Starting phenix.real_space_refine on Fri May 23 23:39:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t4a_41025/05_2025/8t4a_41025.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t4a_41025/05_2025/8t4a_41025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t4a_41025/05_2025/8t4a_41025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t4a_41025/05_2025/8t4a_41025.map" model { file = "/net/cci-nas-00/data/ceres_data/8t4a_41025/05_2025/8t4a_41025.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t4a_41025/05_2025/8t4a_41025.cif" } resolution = 3.4 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 150 5.16 5 C 15660 2.51 5 N 4152 2.21 5 O 4962 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24924 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3459 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 21, 'TRANS': 414} 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: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1019 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 788 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "S" 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: "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: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: E, F, G, I, J, K, M, N, O, P, Q, R, V, Y, W, Z, X, a Time building chain proxies: 13.52, per 1000 atoms: 0.54 Number of scatterers: 24924 At special positions: 0 Unit cell: (156.4, 147.2, 173.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 150 16.00 O 4962 8.00 N 4152 7.00 C 15660 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=2.00 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=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.00 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=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.00 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.00 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 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=2.00 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.00 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 J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 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=2.04 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.04 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 V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA Y 3 " - " MAN Y 4 " " BMA Z 3 " - " MAN Z 4 " 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 V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A 601 " - " ASN A 301 " " NAG A 602 " - " ASN A 88 " " NAG A 603 " - " ASN A 156 " " NAG A 604 " - " ASN A 160 " " NAG A 605 " - " ASN A 197 " " NAG A 606 " - " ASN A 234 " " NAG A 607 " - " ASN A 276 " " NAG A 608 " - " ASN A 295 " " NAG A 609 " - " ASN A 339 " " NAG A 610 " - " ASN A 448 " " NAG A 611 " - " ASN A 289 " " NAG A 612 " - " ASN A 241 " " NAG A 613 " - " ASN A 355 " " NAG A 614 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG E 601 " - " ASN E 301 " " NAG E 602 " - " ASN E 88 " " NAG E 603 " - " ASN E 156 " " NAG E 604 " - " ASN E 160 " " NAG E 605 " - " ASN E 197 " " NAG E 606 " - " ASN E 234 " " NAG E 607 " - " ASN E 276 " " NAG E 608 " - " ASN E 295 " " NAG E 609 " - " ASN E 339 " " NAG E 610 " - " ASN E 448 " " NAG E 611 " - " ASN E 289 " " NAG E 612 " - " ASN E 241 " " NAG E 613 " - " ASN E 355 " " NAG E 614 " - " ASN E 392 " " NAG F 601 " - " ASN F 301 " " NAG F 602 " - " ASN F 88 " " NAG F 603 " - " ASN F 156 " " NAG F 604 " - " ASN F 160 " " NAG F 605 " - " ASN F 197 " " NAG F 606 " - " ASN F 234 " " NAG F 607 " - " ASN F 276 " " NAG F 608 " - " ASN F 295 " " NAG F 609 " - " ASN F 339 " " NAG F 610 " - " ASN F 448 " " NAG F 611 " - " ASN F 289 " " NAG F 612 " - " ASN F 241 " " NAG F 613 " - " ASN F 355 " " NAG F 614 " - " ASN F 392 " " NAG G 701 " - " ASN G 611 " " NAG G 702 " - " ASN G 618 " " NAG G 703 " - " ASN G 637 " " NAG I 701 " - " ASN I 611 " " NAG I 702 " - " ASN I 618 " " NAG I 703 " - " ASN I 637 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 262 " " NAG U 1 " - " ASN A 386 " " NAG V 1 " - " ASN E 332 " " NAG W 1 " - " ASN E 262 " " NAG X 1 " - " ASN E 386 " " NAG Y 1 " - " ASN F 332 " " NAG Z 1 " - " ASN F 262 " " NAG a 1 " - " ASN F 386 " Time building additional restraints: 6.11 Conformation dependent library (CDL) restraints added in 3.0 seconds 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5622 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 63 sheets defined 18.4% alpha, 39.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.77 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.399A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 126 removed outlier: 3.513A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 123 through 126' Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.855A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.378A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.500A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.781A 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: 3.795A pdb=" N GLU D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 546 removed outlier: 3.639A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER B 546 " --> pdb=" O ARG B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.709A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100B through 100F Processing helix chain 'L' and resid 27 through 31 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.399A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 126 removed outlier: 3.513A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 123 through 126' Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.855A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.379A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.500A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.781A 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: 3.794A pdb=" N GLU M 83 " --> pdb=" O ALA M 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 536 through 546 removed outlier: 3.639A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU G 545 " --> pdb=" O ALA G 541 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER G 546 " --> pdb=" O ARG G 542 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 596 Processing helix chain 'G' and resid 618 through 626 removed outlier: 3.709A pdb=" N MET G 626 " --> pdb=" O ILE G 622 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 635 Processing helix chain 'G' and resid 638 through 662 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'O' and resid 100B through 100F Processing helix chain 'Q' and resid 27 through 31 Processing helix chain 'F' and resid 98 through 117 removed outlier: 4.399A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 126 removed outlier: 3.513A pdb=" N CYS F 126 " --> pdb=" O THR F 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 123 through 126' Processing helix chain 'F' and resid 195 through 198 Processing helix chain 'F' and resid 335 through 354 removed outlier: 3.855A pdb=" N HIS F 352 " --> pdb=" O GLN F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 425 through 429 removed outlier: 4.378A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 484 removed outlier: 3.500A pdb=" N TRP F 479 " --> pdb=" O MET F 475 " (cutoff:3.500A) removed outlier: 3.781A 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: 3.795A pdb=" N GLU N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 546 removed outlier: 3.639A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU I 545 " --> pdb=" O ALA I 541 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER I 546 " --> pdb=" O ARG I 542 " (cutoff:3.500A) Processing helix chain 'I' and resid 573 through 596 Processing helix chain 'I' and resid 618 through 626 removed outlier: 3.709A pdb=" N MET I 626 " --> pdb=" O ILE I 622 " (cutoff:3.500A) Processing helix chain 'I' and resid 627 through 635 Processing helix chain 'I' and resid 638 through 662 Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'P' and resid 100B through 100F Processing helix chain 'R' and resid 27 through 31 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.272A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.633A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.518A pdb=" N VAL A 120 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 172 through 177 Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 9.909A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.213A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.498A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.218A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.747A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.218A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.498A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.213A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.909A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 312 removed outlier: 6.887A pdb=" N ASN A 301 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N VAL A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 8 Processing sheet with id=AB2, first strand: chain 'C' and resid 57 through 59 removed outlier: 5.330A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 57 through 59 removed outlier: 5.330A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AB5, first strand: chain 'D' and resid 45 through 48 removed outlier: 6.303A pdb=" N TRP D 35 " --> pdb=" O MET D 47 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N PHE D 95B" --> pdb=" O ALA D 92 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 45 through 48 removed outlier: 6.303A pdb=" N TRP D 35 " --> pdb=" O MET D 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB8, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.689A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ARG H 50 " --> pdb=" O VAL H 35A" (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL H 35A" --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LYS H 96 " --> pdb=" O TYR H 100K" (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.689A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ARG H 50 " --> pdb=" O VAL H 35A" (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL H 35A" --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.561A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.561A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AC4, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.273A pdb=" N VAL G 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL E 38 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N THR G 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N TYR E 40 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N CYS G 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC6, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC7, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.633A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 120 through 121 removed outlier: 3.518A pdb=" N VAL E 120 " --> pdb=" O GLN E 203 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 172 through 177 Processing sheet with id=AD1, first strand: chain 'E' and resid 259 through 261 removed outlier: 9.910A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.214A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.498A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.346A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.219A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.747A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.219A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.346A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.498A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.214A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 301 through 312 removed outlier: 6.888A pdb=" N ASN E 301 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N VAL E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 3 through 8 Processing sheet with id=AD5, first strand: chain 'J' and resid 57 through 59 removed outlier: 5.330A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 57 through 59 removed outlier: 5.330A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=AD8, first strand: chain 'M' and resid 45 through 48 removed outlier: 6.303A pdb=" N TRP M 35 " --> pdb=" O MET M 47 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N PHE M 95B" --> pdb=" O ALA M 92 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 45 through 48 removed outlier: 6.303A pdb=" N TRP M 35 " --> pdb=" O MET M 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AE2, first strand: chain 'O' and resid 57 through 59 removed outlier: 6.689A pdb=" N TRP O 36 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ARG O 50 " --> pdb=" O VAL O 35A" (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL O 35A" --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LYS O 96 " --> pdb=" O TYR O 100K" (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 57 through 59 removed outlier: 6.689A pdb=" N TRP O 36 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ARG O 50 " --> pdb=" O VAL O 35A" (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL O 35A" --> pdb=" O ARG O 50 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 9 through 12 removed outlier: 6.561A pdb=" N VAL Q 11 " --> pdb=" O THR Q 105 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP Q 35 " --> pdb=" O VAL Q 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 9 through 12 removed outlier: 6.561A pdb=" N VAL Q 11 " --> pdb=" O THR Q 105 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 19 through 24 Processing sheet with id=AE7, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.273A pdb=" N VAL I 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL F 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N THR I 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N TYR F 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N CYS I 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AE9, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AF1, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.634A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 120 through 121 removed outlier: 3.518A pdb=" N VAL F 120 " --> pdb=" O GLN F 203 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 172 through 177 Processing sheet with id=AF4, first strand: chain 'F' and resid 259 through 261 removed outlier: 9.909A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.214A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.498A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.219A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA F 329 " --> pdb=" O CYS F 418 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 271 through 274 removed outlier: 6.746A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 10.219A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.498A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.214A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.909A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 301 through 312 removed outlier: 6.887A pdb=" N ASN F 301 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N VAL F 323 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 3 through 8 Processing sheet with id=AF8, first strand: chain 'K' and resid 57 through 59 removed outlier: 5.330A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 57 through 59 removed outlier: 5.330A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AG2, first strand: chain 'N' and resid 45 through 48 removed outlier: 6.303A pdb=" N TRP N 35 " --> pdb=" O MET N 47 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N PHE N 95B" --> pdb=" O ALA N 92 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 45 through 48 removed outlier: 6.303A pdb=" N TRP N 35 " --> pdb=" O MET N 47 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AG5, first strand: chain 'P' and resid 57 through 59 removed outlier: 6.689A pdb=" N TRP P 36 " --> pdb=" O LEU P 48 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ARG P 50 " --> pdb=" O VAL P 35A" (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL P 35A" --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LYS P 96 " --> pdb=" O TYR P 100K" (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'P' and resid 57 through 59 removed outlier: 6.689A pdb=" N TRP P 36 " --> pdb=" O LEU P 48 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ARG P 50 " --> pdb=" O VAL P 35A" (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL P 35A" --> pdb=" O ARG P 50 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'R' and resid 9 through 12 removed outlier: 6.561A pdb=" N VAL R 11 " --> pdb=" O THR R 105 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP R 35 " --> pdb=" O VAL R 47 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'R' and resid 9 through 12 removed outlier: 6.561A pdb=" N VAL R 11 " --> pdb=" O THR R 105 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'R' and resid 19 through 24 1080 hydrogen bonds defined for protein. 2727 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: 9.46 Time building geometry restraints manager: 7.09 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: 7654 1.34 - 1.46: 6465 1.46 - 1.59: 11120 1.59 - 1.71: 0 1.71 - 1.83: 210 Bond restraints: 25449 Sorted by residual: bond pdb=" CG LEU L 4 " pdb=" CD1 LEU L 4 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.68e+00 bond pdb=" CG LEU Q 4 " pdb=" CD1 LEU Q 4 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.68e+00 bond pdb=" CG LEU R 4 " pdb=" CD1 LEU R 4 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.63e+00 bond pdb=" CA ASP H 55 " pdb=" CB ASP H 55 " ideal model delta sigma weight residual 1.532 1.567 -0.035 1.43e-02 4.89e+03 5.91e+00 bond pdb=" CB VAL H 79 " pdb=" CG2 VAL H 79 " ideal model delta sigma weight residual 1.521 1.441 0.080 3.30e-02 9.18e+02 5.89e+00 ... (remaining 25444 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 32318 2.17 - 4.34: 1920 4.34 - 6.51: 268 6.51 - 8.67: 48 8.67 - 10.84: 6 Bond angle restraints: 34560 Sorted by residual: angle pdb=" CA ASP O 55 " pdb=" CB ASP O 55 " pdb=" CG ASP O 55 " ideal model delta sigma weight residual 112.60 117.73 -5.13 1.00e+00 1.00e+00 2.63e+01 angle pdb=" CA ASP H 55 " pdb=" CB ASP H 55 " pdb=" CG ASP H 55 " ideal model delta sigma weight residual 112.60 117.73 -5.13 1.00e+00 1.00e+00 2.63e+01 angle pdb=" CA ASP P 55 " pdb=" CB ASP P 55 " pdb=" CG ASP P 55 " ideal model delta sigma weight residual 112.60 117.72 -5.12 1.00e+00 1.00e+00 2.62e+01 angle pdb=" N THR P 31 " pdb=" CA THR P 31 " pdb=" C THR P 31 " ideal model delta sigma weight residual 112.12 105.63 6.49 1.34e+00 5.57e-01 2.34e+01 angle pdb=" N THR O 31 " pdb=" CA THR O 31 " pdb=" C THR O 31 " ideal model delta sigma weight residual 112.12 105.64 6.48 1.34e+00 5.57e-01 2.34e+01 ... (remaining 34555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.19: 15405 22.19 - 44.38: 546 44.38 - 66.57: 153 66.57 - 88.75: 51 88.75 - 110.94: 24 Dihedral angle restraints: 16179 sinusoidal: 7407 harmonic: 8772 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 158.66 -65.66 1 1.00e+01 1.00e-02 5.64e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 158.66 -65.66 1 1.00e+01 1.00e-02 5.64e+01 dihedral pdb=" CB CYS F 126 " pdb=" SG CYS F 126 " pdb=" SG CYS F 196 " pdb=" CB CYS F 196 " ideal model delta sinusoidal sigma weight residual 93.00 158.66 -65.66 1 1.00e+01 1.00e-02 5.64e+01 ... (remaining 16176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 3588 0.097 - 0.194: 471 0.194 - 0.291: 24 0.291 - 0.388: 6 0.388 - 0.485: 3 Chirality restraints: 4092 Sorted by residual: chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN A 386 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.88e+00 chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN F 386 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.86e+00 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN E 386 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.83e+00 ... (remaining 4089 not shown) Planarity restraints: 4341 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 476 " 0.023 2.00e-02 2.50e+03 4.59e-02 2.11e+01 pdb=" C ARG A 476 " -0.079 2.00e-02 2.50e+03 pdb=" O ARG A 476 " 0.030 2.00e-02 2.50e+03 pdb=" N ASP A 477 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 476 " -0.023 2.00e-02 2.50e+03 4.59e-02 2.11e+01 pdb=" C ARG F 476 " 0.079 2.00e-02 2.50e+03 pdb=" O ARG F 476 " -0.030 2.00e-02 2.50e+03 pdb=" N ASP F 477 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 476 " -0.023 2.00e-02 2.50e+03 4.57e-02 2.09e+01 pdb=" C ARG E 476 " 0.079 2.00e-02 2.50e+03 pdb=" O ARG E 476 " -0.029 2.00e-02 2.50e+03 pdb=" N ASP E 477 " -0.027 2.00e-02 2.50e+03 ... (remaining 4338 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4092 2.77 - 3.31: 22717 3.31 - 3.84: 40823 3.84 - 4.37: 48738 4.37 - 4.90: 82792 Nonbonded interactions: 199162 Sorted by model distance: nonbonded pdb=" NH2 ARG E 500 " pdb=" OG SER J 98 " model vdw 2.243 3.120 nonbonded pdb=" NH2 ARG F 500 " pdb=" OG SER K 98 " model vdw 2.243 3.120 nonbonded pdb=" NH2 ARG A 500 " pdb=" OG SER C 98 " model vdw 2.244 3.120 nonbonded pdb=" OD1 ASN L 27 " pdb=" OG SER L 30 " model vdw 2.244 3.040 nonbonded pdb=" OD1 ASN Q 27 " pdb=" OG SER Q 30 " model vdw 2.244 3.040 ... (remaining 199157 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain 'U' selection = chain 'X' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.880 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 53.610 Find NCS groups from input model: 1.250 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: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 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 0.091 25575 Z= 0.319 Angle : 1.294 52.146 34893 Z= 0.697 Chirality : 0.064 0.485 4092 Planarity : 0.007 0.046 4281 Dihedral : 13.266 110.943 10422 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.23 % Allowed : 4.30 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.15), residues: 2991 helix: 1.09 (0.24), residues: 393 sheet: 1.39 (0.17), residues: 924 loop : 0.61 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP O 100H HIS 0.015 0.002 HIS J 82A PHE 0.023 0.003 PHE R 62 TYR 0.024 0.003 TYR L 95B ARG 0.009 0.001 ARG E 139 Details of bonding type rmsd link_NAG-ASN : bond 0.00482 ( 60) link_NAG-ASN : angle 2.80924 ( 180) link_BETA1-4 : bond 0.00701 ( 15) link_BETA1-4 : angle 3.31728 ( 45) link_ALPHA1-3 : bond 0.00643 ( 6) link_ALPHA1-3 : angle 3.97668 ( 18) hydrogen bonds : bond 0.13325 ( 957) hydrogen bonds : angle 7.56354 ( 2727) SS BOND : bond 0.01201 ( 45) SS BOND : angle 10.71533 ( 90) covalent geometry : bond 0.00715 (25449) covalent geometry : angle 1.15184 (34560) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 435 time to evaluate : 2.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 MET cc_start: 0.8215 (mtm) cc_final: 0.7918 (mtm) REVERT: H 64 LYS cc_start: 0.7932 (mtpp) cc_final: 0.7679 (mttm) REVERT: L 27 ASN cc_start: 0.7741 (t0) cc_final: 0.7422 (t0) REVERT: L 54 ARG cc_start: 0.7167 (ttm110) cc_final: 0.6496 (mtp85) REVERT: L 58 ILE cc_start: 0.6773 (mm) cc_final: 0.6350 (mm) REVERT: L 92 ASP cc_start: 0.7074 (t0) cc_final: 0.6859 (t70) REVERT: J 87 THR cc_start: 0.8978 (m) cc_final: 0.8692 (p) REVERT: M 70 THR cc_start: 0.9443 (m) cc_final: 0.9196 (t) REVERT: M 79 GLN cc_start: 0.7208 (mp10) cc_final: 0.6949 (mp10) REVERT: O 64 LYS cc_start: 0.7672 (mtpp) cc_final: 0.7443 (mttm) REVERT: Q 2 TYR cc_start: 0.3510 (t80) cc_final: 0.2708 (t80) REVERT: Q 58 ILE cc_start: 0.6535 (mm) cc_final: 0.6069 (mm) REVERT: Q 92 ASP cc_start: 0.6843 (t0) cc_final: 0.6625 (t70) REVERT: Q 95 LYS cc_start: 0.8328 (mmmm) cc_final: 0.8062 (mmmm) REVERT: N 70 THR cc_start: 0.9453 (m) cc_final: 0.9184 (p) REVERT: P 52 TYR cc_start: 0.7882 (m-80) cc_final: 0.7644 (m-80) REVERT: P 71 LYS cc_start: 0.7446 (ttpt) cc_final: 0.6729 (pttm) REVERT: P 72 ASP cc_start: 0.8296 (t0) cc_final: 0.8043 (t70) REVERT: R 27 ASN cc_start: 0.7768 (t0) cc_final: 0.7352 (t0) REVERT: R 58 ILE cc_start: 0.6501 (mm) cc_final: 0.5997 (mm) REVERT: R 92 ASP cc_start: 0.7052 (t0) cc_final: 0.6705 (t70) REVERT: R 95 LYS cc_start: 0.8249 (mmmm) cc_final: 0.7894 (mmmm) outliers start: 6 outliers final: 2 residues processed: 441 average time/residue: 0.4174 time to fit residues: 274.9980 Evaluate side-chains 293 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 291 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain R residue 4 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 2.9990 chunk 225 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 151 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 232 optimal weight: 0.7980 chunk 90 optimal weight: 9.9990 chunk 141 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 269 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82BASN L 37 GLN J 3 GLN K 3 GLN P 82BASN ** R 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.096251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.069339 restraints weight = 62294.021| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 3.21 r_work: 0.3082 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 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 : 0.004 0.053 25575 Z= 0.182 Angle : 0.674 8.226 34893 Z= 0.349 Chirality : 0.047 0.228 4092 Planarity : 0.004 0.044 4281 Dihedral : 8.781 70.655 4957 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.51 % Allowed : 6.98 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.15), residues: 2991 helix: 2.53 (0.26), residues: 393 sheet: 1.25 (0.17), residues: 942 loop : 0.20 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 479 HIS 0.007 0.001 HIS K 82A PHE 0.015 0.002 PHE R 62 TYR 0.019 0.002 TYR K 27 ARG 0.005 0.001 ARG J 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00572 ( 60) link_NAG-ASN : angle 2.22215 ( 180) link_BETA1-4 : bond 0.00576 ( 15) link_BETA1-4 : angle 2.45144 ( 45) link_ALPHA1-3 : bond 0.01511 ( 6) link_ALPHA1-3 : angle 2.61783 ( 18) hydrogen bonds : bond 0.05040 ( 957) hydrogen bonds : angle 5.79581 ( 2727) SS BOND : bond 0.00384 ( 45) SS BOND : angle 0.98893 ( 90) covalent geometry : bond 0.00412 (25449) covalent geometry : angle 0.64781 (34560) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 329 time to evaluate : 2.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 MET cc_start: 0.8592 (mtm) cc_final: 0.8249 (mtm) REVERT: H 55 ASP cc_start: 0.7984 (t0) cc_final: 0.7747 (t0) REVERT: H 64 LYS cc_start: 0.8145 (mtpp) cc_final: 0.7875 (mttm) REVERT: L 27 ASN cc_start: 0.7823 (t0) cc_final: 0.7592 (t0) REVERT: L 46 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8283 (tt) REVERT: L 92 ASP cc_start: 0.6921 (t0) cc_final: 0.6686 (t70) REVERT: L 95 LYS cc_start: 0.8289 (mmmm) cc_final: 0.8076 (mmmm) REVERT: M 70 THR cc_start: 0.9539 (m) cc_final: 0.9318 (t) REVERT: M 79 GLN cc_start: 0.7058 (mp10) cc_final: 0.6567 (mp10) REVERT: O 43 LYS cc_start: 0.7358 (mttp) cc_final: 0.7016 (ptmm) REVERT: O 64 LYS cc_start: 0.8120 (mtpp) cc_final: 0.7837 (mttm) REVERT: O 82 MET cc_start: 0.6132 (OUTLIER) cc_final: 0.5856 (ttp) REVERT: Q 95 LYS cc_start: 0.8299 (mmmm) cc_final: 0.8075 (mmmm) REVERT: N 42 LYS cc_start: 0.7959 (mttm) cc_final: 0.7537 (ptmm) REVERT: N 95 THR cc_start: 0.8298 (m) cc_final: 0.8032 (t) REVERT: I 648 GLU cc_start: 0.8338 (tp30) cc_final: 0.8082 (tp30) REVERT: P 38 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7328 (ptp-170) REVERT: P 57 LYS cc_start: 0.8590 (mtpp) cc_final: 0.8376 (mtpp) REVERT: P 82 MET cc_start: 0.6736 (ttp) cc_final: 0.6312 (ttp) REVERT: P 82 ASN cc_start: 0.8440 (OUTLIER) cc_final: 0.8233 (t0) REVERT: P 96 LYS cc_start: 0.7358 (tttt) cc_final: 0.7099 (tttt) REVERT: R 27 ASN cc_start: 0.7662 (t0) cc_final: 0.7340 (t0) REVERT: R 92 ASP cc_start: 0.6933 (t0) cc_final: 0.6692 (t70) REVERT: R 95 LYS cc_start: 0.8291 (mmmm) cc_final: 0.8039 (mmmm) outliers start: 40 outliers final: 22 residues processed: 348 average time/residue: 0.4293 time to fit residues: 222.0218 Evaluate side-chains 301 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 275 time to evaluate : 2.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain O residue 91 TYR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 38 ARG Chi-restraints excluded: chain P residue 82 ASN Chi-restraints excluded: chain P residue 82 MET Chi-restraints excluded: chain P residue 91 TYR Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 218 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 158 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN D 6 GLN M 37 GLN R 17 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.094418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.066143 restraints weight = 62340.214| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.99 r_work: 0.3039 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 25575 Z= 0.198 Angle : 0.651 8.427 34893 Z= 0.334 Chirality : 0.047 0.385 4092 Planarity : 0.004 0.040 4281 Dihedral : 7.565 54.465 4953 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.00 % Allowed : 6.53 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.15), residues: 2991 helix: 2.44 (0.26), residues: 393 sheet: 1.26 (0.17), residues: 888 loop : -0.03 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 479 HIS 0.006 0.001 HIS K 82A PHE 0.015 0.002 PHE R 62 TYR 0.020 0.002 TYR O 100K ARG 0.008 0.001 ARG J 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00348 ( 60) link_NAG-ASN : angle 2.10892 ( 180) link_BETA1-4 : bond 0.00423 ( 15) link_BETA1-4 : angle 2.22232 ( 45) link_ALPHA1-3 : bond 0.01296 ( 6) link_ALPHA1-3 : angle 2.82829 ( 18) hydrogen bonds : bond 0.04628 ( 957) hydrogen bonds : angle 5.47652 ( 2727) SS BOND : bond 0.00459 ( 45) SS BOND : angle 0.90760 ( 90) covalent geometry : bond 0.00463 (25449) covalent geometry : angle 0.62606 (34560) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 305 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8953 (mp) REVERT: C 23 ARG cc_start: 0.8564 (tpp-160) cc_final: 0.8301 (ttm110) REVERT: H 55 ASP cc_start: 0.7921 (t0) cc_final: 0.7676 (t0) REVERT: H 64 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7806 (mttm) REVERT: H 82 ASN cc_start: 0.8430 (t0) cc_final: 0.8179 (t0) REVERT: L 92 ASP cc_start: 0.7462 (t0) cc_final: 0.7256 (t70) REVERT: L 95 LYS cc_start: 0.8407 (mmmm) cc_final: 0.8145 (mmmm) REVERT: E 161 MET cc_start: 0.8954 (tpp) cc_final: 0.8692 (tpt) REVERT: M 79 GLN cc_start: 0.7169 (mp10) cc_final: 0.6601 (mp10) REVERT: O 64 LYS cc_start: 0.8100 (mtpp) cc_final: 0.7711 (mttm) REVERT: O 82 MET cc_start: 0.7210 (mtp) cc_final: 0.6714 (mtp) REVERT: O 100 TYR cc_start: 0.7672 (t80) cc_final: 0.7446 (t80) REVERT: Q 92 ASP cc_start: 0.7673 (t70) cc_final: 0.6592 (p0) REVERT: Q 95 LYS cc_start: 0.8560 (mmmm) cc_final: 0.8186 (mmmt) REVERT: F 111 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8837 (mt) REVERT: K 75 LYS cc_start: 0.9283 (mtpp) cc_final: 0.8974 (mtmm) REVERT: P 5 LYS cc_start: 0.9331 (mttt) cc_final: 0.8794 (tptp) REVERT: P 57 LYS cc_start: 0.8549 (mtpp) cc_final: 0.8322 (mtpp) REVERT: R 27 ASN cc_start: 0.7662 (t0) cc_final: 0.7398 (t0) REVERT: R 36 TYR cc_start: 0.7999 (m-80) cc_final: 0.7379 (m-10) REVERT: R 92 ASP cc_start: 0.7279 (t0) cc_final: 0.7056 (t70) outliers start: 53 outliers final: 32 residues processed: 336 average time/residue: 0.4140 time to fit residues: 209.3464 Evaluate side-chains 305 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 271 time to evaluate : 2.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 91 TYR Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain I residue 544 LEU Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain I residue 657 GLU Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 38 ARG Chi-restraints excluded: chain P residue 82 MET Chi-restraints excluded: chain P residue 91 TYR Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 97 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 20 optimal weight: 1.9990 chunk 269 optimal weight: 1.9990 chunk 247 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 170 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 185 optimal weight: 9.9990 chunk 136 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN M 37 GLN ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.095840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.069398 restraints weight = 62977.410| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.27 r_work: 0.3083 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25575 Z= 0.187 Angle : 0.621 8.285 34893 Z= 0.316 Chirality : 0.046 0.248 4092 Planarity : 0.004 0.040 4281 Dihedral : 6.937 54.436 4953 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.77 % Allowed : 7.40 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.15), residues: 2991 helix: 2.43 (0.27), residues: 393 sheet: 1.30 (0.17), residues: 873 loop : -0.18 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 479 HIS 0.006 0.001 HIS K 82A PHE 0.015 0.002 PHE R 62 TYR 0.021 0.002 TYR H 100K ARG 0.007 0.001 ARG H 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00367 ( 60) link_NAG-ASN : angle 2.04063 ( 180) link_BETA1-4 : bond 0.00380 ( 15) link_BETA1-4 : angle 2.10053 ( 45) link_ALPHA1-3 : bond 0.01241 ( 6) link_ALPHA1-3 : angle 2.89877 ( 18) hydrogen bonds : bond 0.04308 ( 957) hydrogen bonds : angle 5.28791 ( 2727) SS BOND : bond 0.00375 ( 45) SS BOND : angle 0.87489 ( 90) covalent geometry : bond 0.00440 (25449) covalent geometry : angle 0.59665 (34560) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 299 time to evaluate : 2.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8616 (ttt180) REVERT: D 27 ASP cc_start: 0.8208 (p0) cc_final: 0.7998 (p0) REVERT: H 55 ASP cc_start: 0.7959 (t0) cc_final: 0.7727 (t0) REVERT: H 64 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7811 (mttm) REVERT: H 66 ARG cc_start: 0.8104 (mtp-110) cc_final: 0.7123 (ttm110) REVERT: H 82 MET cc_start: 0.6075 (ppp) cc_final: 0.5840 (ppp) REVERT: H 82 ASN cc_start: 0.8489 (t0) cc_final: 0.8056 (t0) REVERT: L 54 ARG cc_start: 0.7487 (ttm110) cc_final: 0.7022 (mmm-85) REVERT: L 92 ASP cc_start: 0.7272 (t0) cc_final: 0.7068 (t70) REVERT: L 95 LYS cc_start: 0.8355 (mmmm) cc_final: 0.8039 (mmmm) REVERT: M 79 GLN cc_start: 0.7243 (mp10) cc_final: 0.6748 (mp10) REVERT: O 64 LYS cc_start: 0.7937 (mtpp) cc_final: 0.7631 (mttm) REVERT: Q 95 LYS cc_start: 0.8424 (mmmm) cc_final: 0.8109 (mmmt) REVERT: F 151 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8475 (ttm-80) REVERT: P 5 LYS cc_start: 0.9296 (mttt) cc_final: 0.8821 (tptp) REVERT: P 57 LYS cc_start: 0.8466 (mtpp) cc_final: 0.8209 (mtpp) REVERT: R 27 ASN cc_start: 0.7609 (t0) cc_final: 0.7405 (t0) REVERT: R 36 TYR cc_start: 0.7845 (m-80) cc_final: 0.7288 (m-10) REVERT: R 92 ASP cc_start: 0.7107 (t0) cc_final: 0.6901 (t70) REVERT: R 95 LYS cc_start: 0.8406 (mmmm) cc_final: 0.8154 (mmmm) outliers start: 47 outliers final: 28 residues processed: 328 average time/residue: 0.4227 time to fit residues: 206.5073 Evaluate side-chains 290 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 260 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 91 TYR Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain F residue 151 ARG Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain I residue 544 LEU Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 91 TYR Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 84 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 240 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 218 optimal weight: 1.9990 chunk 263 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 279 optimal weight: 7.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 6 GLN N 6 GLN P 82BASN R 17 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.095344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.069071 restraints weight = 62448.737| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.20 r_work: 0.3083 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25575 Z= 0.172 Angle : 0.616 13.120 34893 Z= 0.310 Chirality : 0.046 0.348 4092 Planarity : 0.004 0.043 4281 Dihedral : 6.517 54.361 4953 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.43 % Allowed : 8.64 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.15), residues: 2991 helix: 2.48 (0.27), residues: 393 sheet: 1.32 (0.17), residues: 861 loop : -0.29 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 479 HIS 0.006 0.001 HIS K 82A PHE 0.013 0.002 PHE R 62 TYR 0.021 0.002 TYR H 100K ARG 0.008 0.001 ARG P 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00343 ( 60) link_NAG-ASN : angle 1.96024 ( 180) link_BETA1-4 : bond 0.00435 ( 15) link_BETA1-4 : angle 2.01388 ( 45) link_ALPHA1-3 : bond 0.01187 ( 6) link_ALPHA1-3 : angle 2.79736 ( 18) hydrogen bonds : bond 0.04124 ( 957) hydrogen bonds : angle 5.16859 ( 2727) SS BOND : bond 0.00407 ( 45) SS BOND : angle 0.84437 ( 90) covalent geometry : bond 0.00404 (25449) covalent geometry : angle 0.59310 (34560) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 270 time to evaluate : 2.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8588 (ttt180) REVERT: C 75 LYS cc_start: 0.9079 (mtpt) cc_final: 0.8878 (mttm) REVERT: H 5 LYS cc_start: 0.9229 (mttt) cc_final: 0.8734 (tptp) REVERT: H 55 ASP cc_start: 0.7937 (t0) cc_final: 0.7612 (t0) REVERT: H 66 ARG cc_start: 0.8246 (mtp-110) cc_final: 0.7374 (ttm110) REVERT: H 82 MET cc_start: 0.5863 (ppp) cc_final: 0.5056 (ppp) REVERT: H 82 ASN cc_start: 0.8655 (t0) cc_final: 0.8363 (t0) REVERT: L 92 ASP cc_start: 0.7299 (t0) cc_final: 0.7089 (t70) REVERT: L 95 LYS cc_start: 0.8331 (mmmm) cc_final: 0.8019 (mmmm) REVERT: M 17 GLN cc_start: 0.7842 (mm-40) cc_final: 0.7212 (pt0) REVERT: M 47 MET cc_start: 0.8958 (mmm) cc_final: 0.8688 (mmp) REVERT: M 79 GLN cc_start: 0.6970 (mp10) cc_final: 0.6531 (mp10) REVERT: O 46 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8163 (pt0) REVERT: O 64 LYS cc_start: 0.8002 (mtpp) cc_final: 0.7631 (mttm) REVERT: Q 54 ARG cc_start: 0.7281 (ttm110) cc_final: 0.6870 (ttm-80) REVERT: Q 95 LYS cc_start: 0.8380 (mmmm) cc_final: 0.8098 (mmmm) REVERT: F 151 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8507 (ttm-80) REVERT: P 43 LYS cc_start: 0.6925 (ptpp) cc_final: 0.6691 (ptmm) REVERT: P 57 LYS cc_start: 0.8439 (mtpp) cc_final: 0.8103 (mtpp) REVERT: P 66 ARG cc_start: 0.7769 (mtp-110) cc_final: 0.7552 (mtp-110) REVERT: P 82 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.8299 (t0) REVERT: R 27 ASN cc_start: 0.7643 (t0) cc_final: 0.7396 (t0) REVERT: R 36 TYR cc_start: 0.7830 (m-80) cc_final: 0.7260 (m-10) REVERT: R 92 ASP cc_start: 0.7112 (t0) cc_final: 0.6886 (t70) REVERT: R 95 LYS cc_start: 0.8464 (mmmm) cc_final: 0.8072 (mmmm) outliers start: 38 outliers final: 25 residues processed: 298 average time/residue: 0.4131 time to fit residues: 183.6111 Evaluate side-chains 274 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 246 time to evaluate : 2.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 91 TYR Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 151 ARG Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain I residue 544 LEU Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 82 ASN Chi-restraints excluded: chain P residue 91 TYR Chi-restraints excluded: chain R residue 47 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 202 optimal weight: 3.9990 chunk 62 optimal weight: 0.2980 chunk 79 optimal weight: 10.0000 chunk 182 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 chunk 96 optimal weight: 30.0000 chunk 84 optimal weight: 4.9990 chunk 267 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS ** J 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.092714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.065723 restraints weight = 62123.207| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.20 r_work: 0.3033 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 25575 Z= 0.273 Angle : 0.682 11.647 34893 Z= 0.343 Chirality : 0.047 0.234 4092 Planarity : 0.004 0.043 4281 Dihedral : 6.686 56.057 4953 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.85 % Allowed : 8.49 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.15), residues: 2991 helix: 2.15 (0.26), residues: 393 sheet: 1.17 (0.17), residues: 858 loop : -0.46 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 479 HIS 0.006 0.001 HIS K 82A PHE 0.017 0.002 PHE J 29 TYR 0.023 0.002 TYR H 100K ARG 0.008 0.001 ARG O 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 60) link_NAG-ASN : angle 2.05000 ( 180) link_BETA1-4 : bond 0.00397 ( 15) link_BETA1-4 : angle 2.12823 ( 45) link_ALPHA1-3 : bond 0.01120 ( 6) link_ALPHA1-3 : angle 2.78302 ( 18) hydrogen bonds : bond 0.04619 ( 957) hydrogen bonds : angle 5.27825 ( 2727) SS BOND : bond 0.00539 ( 45) SS BOND : angle 0.99051 ( 90) covalent geometry : bond 0.00650 (25449) covalent geometry : angle 0.65937 (34560) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 254 time to evaluate : 2.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8647 (ttt180) REVERT: C 75 LYS cc_start: 0.9068 (mtpt) cc_final: 0.8861 (mttm) REVERT: D 17 GLN cc_start: 0.7992 (mp10) cc_final: 0.7763 (mp10) REVERT: H 5 LYS cc_start: 0.9225 (mttt) cc_final: 0.8777 (tptp) REVERT: H 55 ASP cc_start: 0.7908 (t0) cc_final: 0.7573 (t0) REVERT: H 66 ARG cc_start: 0.8204 (mtp-110) cc_final: 0.7831 (mtp-110) REVERT: L 92 ASP cc_start: 0.7480 (t0) cc_final: 0.7200 (t70) REVERT: L 95 LYS cc_start: 0.8351 (mmmm) cc_final: 0.8057 (mmmm) REVERT: E 161 MET cc_start: 0.8861 (tpp) cc_final: 0.8591 (tpt) REVERT: M 17 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7902 (mp10) REVERT: M 79 GLN cc_start: 0.7088 (mp10) cc_final: 0.6647 (mp10) REVERT: O 64 LYS cc_start: 0.7982 (mtpp) cc_final: 0.7622 (mttm) REVERT: O 82 MET cc_start: 0.6239 (tmm) cc_final: 0.6004 (tmm) REVERT: F 151 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8618 (ttm-80) REVERT: P 57 LYS cc_start: 0.8396 (mtpp) cc_final: 0.8017 (mtpp) REVERT: P 66 ARG cc_start: 0.7893 (mtp-110) cc_final: 0.7668 (mtp-110) REVERT: P 82 ASN cc_start: 0.8359 (t0) cc_final: 0.7982 (t0) REVERT: R 27 ASN cc_start: 0.7660 (t0) cc_final: 0.7445 (t0) REVERT: R 36 TYR cc_start: 0.7931 (m-80) cc_final: 0.7272 (m-10) REVERT: R 95 LYS cc_start: 0.8464 (mmmm) cc_final: 0.8119 (mmmm) outliers start: 49 outliers final: 37 residues processed: 288 average time/residue: 0.4226 time to fit residues: 182.6442 Evaluate side-chains 278 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 239 time to evaluate : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 91 TYR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 151 ARG Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 91 TYR Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 85 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 4 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 194 optimal weight: 7.9990 chunk 201 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 170 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 172 optimal weight: 0.3980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 GLN ** J 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.093115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.066219 restraints weight = 62395.090| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 3.10 r_work: 0.3053 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 25575 Z= 0.212 Angle : 0.638 10.932 34893 Z= 0.323 Chirality : 0.046 0.234 4092 Planarity : 0.004 0.051 4281 Dihedral : 6.518 55.556 4953 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.66 % Allowed : 9.06 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.15), residues: 2991 helix: 2.26 (0.26), residues: 393 sheet: 1.27 (0.18), residues: 822 loop : -0.55 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 479 HIS 0.005 0.001 HIS K 82A PHE 0.012 0.001 PHE C 29 TYR 0.021 0.002 TYR L 95B ARG 0.006 0.000 ARG J 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00352 ( 60) link_NAG-ASN : angle 2.01635 ( 180) link_BETA1-4 : bond 0.00410 ( 15) link_BETA1-4 : angle 1.99804 ( 45) link_ALPHA1-3 : bond 0.01117 ( 6) link_ALPHA1-3 : angle 2.65380 ( 18) hydrogen bonds : bond 0.04268 ( 957) hydrogen bonds : angle 5.18204 ( 2727) SS BOND : bond 0.00466 ( 45) SS BOND : angle 0.90604 ( 90) covalent geometry : bond 0.00502 (25449) covalent geometry : angle 0.61597 (34560) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 252 time to evaluate : 2.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8642 (ttt180) REVERT: D 17 GLN cc_start: 0.8005 (mp10) cc_final: 0.7789 (mp10) REVERT: D 27 ASP cc_start: 0.8264 (p0) cc_final: 0.8047 (p0) REVERT: H 5 LYS cc_start: 0.9206 (mttt) cc_final: 0.8769 (tptp) REVERT: H 55 ASP cc_start: 0.7852 (t0) cc_final: 0.7550 (t0) REVERT: H 82 MET cc_start: 0.5733 (ppp) cc_final: 0.5385 (ppp) REVERT: L 54 ARG cc_start: 0.8078 (ttm-80) cc_final: 0.7706 (ttm-80) REVERT: L 95 LYS cc_start: 0.8364 (mmmm) cc_final: 0.8125 (mmmm) REVERT: M 79 GLN cc_start: 0.7246 (mp10) cc_final: 0.6820 (mp10) REVERT: O 64 LYS cc_start: 0.7928 (mtpp) cc_final: 0.7676 (mttm) REVERT: Q 20 ARG cc_start: 0.8116 (mmt90) cc_final: 0.7893 (mmt90) REVERT: Q 54 ARG cc_start: 0.7130 (ttm110) cc_final: 0.6763 (ttm-80) REVERT: F 151 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8569 (ttm-80) REVERT: F 161 MET cc_start: 0.8732 (tpp) cc_final: 0.8238 (tpt) REVERT: P 43 LYS cc_start: 0.6742 (ptpp) cc_final: 0.6373 (ptmm) REVERT: P 57 LYS cc_start: 0.8385 (mtpp) cc_final: 0.8176 (mtpp) REVERT: P 82 ASN cc_start: 0.8838 (t0) cc_final: 0.8530 (t0) REVERT: R 95 LYS cc_start: 0.8549 (mmmm) cc_final: 0.8295 (mmmm) outliers start: 44 outliers final: 34 residues processed: 283 average time/residue: 0.4227 time to fit residues: 178.0067 Evaluate side-chains 272 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 236 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 91 TYR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 151 ARG Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 91 TYR Chi-restraints excluded: chain R residue 70 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 159 optimal weight: 0.2980 chunk 44 optimal weight: 0.0670 chunk 123 optimal weight: 0.2980 chunk 176 optimal weight: 8.9990 chunk 291 optimal weight: 5.9990 chunk 277 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 234 optimal weight: 0.3980 chunk 268 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 overall best weight: 0.4120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN H 82BASN ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 GLN R 17 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.095366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.068411 restraints weight = 62373.172| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.23 r_work: 0.3092 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25575 Z= 0.112 Angle : 0.595 11.961 34893 Z= 0.301 Chirality : 0.044 0.257 4092 Planarity : 0.004 0.079 4281 Dihedral : 6.145 54.058 4953 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.32 % Allowed : 9.78 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.15), residues: 2991 helix: 2.57 (0.27), residues: 393 sheet: 1.34 (0.18), residues: 822 loop : -0.53 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 479 HIS 0.006 0.001 HIS K 82A PHE 0.011 0.001 PHE C 67 TYR 0.020 0.001 TYR K 27 ARG 0.019 0.001 ARG C 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 60) link_NAG-ASN : angle 1.89321 ( 180) link_BETA1-4 : bond 0.00397 ( 15) link_BETA1-4 : angle 1.88812 ( 45) link_ALPHA1-3 : bond 0.01124 ( 6) link_ALPHA1-3 : angle 2.53252 ( 18) hydrogen bonds : bond 0.03698 ( 957) hydrogen bonds : angle 5.02844 ( 2727) SS BOND : bond 0.00323 ( 45) SS BOND : angle 0.76589 ( 90) covalent geometry : bond 0.00247 (25449) covalent geometry : angle 0.57396 (34560) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 258 time to evaluate : 2.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8610 (ttt180) REVERT: C 72 ASP cc_start: 0.7625 (t0) cc_final: 0.7297 (t0) REVERT: C 75 LYS cc_start: 0.9164 (mttm) cc_final: 0.8928 (mttp) REVERT: H 5 LYS cc_start: 0.9195 (mttt) cc_final: 0.8778 (tptp) REVERT: H 55 ASP cc_start: 0.7913 (t0) cc_final: 0.7612 (t0) REVERT: M 47 MET cc_start: 0.8844 (mmm) cc_final: 0.8483 (mmm) REVERT: M 79 GLN cc_start: 0.7218 (mp10) cc_final: 0.6770 (mp10) REVERT: O 64 LYS cc_start: 0.7988 (mtpp) cc_final: 0.7673 (mttm) REVERT: O 66 ARG cc_start: 0.7914 (mtp-110) cc_final: 0.7288 (mtp-110) REVERT: Q 20 ARG cc_start: 0.8085 (mmt90) cc_final: 0.7876 (mmt90) REVERT: Q 54 ARG cc_start: 0.7122 (ttm110) cc_final: 0.6732 (ttm-80) REVERT: F 151 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8407 (ttm-80) REVERT: F 161 MET cc_start: 0.8715 (tpp) cc_final: 0.8194 (tpt) REVERT: P 43 LYS cc_start: 0.6836 (ptpp) cc_final: 0.6517 (ptmm) REVERT: P 57 LYS cc_start: 0.8350 (mtpp) cc_final: 0.8125 (mtpp) REVERT: P 66 ARG cc_start: 0.7723 (mtp-110) cc_final: 0.7458 (mtp-110) REVERT: P 82 ASN cc_start: 0.8800 (t0) cc_final: 0.8565 (t0) REVERT: R 95 LYS cc_start: 0.8470 (mmmm) cc_final: 0.8231 (mmmm) outliers start: 35 outliers final: 27 residues processed: 281 average time/residue: 0.4140 time to fit residues: 175.4362 Evaluate side-chains 263 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 234 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 91 TYR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 151 ARG Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain I residue 544 LEU Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 91 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 158 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 245 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 283 optimal weight: 20.0000 chunk 190 optimal weight: 0.3980 chunk 242 optimal weight: 0.0470 chunk 278 optimal weight: 9.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN H 82BASN O 82BASN ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN N 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.094978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.068184 restraints weight = 62087.341| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 3.18 r_work: 0.3093 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25575 Z= 0.119 Angle : 0.599 11.269 34893 Z= 0.303 Chirality : 0.044 0.253 4092 Planarity : 0.004 0.108 4281 Dihedral : 5.972 53.736 4953 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.62 % Allowed : 10.04 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.15), residues: 2991 helix: 2.50 (0.27), residues: 399 sheet: 1.31 (0.18), residues: 843 loop : -0.48 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 479 HIS 0.005 0.001 HIS K 82A PHE 0.013 0.001 PHE C 67 TYR 0.016 0.001 TYR H 100K ARG 0.016 0.001 ARG C 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 60) link_NAG-ASN : angle 1.83825 ( 180) link_BETA1-4 : bond 0.00407 ( 15) link_BETA1-4 : angle 1.89848 ( 45) link_ALPHA1-3 : bond 0.01020 ( 6) link_ALPHA1-3 : angle 2.41303 ( 18) hydrogen bonds : bond 0.03583 ( 957) hydrogen bonds : angle 4.95381 ( 2727) SS BOND : bond 0.00341 ( 45) SS BOND : angle 0.75626 ( 90) covalent geometry : bond 0.00269 (25449) covalent geometry : angle 0.57916 (34560) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 243 time to evaluate : 2.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8721 (ttt180) REVERT: H 55 ASP cc_start: 0.7966 (t0) cc_final: 0.7659 (t0) REVERT: J 66 ARG cc_start: 0.8647 (mtm110) cc_final: 0.8118 (mtm110) REVERT: M 47 MET cc_start: 0.8917 (mmm) cc_final: 0.8580 (mmm) REVERT: M 79 GLN cc_start: 0.7255 (mp10) cc_final: 0.6797 (mp10) REVERT: O 64 LYS cc_start: 0.7980 (mtpp) cc_final: 0.7700 (mttm) REVERT: Q 20 ARG cc_start: 0.8048 (mmt90) cc_final: 0.7831 (mmt90) REVERT: Q 54 ARG cc_start: 0.7121 (ttm110) cc_final: 0.6722 (ttm-80) REVERT: F 161 MET cc_start: 0.8762 (tpp) cc_final: 0.8316 (tpt) REVERT: N 47 MET cc_start: 0.8983 (mmm) cc_final: 0.8570 (mmm) REVERT: P 34 MET cc_start: 0.8255 (mtm) cc_final: 0.7889 (mtm) REVERT: P 66 ARG cc_start: 0.7982 (mtp-110) cc_final: 0.7745 (mtp-110) REVERT: P 82 ASN cc_start: 0.8876 (t0) cc_final: 0.8602 (t0) REVERT: R 95 LYS cc_start: 0.8571 (mmmm) cc_final: 0.8335 (mmmm) outliers start: 43 outliers final: 27 residues processed: 269 average time/residue: 0.4187 time to fit residues: 169.2594 Evaluate side-chains 263 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 235 time to evaluate : 2.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 91 TYR Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain I residue 544 LEU Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 91 TYR Chi-restraints excluded: chain R residue 85 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 295 optimal weight: 8.9990 chunk 159 optimal weight: 0.0270 chunk 81 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 241 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 266 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82BASN ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.095234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.068171 restraints weight = 62761.974| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.27 r_work: 0.3082 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25575 Z= 0.147 Angle : 0.606 11.262 34893 Z= 0.306 Chirality : 0.044 0.247 4092 Planarity : 0.004 0.095 4281 Dihedral : 5.920 54.342 4953 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.21 % Allowed : 10.27 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.15), residues: 2991 helix: 2.43 (0.27), residues: 399 sheet: 1.36 (0.18), residues: 831 loop : -0.53 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 479 HIS 0.005 0.001 HIS K 82A PHE 0.009 0.001 PHE C 67 TYR 0.018 0.002 TYR R 95B ARG 0.013 0.001 ARG C 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 60) link_NAG-ASN : angle 1.88181 ( 180) link_BETA1-4 : bond 0.00383 ( 15) link_BETA1-4 : angle 1.96231 ( 45) link_ALPHA1-3 : bond 0.00978 ( 6) link_ALPHA1-3 : angle 2.32783 ( 18) hydrogen bonds : bond 0.03713 ( 957) hydrogen bonds : angle 4.94483 ( 2727) SS BOND : bond 0.00385 ( 45) SS BOND : angle 0.77759 ( 90) covalent geometry : bond 0.00343 (25449) covalent geometry : angle 0.58585 (34560) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 244 time to evaluate : 2.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8660 (ttt180) REVERT: C 72 ASP cc_start: 0.7582 (t0) cc_final: 0.7069 (t0) REVERT: C 75 LYS cc_start: 0.9123 (mtpt) cc_final: 0.8733 (mttp) REVERT: D 27 ASP cc_start: 0.8296 (p0) cc_final: 0.8068 (p0) REVERT: H 55 ASP cc_start: 0.7776 (t0) cc_final: 0.7463 (t0) REVERT: M 47 MET cc_start: 0.8875 (mmm) cc_final: 0.8530 (mmm) REVERT: M 79 GLN cc_start: 0.7236 (mp10) cc_final: 0.6812 (mp10) REVERT: O 64 LYS cc_start: 0.7986 (mtpp) cc_final: 0.7707 (mttm) REVERT: Q 20 ARG cc_start: 0.8103 (mmt90) cc_final: 0.7885 (mmt90) REVERT: Q 54 ARG cc_start: 0.7019 (ttm110) cc_final: 0.6631 (ttm-80) REVERT: P 34 MET cc_start: 0.7971 (mtm) cc_final: 0.7609 (mtm) REVERT: P 66 ARG cc_start: 0.7978 (mtp-110) cc_final: 0.7741 (mtp-110) REVERT: P 82 ASN cc_start: 0.8851 (t0) cc_final: 0.8556 (t0) outliers start: 32 outliers final: 28 residues processed: 266 average time/residue: 0.4174 time to fit residues: 167.5139 Evaluate side-chains 265 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 236 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 91 TYR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 91 TYR Chi-restraints excluded: chain R residue 85 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 11 optimal weight: 3.9990 chunk 227 optimal weight: 0.6980 chunk 274 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 275 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN H 82BASN E 170 GLN ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 54 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.094675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.067856 restraints weight = 62006.887| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 3.17 r_work: 0.3092 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25575 Z= 0.138 Angle : 0.605 10.905 34893 Z= 0.305 Chirality : 0.044 0.253 4092 Planarity : 0.004 0.079 4281 Dihedral : 5.805 54.450 4953 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.28 % Allowed : 10.34 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.15), residues: 2991 helix: 2.47 (0.27), residues: 399 sheet: 1.37 (0.18), residues: 831 loop : -0.54 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 479 HIS 0.005 0.001 HIS K 82A PHE 0.010 0.001 PHE R 98 TYR 0.023 0.001 TYR O 58 ARG 0.012 0.001 ARG H 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 60) link_NAG-ASN : angle 1.89139 ( 180) link_BETA1-4 : bond 0.00370 ( 15) link_BETA1-4 : angle 1.96707 ( 45) link_ALPHA1-3 : bond 0.00928 ( 6) link_ALPHA1-3 : angle 2.25976 ( 18) hydrogen bonds : bond 0.03633 ( 957) hydrogen bonds : angle 4.91716 ( 2727) SS BOND : bond 0.00371 ( 45) SS BOND : angle 0.77299 ( 90) covalent geometry : bond 0.00321 (25449) covalent geometry : angle 0.58418 (34560) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11452.62 seconds wall clock time: 199 minutes 44.25 seconds (11984.25 seconds total)