb=" N TRP N 35 " --> pdb=" O MET N 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 45 through 48 current: chain 'N' and resid 95A through 98 Processing sheet with id=AE8, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AE9, first strand: chain 'P' and resid 33 through 39 removed outlier: 6.580A pdb=" N TRP P 34 " --> pdb=" O TYR P 50 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR P 50 " --> pdb=" O TRP P 34 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TRP P 36 " --> pdb=" O ILE P 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 57 through 59 current: chain 'P' and resid 102 through 103 Processing sheet with id=AF1, first strand: chain 'P' and resid 98 through 99 Processing sheet with id=AF2, first strand: chain 'R' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'R' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 10 through 12 current: chain 'R' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 53 through 54 current: chain 'R' and resid 97 through 98 699 hydrogen bonds defined for protein. 1728 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: 9.03 Time building geometry restraints manager: 8.13 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: 7708 1.34 - 1.47: 6546 1.47 - 1.60: 10604 1.60 - 1.72: 0 1.72 - 1.85: 201 Bond restraints: 25059 Sorted by residual: bond pdb=" CG PRO Q 80 " pdb=" CD PRO Q 80 " ideal model delta sigma weight residual 1.503 1.303 0.200 3.40e-02 8.65e+02 3.47e+01 bond pdb=" CG PRO L 80 " pdb=" CD PRO L 80 " ideal model delta sigma weight residual 1.503 1.303 0.200 3.40e-02 8.65e+02 3.47e+01 bond pdb=" CG PRO R 80 " pdb=" CD PRO R 80 " ideal model delta sigma weight residual 1.503 1.303 0.200 3.40e-02 8.65e+02 3.46e+01 bond pdb=" CB CYS E 331 " pdb=" SG CYS E 331 " ideal model delta sigma weight residual 1.808 1.727 0.081 3.30e-02 9.18e+02 6.02e+00 bond pdb=" CB CYS F 331 " pdb=" SG CYS F 331 " ideal model delta sigma weight residual 1.808 1.727 0.081 3.30e-02 9.18e+02 6.00e+00 ... (remaining 25054 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 33076 2.83 - 5.67: 867 5.67 - 8.50: 71 8.50 - 11.34: 9 11.34 - 14.17: 3 Bond angle restraints: 34026 Sorted by residual: angle pdb=" CA PRO Q 80 " pdb=" N PRO Q 80 " pdb=" CD PRO Q 80 " ideal model delta sigma weight residual 112.00 97.83 14.17 1.40e+00 5.10e-01 1.03e+02 angle pdb=" CA PRO R 80 " pdb=" N PRO R 80 " pdb=" CD PRO R 80 " ideal model delta sigma weight residual 112.00 97.83 14.17 1.40e+00 5.10e-01 1.03e+02 angle pdb=" CA PRO L 80 " pdb=" N PRO L 80 " pdb=" CD PRO L 80 " ideal model delta sigma weight residual 112.00 97.86 14.14 1.40e+00 5.10e-01 1.02e+02 angle pdb=" N PRO L 80 " pdb=" CD PRO L 80 " pdb=" CG PRO L 80 " ideal model delta sigma weight residual 103.20 92.65 10.55 1.50e+00 4.44e-01 4.94e+01 angle pdb=" N PRO R 80 " pdb=" CD PRO R 80 " pdb=" CG PRO R 80 " ideal model delta sigma weight residual 103.20 92.66 10.54 1.50e+00 4.44e-01 4.93e+01 ... (remaining 34021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.53: 15054 21.53 - 43.06: 522 43.06 - 64.59: 144 64.59 - 86.12: 45 86.12 - 107.64: 27 Dihedral angle restraints: 15792 sinusoidal: 7092 harmonic: 8700 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 42.86 50.14 1 1.00e+01 1.00e-02 3.45e+01 dihedral pdb=" CB CYS O 22 " pdb=" SG CYS O 22 " pdb=" SG CYS O 92 " pdb=" CB CYS O 92 " ideal model delta sinusoidal sigma weight residual 93.00 42.88 50.12 1 1.00e+01 1.00e-02 3.45e+01 dihedral pdb=" CB CYS P 22 " pdb=" SG CYS P 22 " pdb=" SG CYS P 92 " pdb=" CB CYS P 92 " ideal model delta sinusoidal sigma weight residual 93.00 42.88 50.12 1 1.00e+01 1.00e-02 3.44e+01 ... (remaining 15789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.171: 3939 0.171 - 0.343: 30 0.343 - 0.514: 0 0.514 - 0.685: 3 0.685 - 0.857: 3 Chirality restraints: 3975 Sorted by residual: chirality pdb=" C1 NAG F 607 " pdb=" ND2 ASN F 234 " pdb=" C2 NAG F 607 " pdb=" O5 NAG F 607 " both_signs ideal model delta sigma weight residual False -2.40 -1.54 -0.86 2.00e-01 2.50e+01 1.83e+01 chirality pdb=" C1 NAG E 607 " pdb=" ND2 ASN E 234 " pdb=" C2 NAG E 607 " pdb=" O5 NAG E 607 " both_signs ideal model delta sigma weight residual False -2.40 -1.54 -0.86 2.00e-01 2.50e+01 1.83e+01 chirality pdb=" C1 NAG A 607 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A 607 " pdb=" O5 NAG A 607 " both_signs ideal model delta sigma weight residual False -2.40 -1.55 -0.85 2.00e-01 2.50e+01 1.82e+01 ... (remaining 3972 not shown) Planarity restraints: 4287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN R 79 " -0.099 5.00e-02 4.00e+02 1.38e-01 3.05e+01 pdb=" N PRO R 80 " 0.238 5.00e-02 4.00e+02 pdb=" CA PRO R 80 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO R 80 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN L 79 " -0.099 5.00e-02 4.00e+02 1.38e-01 3.05e+01 pdb=" N PRO L 80 " 0.238 5.00e-02 4.00e+02 pdb=" CA PRO L 80 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO L 80 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN Q 79 " -0.099 5.00e-02 4.00e+02 1.38e-01 3.04e+01 pdb=" N PRO Q 80 " 0.238 5.00e-02 4.00e+02 pdb=" CA PRO Q 80 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO Q 80 " -0.075 5.00e-02 4.00e+02 ... (remaining 4284 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3395 2.76 - 3.30: 22450 3.30 - 3.83: 39817 3.83 - 4.37: 48129 4.37 - 4.90: 82373 Nonbonded interactions: 196164 Sorted by model distance: nonbonded pdb=" NH2 ARG E 500 " pdb=" OG SER J 98 " model vdw 2.227 3.120 nonbonded pdb=" NH2 ARG A 500 " pdb=" OG SER C 98 " model vdw 2.228 3.120 nonbonded pdb=" NH2 ARG F 500 " pdb=" OG SER K 98 " model vdw 2.228 3.120 nonbonded pdb=" NH1 ARG R 61 " pdb=" O SER R 77 " model vdw 2.265 3.120 nonbonded pdb=" NH1 ARG L 61 " pdb=" O SER L 77 " model vdw 2.265 3.120 ... (remaining 196159 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.16 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'C' selection = chain 'K' selection = chain 'J' } ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'T' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'D' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'S' selection = chain 'U' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.480 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: 0.040 Extract box with map and model: 1.080 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 58.440 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.200 25173 Z= 0.293 Angle : 1.120 18.831 34323 Z= 0.599 Chirality : 0.065 0.857 3975 Planarity : 0.007 0.138 4239 Dihedral : 13.170 107.645 10095 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.34 % Allowed : 5.30 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.15), residues: 2973 helix: 0.56 (0.26), residues: 357 sheet: 0.80 (0.17), residues: 942 loop : 0.61 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP O 34 HIS 0.010 0.001 HIS F 374 PHE 0.054 0.004 PHE A 320 TYR 0.043 0.003 TYR H 50 ARG 0.005 0.001 ARG P 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 48) link_NAG-ASN : angle 3.90767 ( 144) link_ALPHA1-6 : bond 0.00471 ( 3) link_ALPHA1-6 : angle 1.13353 ( 9) link_BETA1-4 : bond 0.00487 ( 12) link_BETA1-4 : angle 2.15424 ( 36) link_ALPHA1-3 : bond 0.00305 ( 6) link_ALPHA1-3 : angle 2.54094 ( 18) hydrogen bonds : bond 0.14335 ( 699) hydrogen bonds : angle 6.19108 ( 1728) SS BOND : bond 0.00702 ( 45) SS BOND : angle 2.22366 ( 90) covalent geometry : bond 0.00694 (25059) covalent geometry : angle 1.08611 (34026) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 391 time to evaluate : 2.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 ASN cc_start: 0.8449 (t0) cc_final: 0.8187 (t0) REVERT: D 42 LYS cc_start: 0.7750 (mmmm) cc_final: 0.7516 (mtpt) REVERT: B 657 GLU cc_start: 0.8495 (tp30) cc_final: 0.8236 (mt-10) REVERT: H 72 ASP cc_start: 0.6771 (t0) cc_final: 0.6138 (t0) REVERT: H 75 GLU cc_start: 0.7777 (mp0) cc_final: 0.7367 (mp0) REVERT: E 434 MET cc_start: 0.8182 (ttt) cc_final: 0.7743 (ttt) REVERT: J 28 THR cc_start: 0.8789 (p) cc_final: 0.8406 (p) REVERT: J 72 ASP cc_start: 0.7981 (t0) cc_final: 0.7687 (t0) REVERT: M 50 ASP cc_start: 0.8358 (t70) cc_final: 0.7673 (t0) REVERT: M 91 TYR cc_start: 0.9006 (t80) cc_final: 0.8756 (t80) REVERT: O 72 ASP cc_start: 0.7105 (t0) cc_final: 0.6419 (t0) REVERT: O 75 GLU cc_start: 0.8047 (mp0) cc_final: 0.7455 (mp0) REVERT: Q 73 LEU cc_start: 0.8236 (tp) cc_final: 0.8023 (tp) REVERT: F 434 MET cc_start: 0.8261 (ttt) cc_final: 0.7794 (ttt) REVERT: K 28 THR cc_start: 0.8820 (p) cc_final: 0.8486 (p) REVERT: K 52 ASP cc_start: 0.8683 (p0) cc_final: 0.8362 (p0) REVERT: K 72 ASP cc_start: 0.7777 (t0) cc_final: 0.7496 (t0) REVERT: N 50 ASP cc_start: 0.8040 (t70) cc_final: 0.7741 (t0) REVERT: I 607 ASN cc_start: 0.8067 (m-40) cc_final: 0.7857 (m-40) REVERT: I 647 GLU cc_start: 0.7595 (tt0) cc_final: 0.7163 (tt0) REVERT: P 72 ASP cc_start: 0.6894 (t0) cc_final: 0.6114 (t0) REVERT: P 75 GLU cc_start: 0.8020 (mp0) cc_final: 0.7507 (mp0) REVERT: R 69 THR cc_start: 0.7586 (p) cc_final: 0.6986 (p) outliers start: 9 outliers final: 5 residues processed: 397 average time/residue: 0.4199 time to fit residues: 257.2963 Evaluate side-chains 260 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 255 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain F residue 88 ASN Chi-restraints excluded: chain F residue 188 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 4.9990 chunk 225 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 232 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 chunk 173 optimal weight: 0.6980 chunk 269 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN H 39 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 GLN O 39 GLN ** Q 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 GLN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.087267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.068360 restraints weight = 54426.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.070598 restraints weight = 31391.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.072054 restraints weight = 21861.485| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 25173 Z= 0.213 Angle : 0.690 13.230 34323 Z= 0.352 Chirality : 0.048 0.388 3975 Planarity : 0.005 0.048 4239 Dihedral : 9.501 82.815 4684 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.02 % Favored : 97.88 % Rotamer: Outliers : 1.37 % Allowed : 7.44 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.15), residues: 2973 helix: 1.91 (0.28), residues: 372 sheet: 0.97 (0.17), residues: 963 loop : 0.17 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 479 HIS 0.008 0.001 HIS A 374 PHE 0.031 0.003 PHE F 320 TYR 0.028 0.002 TYR R 49 ARG 0.008 0.001 ARG N 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00453 ( 48) link_NAG-ASN : angle 3.04746 ( 144) link_ALPHA1-6 : bond 0.00168 ( 3) link_ALPHA1-6 : angle 1.95984 ( 9) link_BETA1-4 : bond 0.00397 ( 12) link_BETA1-4 : angle 2.10893 ( 36) link_ALPHA1-3 : bond 0.00611 ( 6) link_ALPHA1-3 : angle 2.15662 ( 18) hydrogen bonds : bond 0.04554 ( 699) hydrogen bonds : angle 5.16971 ( 1728) SS BOND : bond 0.00386 ( 45) SS BOND : angle 1.17640 ( 90) covalent geometry : bond 0.00504 (25059) covalent geometry : angle 0.65467 (34026) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 267 time to evaluate : 2.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 THR cc_start: 0.8899 (p) cc_final: 0.8512 (p) REVERT: C 72 ASP cc_start: 0.8005 (t0) cc_final: 0.7803 (t0) REVERT: H 72 ASP cc_start: 0.6932 (t0) cc_final: 0.6590 (t0) REVERT: H 75 GLU cc_start: 0.7941 (mp0) cc_final: 0.7554 (mp0) REVERT: L 78 LEU cc_start: 0.8247 (tt) cc_final: 0.7951 (tt) REVERT: J 28 THR cc_start: 0.8733 (OUTLIER) cc_final: 0.8371 (p) REVERT: J 72 ASP cc_start: 0.8099 (t0) cc_final: 0.7888 (t0) REVERT: M 50 ASP cc_start: 0.8373 (t70) cc_final: 0.7724 (t0) REVERT: O 72 ASP cc_start: 0.7312 (t0) cc_final: 0.6779 (t0) REVERT: O 75 GLU cc_start: 0.7884 (mp0) cc_final: 0.7599 (mp0) REVERT: Q 78 LEU cc_start: 0.8140 (tt) cc_final: 0.7775 (tt) REVERT: F 434 MET cc_start: 0.8712 (ttt) cc_final: 0.8211 (ttt) REVERT: F 475 MET cc_start: 0.8358 (tpp) cc_final: 0.8157 (tpp) REVERT: K 28 THR cc_start: 0.8829 (OUTLIER) cc_final: 0.8408 (p) REVERT: K 72 ASP cc_start: 0.7944 (t0) cc_final: 0.7634 (t0) REVERT: N 50 ASP cc_start: 0.8194 (t70) cc_final: 0.7899 (t0) REVERT: I 607 ASN cc_start: 0.8247 (m-40) cc_final: 0.7976 (m-40) REVERT: P 72 ASP cc_start: 0.7155 (t0) cc_final: 0.6642 (t0) REVERT: P 75 GLU cc_start: 0.8017 (mp0) cc_final: 0.7640 (mp0) outliers start: 36 outliers final: 20 residues processed: 284 average time/residue: 0.3387 time to fit residues: 155.3301 Evaluate side-chains 252 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 230 time to evaluate : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain Q residue 23 CYS Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain R residue 94 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 164 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 286 optimal weight: 0.7980 chunk 258 optimal weight: 3.9990 chunk 282 optimal weight: 2.9990 chunk 43 optimal weight: 0.0370 chunk 179 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 269 optimal weight: 4.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN L 37 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN ** Q 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN R 37 GLN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.088072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.069309 restraints weight = 54057.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.071585 restraints weight = 30898.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.073062 restraints weight = 21419.784| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25173 Z= 0.122 Angle : 0.580 12.849 34323 Z= 0.292 Chirality : 0.044 0.335 3975 Planarity : 0.004 0.037 4239 Dihedral : 8.425 79.004 4674 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.37 % Allowed : 8.31 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.16), residues: 2973 helix: 2.42 (0.29), residues: 372 sheet: 0.76 (0.16), residues: 1011 loop : 0.14 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 47 HIS 0.006 0.001 HIS A 374 PHE 0.027 0.002 PHE A 320 TYR 0.023 0.001 TYR Q 49 ARG 0.006 0.000 ARG A 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00443 ( 48) link_NAG-ASN : angle 2.89068 ( 144) link_ALPHA1-6 : bond 0.00404 ( 3) link_ALPHA1-6 : angle 1.87570 ( 9) link_BETA1-4 : bond 0.00406 ( 12) link_BETA1-4 : angle 1.76801 ( 36) link_ALPHA1-3 : bond 0.00874 ( 6) link_ALPHA1-3 : angle 1.66755 ( 18) hydrogen bonds : bond 0.03613 ( 699) hydrogen bonds : angle 4.77445 ( 1728) SS BOND : bond 0.00302 ( 45) SS BOND : angle 0.93708 ( 90) covalent geometry : bond 0.00277 (25059) covalent geometry : angle 0.54364 (34026) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 275 time to evaluate : 2.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 THR cc_start: 0.8848 (p) cc_final: 0.8437 (p) REVERT: C 72 ASP cc_start: 0.7965 (t0) cc_final: 0.7697 (t0) REVERT: D 78 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8223 (mp) REVERT: H 3 GLN cc_start: 0.7530 (tm-30) cc_final: 0.7284 (tm-30) REVERT: H 72 ASP cc_start: 0.6933 (t0) cc_final: 0.6686 (t0) REVERT: H 75 GLU cc_start: 0.7884 (mp0) cc_final: 0.7518 (mp0) REVERT: L 78 LEU cc_start: 0.8391 (tt) cc_final: 0.8148 (tt) REVERT: J 28 THR cc_start: 0.8727 (p) cc_final: 0.8337 (p) REVERT: J 72 ASP cc_start: 0.8064 (t0) cc_final: 0.7805 (t0) REVERT: M 50 ASP cc_start: 0.8177 (t70) cc_final: 0.7583 (t0) REVERT: O 72 ASP cc_start: 0.7241 (t0) cc_final: 0.6614 (t0) REVERT: O 75 GLU cc_start: 0.7821 (mp0) cc_final: 0.7545 (mp0) REVERT: Q 78 LEU cc_start: 0.8364 (tt) cc_final: 0.8061 (tt) REVERT: F 426 MET cc_start: 0.8399 (mmm) cc_final: 0.8127 (mtp) REVERT: F 434 MET cc_start: 0.8641 (ttt) cc_final: 0.8189 (ttt) REVERT: F 475 MET cc_start: 0.8313 (tpp) cc_final: 0.8067 (tpp) REVERT: K 28 THR cc_start: 0.8876 (p) cc_final: 0.8443 (p) REVERT: K 72 ASP cc_start: 0.7927 (t0) cc_final: 0.7564 (t0) REVERT: N 50 ASP cc_start: 0.8224 (t70) cc_final: 0.7920 (t0) REVERT: I 607 ASN cc_start: 0.8271 (m-40) cc_final: 0.7994 (m-40) REVERT: P 72 ASP cc_start: 0.7129 (t0) cc_final: 0.6706 (t0) REVERT: P 75 GLU cc_start: 0.7926 (mp0) cc_final: 0.7569 (mp0) REVERT: R 78 LEU cc_start: 0.8329 (tt) cc_final: 0.8046 (tt) outliers start: 36 outliers final: 23 residues processed: 302 average time/residue: 0.3386 time to fit residues: 167.2275 Evaluate side-chains 264 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 240 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 616 ASN Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain Q residue 23 CYS Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain R residue 94 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 168 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 255 optimal weight: 0.1980 chunk 293 optimal weight: 10.0000 chunk 6 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 217 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN M 31 ASN Q 37 GLN Q 90 GLN R 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.087717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.068833 restraints weight = 55002.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.071073 restraints weight = 31525.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.072527 restraints weight = 21956.137| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25173 Z= 0.123 Angle : 0.577 12.750 34323 Z= 0.290 Chirality : 0.044 0.319 3975 Planarity : 0.003 0.037 4239 Dihedral : 7.904 77.024 4674 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.45 % Allowed : 9.00 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.16), residues: 2973 helix: 2.54 (0.29), residues: 372 sheet: 0.83 (0.17), residues: 984 loop : -0.01 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 47 HIS 0.005 0.001 HIS E 374 PHE 0.025 0.002 PHE A 320 TYR 0.024 0.001 TYR Q 49 ARG 0.004 0.000 ARG A 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 48) link_NAG-ASN : angle 2.79984 ( 144) link_ALPHA1-6 : bond 0.00426 ( 3) link_ALPHA1-6 : angle 1.91792 ( 9) link_BETA1-4 : bond 0.00381 ( 12) link_BETA1-4 : angle 1.77349 ( 36) link_ALPHA1-3 : bond 0.00903 ( 6) link_ALPHA1-3 : angle 1.83458 ( 18) hydrogen bonds : bond 0.03357 ( 699) hydrogen bonds : angle 4.59243 ( 1728) SS BOND : bond 0.01084 ( 45) SS BOND : angle 1.23702 ( 90) covalent geometry : bond 0.00279 (25059) covalent geometry : angle 0.54058 (34026) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 257 time to evaluate : 2.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 THR cc_start: 0.8831 (p) cc_final: 0.8398 (p) REVERT: C 72 ASP cc_start: 0.7976 (t0) cc_final: 0.7635 (t0) REVERT: D 78 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8314 (mp) REVERT: H 75 GLU cc_start: 0.7907 (mp0) cc_final: 0.7563 (mp0) REVERT: L 21 ILE cc_start: 0.8138 (mm) cc_final: 0.7932 (tp) REVERT: L 78 LEU cc_start: 0.8407 (tt) cc_final: 0.8140 (tt) REVERT: J 28 THR cc_start: 0.8738 (OUTLIER) cc_final: 0.8394 (p) REVERT: J 72 ASP cc_start: 0.8034 (t0) cc_final: 0.7749 (t0) REVERT: J 81 GLN cc_start: 0.7799 (tm-30) cc_final: 0.7418 (tm-30) REVERT: M 50 ASP cc_start: 0.8225 (t70) cc_final: 0.7650 (t0) REVERT: M 74 THR cc_start: 0.8096 (m) cc_final: 0.7377 (p) REVERT: O 72 ASP cc_start: 0.7255 (t0) cc_final: 0.6664 (t0) REVERT: O 75 GLU cc_start: 0.7837 (mp0) cc_final: 0.7561 (mp0) REVERT: F 426 MET cc_start: 0.8331 (mmm) cc_final: 0.8053 (mtp) REVERT: F 434 MET cc_start: 0.8689 (ttt) cc_final: 0.8222 (ttt) REVERT: F 475 MET cc_start: 0.8349 (tpp) cc_final: 0.8118 (tpp) REVERT: K 28 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8417 (p) REVERT: K 72 ASP cc_start: 0.8000 (t0) cc_final: 0.7588 (t0) REVERT: N 50 ASP cc_start: 0.8206 (t70) cc_final: 0.7946 (t0) REVERT: P 72 ASP cc_start: 0.7158 (t0) cc_final: 0.6787 (t0) REVERT: P 75 GLU cc_start: 0.7932 (mp0) cc_final: 0.7573 (mp0) REVERT: R 78 LEU cc_start: 0.8239 (tt) cc_final: 0.7968 (tt) outliers start: 38 outliers final: 21 residues processed: 285 average time/residue: 0.3224 time to fit residues: 150.5431 Evaluate side-chains 264 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 240 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 616 ASN Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain Q residue 23 CYS Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain R residue 94 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 52 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 140 optimal weight: 0.7980 chunk 163 optimal weight: 3.9990 chunk 195 optimal weight: 8.9990 chunk 280 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN A 302 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.084249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.065108 restraints weight = 55481.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.067230 restraints weight = 32285.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.068633 restraints weight = 22766.690| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 25173 Z= 0.255 Angle : 0.674 14.089 34323 Z= 0.339 Chirality : 0.047 0.323 3975 Planarity : 0.004 0.047 4239 Dihedral : 8.069 78.759 4674 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.41 % Allowed : 9.31 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.15), residues: 2973 helix: 2.21 (0.29), residues: 372 sheet: 0.54 (0.17), residues: 957 loop : -0.30 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 103 HIS 0.006 0.001 HIS E 330 PHE 0.031 0.002 PHE A 320 TYR 0.023 0.002 TYR Q 49 ARG 0.012 0.001 ARG A 139 Details of bonding type rmsd link_NAG-ASN : bond 0.00529 ( 48) link_NAG-ASN : angle 2.93716 ( 144) link_ALPHA1-6 : bond 0.00203 ( 3) link_ALPHA1-6 : angle 1.89022 ( 9) link_BETA1-4 : bond 0.00378 ( 12) link_BETA1-4 : angle 1.97126 ( 36) link_ALPHA1-3 : bond 0.00835 ( 6) link_ALPHA1-3 : angle 1.71392 ( 18) hydrogen bonds : bond 0.04182 ( 699) hydrogen bonds : angle 4.86535 ( 1728) SS BOND : bond 0.00545 ( 45) SS BOND : angle 1.62670 ( 90) covalent geometry : bond 0.00614 (25059) covalent geometry : angle 0.63881 (34026) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 253 time to evaluate : 2.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8446 (p) REVERT: C 72 ASP cc_start: 0.8108 (t0) cc_final: 0.7783 (t0) REVERT: D 95 THR cc_start: 0.8671 (OUTLIER) cc_final: 0.8405 (p) REVERT: H 75 GLU cc_start: 0.8228 (mp0) cc_final: 0.8009 (mp0) REVERT: L 21 ILE cc_start: 0.8182 (mm) cc_final: 0.7948 (tp) REVERT: L 90 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8021 (pp30) REVERT: L 93 ASP cc_start: 0.8354 (t0) cc_final: 0.8149 (t0) REVERT: J 28 THR cc_start: 0.8754 (OUTLIER) cc_final: 0.8274 (p) REVERT: M 50 ASP cc_start: 0.8413 (t70) cc_final: 0.7960 (t0) REVERT: M 74 THR cc_start: 0.8155 (m) cc_final: 0.7486 (p) REVERT: O 72 ASP cc_start: 0.7343 (t0) cc_final: 0.6720 (t0) REVERT: O 75 GLU cc_start: 0.7966 (mp0) cc_final: 0.7613 (mp0) REVERT: Q 78 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7773 (tt) REVERT: F 434 MET cc_start: 0.8697 (ttt) cc_final: 0.8250 (ttt) REVERT: K 28 THR cc_start: 0.8882 (OUTLIER) cc_final: 0.8462 (p) REVERT: K 72 ASP cc_start: 0.8089 (t0) cc_final: 0.7750 (t0) REVERT: K 97 MET cc_start: 0.8511 (ttm) cc_final: 0.8236 (ttm) REVERT: N 50 ASP cc_start: 0.8332 (t70) cc_final: 0.8082 (t0) REVERT: P 72 ASP cc_start: 0.7186 (t0) cc_final: 0.6771 (t0) REVERT: P 75 GLU cc_start: 0.7877 (mp0) cc_final: 0.7360 (mp0) outliers start: 37 outliers final: 24 residues processed: 275 average time/residue: 0.3379 time to fit residues: 152.9921 Evaluate side-chains 264 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 234 time to evaluate : 2.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 616 ASN Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain Q residue 23 CYS Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 52 ASP Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain R residue 94 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 157 optimal weight: 3.9990 chunk 266 optimal weight: 2.9990 chunk 213 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 283 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 214 optimal weight: 0.0670 chunk 100 optimal weight: 2.9990 chunk 232 optimal weight: 2.9990 chunk 201 optimal weight: 0.3980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.086270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.067366 restraints weight = 54339.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.069561 restraints weight = 31347.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.070978 restraints weight = 21914.041| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 25173 Z= 0.117 Angle : 0.577 12.962 34323 Z= 0.289 Chirality : 0.044 0.295 3975 Planarity : 0.003 0.034 4239 Dihedral : 7.723 75.815 4674 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.18 % Allowed : 10.03 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.15), residues: 2973 helix: 2.55 (0.29), residues: 372 sheet: 0.51 (0.17), residues: 936 loop : -0.23 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 479 HIS 0.005 0.001 HIS E 374 PHE 0.023 0.002 PHE F 320 TYR 0.024 0.001 TYR Q 49 ARG 0.004 0.000 ARG E 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00497 ( 48) link_NAG-ASN : angle 2.81793 ( 144) link_ALPHA1-6 : bond 0.00419 ( 3) link_ALPHA1-6 : angle 1.85811 ( 9) link_BETA1-4 : bond 0.00342 ( 12) link_BETA1-4 : angle 1.77073 ( 36) link_ALPHA1-3 : bond 0.00852 ( 6) link_ALPHA1-3 : angle 1.71136 ( 18) hydrogen bonds : bond 0.03374 ( 699) hydrogen bonds : angle 4.55318 ( 1728) SS BOND : bond 0.00596 ( 45) SS BOND : angle 1.32359 ( 90) covalent geometry : bond 0.00271 (25059) covalent geometry : angle 0.54008 (34026) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 253 time to evaluate : 2.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 52 ASP cc_start: 0.9037 (OUTLIER) cc_final: 0.8736 (p0) REVERT: C 72 ASP cc_start: 0.8041 (t0) cc_final: 0.7701 (t0) REVERT: D 95 THR cc_start: 0.8674 (p) cc_final: 0.8397 (p) REVERT: J 28 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8307 (p) REVERT: M 50 ASP cc_start: 0.8252 (t70) cc_final: 0.7768 (t0) REVERT: M 74 THR cc_start: 0.8139 (m) cc_final: 0.7441 (p) REVERT: O 72 ASP cc_start: 0.7302 (t0) cc_final: 0.6756 (t0) REVERT: O 75 GLU cc_start: 0.8006 (mp0) cc_final: 0.7726 (mp0) REVERT: Q 71 TYR cc_start: 0.8168 (m-80) cc_final: 0.7808 (m-10) REVERT: Q 78 LEU cc_start: 0.7998 (tp) cc_final: 0.7745 (tt) REVERT: F 426 MET cc_start: 0.8336 (mmm) cc_final: 0.8084 (mtp) REVERT: F 434 MET cc_start: 0.8673 (ttt) cc_final: 0.8215 (ttt) REVERT: K 28 THR cc_start: 0.8815 (OUTLIER) cc_final: 0.8362 (p) REVERT: K 72 ASP cc_start: 0.8025 (t0) cc_final: 0.7723 (t0) REVERT: K 97 MET cc_start: 0.8443 (ttm) cc_final: 0.8142 (ttm) REVERT: N 50 ASP cc_start: 0.8287 (t70) cc_final: 0.8038 (t0) REVERT: P 72 ASP cc_start: 0.7169 (t0) cc_final: 0.6809 (t0) REVERT: P 75 GLU cc_start: 0.7990 (mp0) cc_final: 0.7594 (mp0) REVERT: R 78 LEU cc_start: 0.8212 (tt) cc_final: 0.7960 (tt) outliers start: 31 outliers final: 22 residues processed: 272 average time/residue: 0.3594 time to fit residues: 161.9265 Evaluate side-chains 265 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 240 time to evaluate : 2.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain Q residue 23 CYS Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain I residue 621 GLU Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain R residue 94 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 217 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 163 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 213 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 167 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 200 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 202 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN E 170 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** P 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.085930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.066919 restraints weight = 54774.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.069108 restraints weight = 31616.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.070545 restraints weight = 22157.823| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 25173 Z= 0.132 Angle : 0.580 12.551 34323 Z= 0.290 Chirality : 0.044 0.294 3975 Planarity : 0.003 0.035 4239 Dihedral : 7.548 74.962 4674 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.22 % Allowed : 10.45 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.15), residues: 2973 helix: 2.26 (0.29), residues: 393 sheet: 0.56 (0.17), residues: 885 loop : -0.24 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP L 35 HIS 0.005 0.001 HIS E 374 PHE 0.025 0.002 PHE A 320 TYR 0.026 0.001 TYR D 91 ARG 0.004 0.000 ARG A 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00468 ( 48) link_NAG-ASN : angle 2.75981 ( 144) link_ALPHA1-6 : bond 0.00407 ( 3) link_ALPHA1-6 : angle 1.86105 ( 9) link_BETA1-4 : bond 0.00362 ( 12) link_BETA1-4 : angle 1.77261 ( 36) link_ALPHA1-3 : bond 0.00832 ( 6) link_ALPHA1-3 : angle 1.61357 ( 18) hydrogen bonds : bond 0.03328 ( 699) hydrogen bonds : angle 4.51706 ( 1728) SS BOND : bond 0.00594 ( 45) SS BOND : angle 1.30290 ( 90) covalent geometry : bond 0.00315 (25059) covalent geometry : angle 0.54536 (34026) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 257 time to evaluate : 2.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 52 ASP cc_start: 0.9062 (OUTLIER) cc_final: 0.8761 (p0) REVERT: C 72 ASP cc_start: 0.8049 (t0) cc_final: 0.7720 (t0) REVERT: D 95 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.8382 (p) REVERT: H 75 GLU cc_start: 0.8114 (mp0) cc_final: 0.7807 (pm20) REVERT: L 90 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7953 (pp30) REVERT: J 28 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8281 (p) REVERT: J 72 ASP cc_start: 0.8041 (t0) cc_final: 0.7753 (t0) REVERT: M 50 ASP cc_start: 0.8213 (t70) cc_final: 0.7723 (t0) REVERT: M 74 THR cc_start: 0.8167 (m) cc_final: 0.7474 (p) REVERT: O 72 ASP cc_start: 0.7323 (t0) cc_final: 0.6792 (t0) REVERT: O 75 GLU cc_start: 0.8021 (mp0) cc_final: 0.7748 (mp0) REVERT: O 86 ASP cc_start: 0.8733 (m-30) cc_final: 0.8259 (m-30) REVERT: Q 71 TYR cc_start: 0.8222 (m-80) cc_final: 0.7760 (m-80) REVERT: Q 78 LEU cc_start: 0.8030 (tp) cc_final: 0.7757 (tt) REVERT: F 426 MET cc_start: 0.8333 (mmm) cc_final: 0.8080 (mtp) REVERT: F 434 MET cc_start: 0.8696 (ttt) cc_final: 0.8235 (ttt) REVERT: K 28 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8370 (p) REVERT: K 72 ASP cc_start: 0.8027 (t0) cc_final: 0.7732 (t0) REVERT: K 97 MET cc_start: 0.8480 (ttm) cc_final: 0.8163 (ttm) REVERT: N 50 ASP cc_start: 0.8291 (t70) cc_final: 0.8045 (t0) REVERT: P 72 ASP cc_start: 0.7175 (t0) cc_final: 0.6797 (t0) REVERT: P 75 GLU cc_start: 0.8027 (mp0) cc_final: 0.7641 (mp0) REVERT: R 78 LEU cc_start: 0.8187 (tt) cc_final: 0.7939 (tt) outliers start: 32 outliers final: 22 residues processed: 277 average time/residue: 0.3416 time to fit residues: 155.1344 Evaluate side-chains 269 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 242 time to evaluate : 2.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain Q residue 23 CYS Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain I residue 621 GLU Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain R residue 94 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 227 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 chunk 277 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 210 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** P 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.085408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.066382 restraints weight = 54770.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.068557 restraints weight = 31783.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.069990 restraints weight = 22324.109| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 25173 Z= 0.158 Angle : 0.594 12.589 34323 Z= 0.297 Chirality : 0.044 0.293 3975 Planarity : 0.004 0.035 4239 Dihedral : 7.534 74.623 4674 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.45 % Allowed : 10.68 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.15), residues: 2973 helix: 2.22 (0.29), residues: 393 sheet: 0.50 (0.17), residues: 885 loop : -0.29 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP L 35 HIS 0.005 0.001 HIS E 330 PHE 0.024 0.002 PHE A 320 TYR 0.023 0.001 TYR Q 49 ARG 0.003 0.000 ARG A 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00468 ( 48) link_NAG-ASN : angle 2.75807 ( 144) link_ALPHA1-6 : bond 0.00354 ( 3) link_ALPHA1-6 : angle 1.87948 ( 9) link_BETA1-4 : bond 0.00327 ( 12) link_BETA1-4 : angle 1.79993 ( 36) link_ALPHA1-3 : bond 0.00777 ( 6) link_ALPHA1-3 : angle 1.59066 ( 18) hydrogen bonds : bond 0.03458 ( 699) hydrogen bonds : angle 4.55200 ( 1728) SS BOND : bond 0.00605 ( 45) SS BOND : angle 1.44228 ( 90) covalent geometry : bond 0.00380 (25059) covalent geometry : angle 0.55944 (34026) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 251 time to evaluate : 2.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 52 ASP cc_start: 0.9063 (OUTLIER) cc_final: 0.8749 (p0) REVERT: C 72 ASP cc_start: 0.8084 (t0) cc_final: 0.7755 (t0) REVERT: D 95 THR cc_start: 0.8713 (p) cc_final: 0.8443 (p) REVERT: L 90 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7922 (pp30) REVERT: J 28 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8289 (p) REVERT: J 72 ASP cc_start: 0.8024 (t0) cc_final: 0.7820 (t0) REVERT: M 50 ASP cc_start: 0.8144 (t70) cc_final: 0.7654 (t0) REVERT: M 74 THR cc_start: 0.8247 (m) cc_final: 0.7566 (p) REVERT: O 72 ASP cc_start: 0.7380 (t0) cc_final: 0.6821 (t0) REVERT: O 75 GLU cc_start: 0.8055 (mp0) cc_final: 0.7751 (mp0) REVERT: Q 71 TYR cc_start: 0.8179 (m-80) cc_final: 0.7707 (m-10) REVERT: Q 78 LEU cc_start: 0.8036 (tp) cc_final: 0.7788 (tt) REVERT: Q 90 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8181 (pp30) REVERT: F 426 MET cc_start: 0.8364 (mmm) cc_final: 0.8105 (mtp) REVERT: F 434 MET cc_start: 0.8668 (ttt) cc_final: 0.8210 (ttt) REVERT: K 28 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8388 (p) REVERT: K 72 ASP cc_start: 0.8055 (t0) cc_final: 0.7755 (t0) REVERT: K 97 MET cc_start: 0.8497 (ttm) cc_final: 0.8165 (ttm) REVERT: N 50 ASP cc_start: 0.8319 (t70) cc_final: 0.8068 (t0) REVERT: P 72 ASP cc_start: 0.7190 (t0) cc_final: 0.6811 (t0) REVERT: P 75 GLU cc_start: 0.8048 (mp0) cc_final: 0.7635 (mp0) REVERT: R 78 LEU cc_start: 0.8219 (tt) cc_final: 0.7956 (tt) outliers start: 38 outliers final: 30 residues processed: 272 average time/residue: 0.3380 time to fit residues: 149.6569 Evaluate side-chains 271 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 236 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain Q residue 23 CYS Chi-restraints excluded: chain Q residue 90 GLN Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 103 LYS Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 52 ASP Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain I residue 621 GLU Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain R residue 94 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 74 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 232 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 191 optimal weight: 2.9990 chunk 265 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 198 optimal weight: 0.3980 chunk 254 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 585 HIS F 170 GLN ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** P 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.085249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.066220 restraints weight = 54931.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.068389 restraints weight = 31852.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.069819 restraints weight = 22380.163| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 25173 Z= 0.159 Angle : 0.603 12.554 34323 Z= 0.300 Chirality : 0.044 0.289 3975 Planarity : 0.004 0.035 4239 Dihedral : 7.494 74.118 4674 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.30 % Allowed : 11.25 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.15), residues: 2973 helix: 2.20 (0.29), residues: 393 sheet: 0.48 (0.18), residues: 885 loop : -0.35 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP L 35 HIS 0.005 0.001 HIS E 330 PHE 0.031 0.002 PHE A 320 TYR 0.025 0.001 TYR D 91 ARG 0.004 0.000 ARG Q 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 48) link_NAG-ASN : angle 2.75095 ( 144) link_ALPHA1-6 : bond 0.00353 ( 3) link_ALPHA1-6 : angle 1.86483 ( 9) link_BETA1-4 : bond 0.00312 ( 12) link_BETA1-4 : angle 1.79519 ( 36) link_ALPHA1-3 : bond 0.00756 ( 6) link_ALPHA1-3 : angle 1.56460 ( 18) hydrogen bonds : bond 0.03461 ( 699) hydrogen bonds : angle 4.55567 ( 1728) SS BOND : bond 0.00601 ( 45) SS BOND : angle 1.42847 ( 90) covalent geometry : bond 0.00381 (25059) covalent geometry : angle 0.56849 (34026) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 251 time to evaluate : 2.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 52 ASP cc_start: 0.9046 (OUTLIER) cc_final: 0.8730 (p0) REVERT: C 72 ASP cc_start: 0.8112 (t0) cc_final: 0.7802 (t0) REVERT: D 95 THR cc_start: 0.8712 (p) cc_final: 0.8432 (p) REVERT: H 64 LYS cc_start: 0.8439 (mppt) cc_final: 0.8164 (mtmm) REVERT: H 75 GLU cc_start: 0.8624 (mp0) cc_final: 0.8412 (pm20) REVERT: L 90 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7966 (pp30) REVERT: J 28 THR cc_start: 0.8623 (OUTLIER) cc_final: 0.8270 (p) REVERT: J 72 ASP cc_start: 0.8035 (t0) cc_final: 0.7826 (t0) REVERT: M 50 ASP cc_start: 0.8153 (t70) cc_final: 0.7672 (t0) REVERT: M 74 THR cc_start: 0.8147 (m) cc_final: 0.7513 (p) REVERT: O 72 ASP cc_start: 0.7400 (t0) cc_final: 0.6854 (t0) REVERT: O 75 GLU cc_start: 0.8058 (mp0) cc_final: 0.7742 (mp0) REVERT: Q 71 TYR cc_start: 0.8154 (m-80) cc_final: 0.7676 (m-10) REVERT: Q 90 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8290 (pp30) REVERT: F 426 MET cc_start: 0.8419 (mmm) cc_final: 0.8136 (mtp) REVERT: F 434 MET cc_start: 0.8672 (ttt) cc_final: 0.8220 (ttt) REVERT: K 28 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8372 (p) REVERT: K 72 ASP cc_start: 0.8091 (t0) cc_final: 0.7801 (t0) REVERT: K 81 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7090 (tm-30) REVERT: K 97 MET cc_start: 0.8492 (ttm) cc_final: 0.8216 (ttm) REVERT: N 50 ASP cc_start: 0.8308 (t70) cc_final: 0.8067 (t0) REVERT: P 72 ASP cc_start: 0.7209 (t0) cc_final: 0.6797 (t0) REVERT: P 75 GLU cc_start: 0.7998 (mp0) cc_final: 0.7568 (mp0) REVERT: R 3 GLN cc_start: 0.7811 (mm-40) cc_final: 0.7574 (mm-40) REVERT: R 78 LEU cc_start: 0.8223 (tt) cc_final: 0.7972 (tt) outliers start: 34 outliers final: 26 residues processed: 271 average time/residue: 0.3204 time to fit residues: 142.5921 Evaluate side-chains 272 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 241 time to evaluate : 2.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain Q residue 23 CYS Chi-restraints excluded: chain Q residue 90 GLN Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 103 LYS Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 52 ASP Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain I residue 621 GLU Chi-restraints excluded: chain R residue 94 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 195 optimal weight: 10.0000 chunk 273 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 234 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 192 optimal weight: 1.9990 chunk 232 optimal weight: 2.9990 chunk 212 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 585 HIS ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** P 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.084751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.065674 restraints weight = 55223.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.067842 restraints weight = 32070.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.069260 restraints weight = 22561.271| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 25173 Z= 0.178 Angle : 0.620 12.598 34323 Z= 0.308 Chirality : 0.045 0.287 3975 Planarity : 0.004 0.035 4239 Dihedral : 7.501 73.873 4674 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.26 % Allowed : 11.44 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 2973 helix: 2.16 (0.29), residues: 393 sheet: 0.41 (0.18), residues: 885 loop : -0.41 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP L 35 HIS 0.006 0.001 HIS E 330 PHE 0.025 0.002 PHE A 320 TYR 0.023 0.001 TYR Q 49 ARG 0.003 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00480 ( 48) link_NAG-ASN : angle 2.76942 ( 144) link_ALPHA1-6 : bond 0.00329 ( 3) link_ALPHA1-6 : angle 1.85456 ( 9) link_BETA1-4 : bond 0.00307 ( 12) link_BETA1-4 : angle 1.81974 ( 36) link_ALPHA1-3 : bond 0.00728 ( 6) link_ALPHA1-3 : angle 1.55338 ( 18) hydrogen bonds : bond 0.03576 ( 699) hydrogen bonds : angle 4.60006 ( 1728) SS BOND : bond 0.00603 ( 45) SS BOND : angle 1.44404 ( 90) covalent geometry : bond 0.00427 (25059) covalent geometry : angle 0.58703 (34026) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 240 time to evaluate : 2.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 52 ASP cc_start: 0.9065 (OUTLIER) cc_final: 0.8744 (p0) REVERT: C 72 ASP cc_start: 0.8144 (t0) cc_final: 0.7838 (t0) REVERT: D 95 THR cc_start: 0.8724 (p) cc_final: 0.8444 (p) REVERT: L 90 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.7981 (pp30) REVERT: J 28 THR cc_start: 0.8580 (OUTLIER) cc_final: 0.8240 (p) REVERT: M 50 ASP cc_start: 0.8157 (t70) cc_final: 0.7689 (t0) REVERT: M 74 THR cc_start: 0.8159 (m) cc_final: 0.7531 (p) REVERT: O 72 ASP cc_start: 0.7380 (t0) cc_final: 0.6837 (t0) REVERT: O 75 GLU cc_start: 0.8035 (mp0) cc_final: 0.7713 (mp0) REVERT: Q 71 TYR cc_start: 0.8147 (m-80) cc_final: 0.7649 (m-10) REVERT: Q 90 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8308 (pp30) REVERT: F 95 MET cc_start: 0.8893 (ptm) cc_final: 0.8670 (ttp) REVERT: F 426 MET cc_start: 0.8436 (mmm) cc_final: 0.8138 (mtp) REVERT: F 434 MET cc_start: 0.8666 (ttt) cc_final: 0.8244 (ttt) REVERT: K 28 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8268 (p) REVERT: K 72 ASP cc_start: 0.8075 (t0) cc_final: 0.7789 (t0) REVERT: K 97 MET cc_start: 0.8524 (ttm) cc_final: 0.8251 (ttm) REVERT: N 50 ASP cc_start: 0.8323 (t70) cc_final: 0.8081 (t0) REVERT: P 72 ASP cc_start: 0.7232 (t0) cc_final: 0.6846 (t0) REVERT: P 75 GLU cc_start: 0.8058 (mp0) cc_final: 0.7565 (mp0) REVERT: R 3 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7751 (mm-40) REVERT: R 78 LEU cc_start: 0.8215 (tt) cc_final: 0.7960 (tt) outliers start: 33 outliers final: 25 residues processed: 260 average time/residue: 0.3334 time to fit residues: 143.6112 Evaluate side-chains 267 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 237 time to evaluate : 2.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain Q residue 23 CYS Chi-restraints excluded: chain Q residue 90 GLN Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 52 ASP Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain I residue 621 GLU Chi-restraints excluded: chain R residue 94 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 191 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 126 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 197 optimal weight: 0.8980 chunk 261 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 284 optimal weight: 3.9990 chunk 259 optimal weight: 0.9990 chunk 286 optimal weight: 2.9990 chunk 264 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 585 HIS ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** P 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.084810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.065797 restraints weight = 54924.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.067935 restraints weight = 31892.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.069356 restraints weight = 22484.392| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.163 25173 Z= 0.211 Angle : 0.741 59.185 34323 Z= 0.406 Chirality : 0.046 0.776 3975 Planarity : 0.004 0.081 4239 Dihedral : 7.491 73.879 4674 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.18 % Allowed : 11.71 % Favored : 87.11 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.15), residues: 2973 helix: 2.14 (0.29), residues: 393 sheet: 0.41 (0.18), residues: 885 loop : -0.41 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 35 HIS 0.005 0.001 HIS E 330 PHE 0.024 0.002 PHE A 320 TYR 0.022 0.001 TYR Q 49 ARG 0.005 0.000 ARG Q 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00479 ( 48) link_NAG-ASN : angle 2.76897 ( 144) link_ALPHA1-6 : bond 0.00371 ( 3) link_ALPHA1-6 : angle 1.88531 ( 9) link_BETA1-4 : bond 0.00375 ( 12) link_BETA1-4 : angle 1.80698 ( 36) link_ALPHA1-3 : bond 0.00793 ( 6) link_ALPHA1-3 : angle 1.58159 ( 18) hydrogen bonds : bond 0.03594 ( 699) hydrogen bonds : angle 4.60103 ( 1728) SS BOND : bond 0.00605 ( 45) SS BOND : angle 1.44067 ( 90) covalent geometry : bond 0.00474 (25059) covalent geometry : angle 0.71449 (34026) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7478.95 seconds wall clock time: 131 minutes 25.20 seconds (7885.20 seconds total)