Starting phenix.real_space_refine on Thu May 22 15:16:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d8y_46653/05_2025/9d8y_46653.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d8y_46653/05_2025/9d8y_46653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d8y_46653/05_2025/9d8y_46653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d8y_46653/05_2025/9d8y_46653.map" model { file = "/net/cci-nas-00/data/ceres_data/9d8y_46653/05_2025/9d8y_46653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d8y_46653/05_2025/9d8y_46653.cif" } resolution = 4.06 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5508 atoms to isotropic. 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 110 5.16 5 C 11846 2.51 5 N 3238 2.21 5 O 3606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 18800 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2781 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 21, 'TRANS': 345} Chain breaks: 4 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 10, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "B" Number of atoms: 2546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2546 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 18, 'TRANS': 304} Chain breaks: 5 Chain: "C" Number of atoms: 2633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2633 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 19, 'TRANS': 316} Chain breaks: 4 Chain: "D" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1035 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "E" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1060 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 133} Chain breaks: 1 Chain: "F" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1035 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "G" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "H" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 800 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 98} Chain: "I" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "J" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 800 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 98} Chain: "K" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 800 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 98} Chain: "M" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 768 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "N" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 760 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "O" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 768 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "e" 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: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.67, per 1000 atoms: 0.62 Number of scatterers: 18800 At special positions: 0 Unit cell: (106.92, 146.88, 146.88, 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 110 16.00 O 3606 8.00 N 3238 7.00 C 11846 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.05 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.04 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 445 " distance=2.04 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 378 " distance=2.05 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS M 16 " - pdb=" SG CYS M 84 " distance=2.04 Simple disulfide: pdb=" SG CYS N 16 " - pdb=" SG CYS N 84 " distance=2.03 Simple disulfide: pdb=" SG CYS O 16 " - pdb=" SG CYS O 84 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA P 3 " - " MAN P 4 " " BMA U 3 " - " MAN U 4 " " BMA Z 3 " - " MAN Z 4 " ALPHA1-6 " BMA P 3 " - " MAN P 5 " " BMA U 3 " - " MAN U 5 " " BMA Z 3 " - " MAN Z 5 " BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG e 1 " - " NAG e 2 " NAG-ASN " NAG E 701 " - " ASN E 611 " " NAG F 701 " - " ASN F 611 " " NAG P 1 " - " ASN A 88 " " NAG U 1 " - " ASN B 88 " " NAG Z 1 " - " ASN C 88 " " NAG e 1 " - " ASN D 611 " Time building additional restraints: 4.74 Conformation dependent library (CDL) restraints added in 2.4 seconds 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4394 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 43 sheets defined 17.1% alpha, 31.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.97 Creating SS restraints... Processing helix chain 'A' and resid 66 through 72 removed outlier: 3.761A pdb=" N HIS A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.810A pdb=" N GLN A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.762A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 480 Processing helix chain 'B' and resid 100 through 115 removed outlier: 3.643A pdb=" N SER B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 353 Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.853A pdb=" N THR B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 481 removed outlier: 3.709A pdb=" N ASN B 478 " --> pdb=" O ASP B 474 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 74 removed outlier: 3.685A pdb=" N ALA C 73 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS C 74 " --> pdb=" O THR C 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 70 through 74' Processing helix chain 'C' and resid 100 through 114 removed outlier: 3.548A pdb=" N GLN C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 354 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 476 through 480 Processing helix chain 'D' and resid 536 through 543 removed outlier: 3.890A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG D 542 " --> pdb=" O THR D 538 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 596 removed outlier: 3.689A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 removed outlier: 3.518A pdb=" N ASN D 625 " --> pdb=" O GLU D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.603A pdb=" N TRP D 631 " --> pdb=" O THR D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 650 removed outlier: 3.835A pdb=" N ILE D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 662 Processing helix chain 'E' and resid 567 through 596 removed outlier: 3.689A pdb=" N GLY E 572 " --> pdb=" O LEU E 568 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ILE E 573 " --> pdb=" O THR E 569 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP E 589 " --> pdb=" O ARG E 585 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU E 592 " --> pdb=" O ARG E 588 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU E 593 " --> pdb=" O ASP E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 623 Processing helix chain 'E' and resid 627 through 636 Processing helix chain 'E' and resid 638 through 649 removed outlier: 3.514A pdb=" N ILE E 642 " --> pdb=" O TYR E 638 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 655 removed outlier: 3.538A pdb=" N LYS E 655 " --> pdb=" O ASN E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 657 through 662 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.919A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 596 removed outlier: 3.748A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 654 removed outlier: 3.589A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLN F 650 " --> pdb=" O LEU F 646 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) Processing helix chain 'F' and resid 656 through 662 removed outlier: 3.523A pdb=" N LEU F 660 " --> pdb=" O ASN F 656 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.711A pdb=" N GLY G 31 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 28 through 32' Processing helix chain 'I' and resid 28 through 32 removed outlier: 4.070A pdb=" N ASN I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 removed outlier: 4.173A pdb=" N GLN I 64 " --> pdb=" O GLN I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.854A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 4.128A pdb=" N ASN K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.859A pdb=" N THR K 87 " --> pdb=" O SER K 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 64 removed outlier: 3.812A pdb=" N ASP M 63 " --> pdb=" O SER M 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 51 through 53 No H-bonds generated for 'chain 'N' and resid 51 through 53' Processing helix chain 'O' and resid 59 through 64 removed outlier: 4.034A pdb=" N ASP O 63 " --> pdb=" O SER O 60 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 79 removed outlier: 3.509A pdb=" N ASP O 78 " --> pdb=" O LYS O 75 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER O 79 " --> pdb=" O ILE O 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 75 through 79' Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.132A pdb=" N VAL A 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N CYS D 604 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.012A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.744A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 202 Processing sheet with id=AA5, first strand: chain 'A' and resid 260 through 261 removed outlier: 6.743A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.594A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.058A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 12.064A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.745A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.647A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.154A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 12.848A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR A 384 " --> pdb=" O ARG A 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273 removed outlier: 12.848A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 11.154A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 10.647A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.745A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.064A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 12.058A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.594A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 494 through 499 removed outlier: 3.930A pdb=" N VAL B 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 45 through 47 removed outlier: 4.066A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 86 " --> pdb=" O VAL B 242 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 75 through 76 removed outlier: 6.694A pdb=" N CYS B 54 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 91 through 93 removed outlier: 3.752A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 259 through 261 removed outlier: 3.736A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS B 296 " --> pdb=" O CYS B 445 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER B 447 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N GLY B 451 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 11.269A pdb=" N THR B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 12.205A pdb=" N ILE B 453 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 11.715A pdb=" N PHE B 288 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 10.869A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 11.082A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 259 through 261 removed outlier: 3.736A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 374 through 378 Processing sheet with id=AB5, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.400A pdb=" N VAL F 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL C 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N THR F 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N TYR C 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N CYS F 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.790A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.905A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB9, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.737A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.847A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.928A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 11.921A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.659A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.101A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE C 376 " --> pdb=" O PHE C 383 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 271 through 273 removed outlier: 11.101A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.659A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.921A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.928A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.847A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 423 through 424 Processing sheet with id=AC3, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AC4, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.463A pdb=" N LEU G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N TRP G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 10 through 11 removed outlier: 4.182A pdb=" N VAL G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AC7, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.716A pdb=" N THR H 102 " --> pdb=" O TYR H 86 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.485A pdb=" N LEU I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N TRP I 50 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.934A pdb=" N VAL I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.693A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'J' and resid 53 through 54 removed outlier: 6.383A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AD6, first strand: chain 'K' and resid 10 through 11 removed outlier: 7.204A pdb=" N GLU K 10 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TRP K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 10 through 11 removed outlier: 7.204A pdb=" N GLU K 10 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD9, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.586A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 2 through 5 removed outlier: 4.184A pdb=" N LYS M 2 " --> pdb=" O GLU M 92 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N TRP M 28 " --> pdb=" O ILE M 36 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 11 through 17 removed outlier: 3.750A pdb=" N CYS M 16 " --> pdb=" O PHE M 67 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 2 through 3 removed outlier: 6.741A pdb=" N LYS N 2 " --> pdb=" O GLN N 94 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 12 through 14 Processing sheet with id=AE5, first strand: chain 'N' and resid 37 through 39 Processing sheet with id=AE6, first strand: chain 'O' and resid 2 through 5 removed outlier: 6.655A pdb=" N LYS O 2 " --> pdb=" O GLN O 94 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N LEU O 96 " --> pdb=" O LYS O 2 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL O 4 " --> pdb=" O LEU O 96 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N PHE O 26 " --> pdb=" O GLY O 38 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLY O 38 " --> pdb=" O PHE O 26 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TRP O 28 " --> pdb=" O ILE O 36 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 12 through 17 666 hydrogen bonds defined for protein. 1749 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: 6.58 Time building geometry restraints manager: 5.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6077 1.35 - 1.48: 4888 1.48 - 1.61: 8077 1.61 - 1.75: 1 1.75 - 1.88: 149 Bond restraints: 19192 Sorted by residual: bond pdb=" C1 BMA Z 3 " pdb=" C2 BMA Z 3 " ideal model delta sigma weight residual 1.519 1.617 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" CA ASN E 616 " pdb=" CB ASN E 616 " ideal model delta sigma weight residual 1.526 1.604 -0.078 1.76e-02 3.23e+03 1.97e+01 bond pdb=" C5 MAN Z 4 " pdb=" O5 MAN Z 4 " ideal model delta sigma weight residual 1.418 1.481 -0.063 2.00e-02 2.50e+03 9.87e+00 bond pdb=" C1 MAN Z 4 " pdb=" O5 MAN Z 4 " ideal model delta sigma weight residual 1.399 1.451 -0.052 2.00e-02 2.50e+03 6.64e+00 bond pdb=" C1 NAG U 2 " pdb=" O5 NAG U 2 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.36e+00 ... (remaining 19187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.13: 25794 4.13 - 8.26: 219 8.26 - 12.39: 23 12.39 - 16.53: 1 16.53 - 20.66: 1 Bond angle restraints: 26038 Sorted by residual: angle pdb=" C CYS B 218 " pdb=" N ALA B 219 " pdb=" CA ALA B 219 " ideal model delta sigma weight residual 120.69 141.35 -20.66 2.95e+00 1.15e-01 4.90e+01 angle pdb=" C LYS F 601 " pdb=" N LEU F 602 " pdb=" CA LEU F 602 " ideal model delta sigma weight residual 121.54 132.66 -11.12 1.91e+00 2.74e-01 3.39e+01 angle pdb=" C LYS E 601 " pdb=" N LEU E 602 " pdb=" CA LEU E 602 " ideal model delta sigma weight residual 121.54 131.50 -9.96 1.91e+00 2.74e-01 2.72e+01 angle pdb=" C LYS D 601 " pdb=" N LEU D 602 " pdb=" CA LEU D 602 " ideal model delta sigma weight residual 121.54 131.29 -9.75 1.91e+00 2.74e-01 2.61e+01 angle pdb=" C ILE C 439 " pdb=" N GLN C 440 " pdb=" CA GLN C 440 " ideal model delta sigma weight residual 121.54 131.16 -9.62 1.91e+00 2.74e-01 2.54e+01 ... (remaining 26033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.02: 10848 23.02 - 46.05: 720 46.05 - 69.07: 79 69.07 - 92.10: 41 92.10 - 115.12: 9 Dihedral angle restraints: 11697 sinusoidal: 4883 harmonic: 6814 Sorted by residual: dihedral pdb=" CB CYS C 501 " pdb=" SG CYS C 501 " pdb=" SG CYS F 605 " pdb=" CB CYS F 605 " ideal model delta sinusoidal sigma weight residual -86.00 -0.30 -85.70 1 1.00e+01 1.00e-02 8.88e+01 dihedral pdb=" CB CYS C 296 " pdb=" SG CYS C 296 " pdb=" SG CYS C 378 " pdb=" CB CYS C 378 " ideal model delta sinusoidal sigma weight residual -86.00 -2.72 -83.28 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" CB CYS B 296 " pdb=" SG CYS B 296 " pdb=" SG CYS B 445 " pdb=" CB CYS B 445 " ideal model delta sinusoidal sigma weight residual -86.00 -9.97 -76.03 1 1.00e+01 1.00e-02 7.28e+01 ... (remaining 11694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2393 0.067 - 0.133: 493 0.133 - 0.200: 68 0.200 - 0.267: 14 0.267 - 0.333: 7 Chirality restraints: 2975 Sorted by residual: chirality pdb=" CB ILE C 84 " pdb=" CA ILE C 84 " pdb=" CG1 ILE C 84 " pdb=" CG2 ILE C 84 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CG LEU A 259 " pdb=" CB LEU A 259 " pdb=" CD1 LEU A 259 " pdb=" CD2 LEU A 259 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C5 BMA P 3 " pdb=" C4 BMA P 3 " pdb=" C6 BMA P 3 " pdb=" O5 BMA P 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 2972 not shown) Planarity restraints: 3299 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP K 50 " 0.042 2.00e-02 2.50e+03 3.39e-02 2.88e+01 pdb=" CG TRP K 50 " -0.089 2.00e-02 2.50e+03 pdb=" CD1 TRP K 50 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP K 50 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP K 50 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP K 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP K 50 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 50 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 50 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP K 50 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS C 239 " 0.053 5.00e-02 4.00e+02 8.16e-02 1.07e+01 pdb=" N PRO C 240 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO C 240 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 240 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE N 67 " -0.017 2.00e-02 2.50e+03 2.28e-02 9.09e+00 pdb=" CG PHE N 67 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE N 67 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE N 67 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE N 67 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE N 67 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE N 67 " 0.000 2.00e-02 2.50e+03 ... (remaining 3296 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 4238 2.79 - 3.32: 15327 3.32 - 3.85: 29980 3.85 - 4.37: 32638 4.37 - 4.90: 57586 Nonbonded interactions: 139769 Sorted by model distance: nonbonded pdb=" OD1 ASP H 82 " pdb=" OH TYR H 86 " model vdw 2.268 3.040 nonbonded pdb=" OG SER C 365 " pdb=" O LYS O 46 " model vdw 2.307 3.040 nonbonded pdb=" O PRO L 8 " pdb=" OG1 THR L 102 " model vdw 2.314 3.040 nonbonded pdb=" O GLY E 516 " pdb=" OH TYR I 97 " model vdw 2.320 3.040 nonbonded pdb=" OG SER B 365 " pdb=" O LYS N 46 " model vdw 2.330 3.040 ... (remaining 139764 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 56 or resid 69 through 115 or resid 207 through \ 299 or resid 329 through 397 or resid 413 through 457 or resid 460 through 503) \ ) selection = (chain 'B' and (resid 33 through 48 or (resid 49 and (name N or name CA or name \ C or name O or name CB )) or resid 50 through 86 or (resid 87 and (name N or nam \ e CA or name C or name O or name CB )) or resid 88 through 96 or (resid 97 and ( \ name N or name CA or name C or name O or name CB )) or resid 98 through 207 or ( \ resid 208 and (name N or name CA or name C or name O or name CB )) or resid 209 \ through 210 or (resid 211 and (name N or name CA or name C or name O or name CB \ )) or resid 212 through 230 or (resid 231 through 232 and (name N or name CA or \ name C or name O or name CB )) or resid 233 through 266 or (resid 267 through 26 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 270 through \ 274 or (resid 275 and (name N or name CA or name C or name O or name CB )) or re \ sid 276 through 299 or resid 329 through 357 or (resid 358 and (name N or name C \ A or name C or name O or name CB )) or resid 359 through 369 or (resid 370 and ( \ name N or name CA or name C or name O or name CB )) or resid 371 through 380 or \ (resid 381 and (name N or name CA or name C or name O or name CB )) or resid 382 \ through 395 or (resid 396 and (name N or name CA or name C or name O or name CB \ )) or resid 397 or resid 413 through 439 or (resid 440 and (name N or name CA o \ r name C or name O or name CB )) or resid 441 through 456 or (resid 457 and (nam \ e N or name CA or name C or name O or name CB )) or resid 463 through 464 or (re \ sid 465 and (name N or name CA or name C or name O or name CB or name OG1)) or ( \ resid 466 and (name N or name CA or name C or name O or name CB or name CG )) or \ (resid 467 and (name N or name CA or name C or name O or name CB )) or resid 46 \ 8 through 473 or (resid 474 and (name N or name CA or name C or name O or name C \ B )) or resid 475 through 501 or (resid 502 and (name N or name CA or name C or \ name O or name CB )) or resid 503)) selection = (chain 'C' and (resid 33 through 48 or (resid 49 and (name N or name CA or name \ C or name O or name CB )) or resid 50 through 56 or resid 69 through 86 or (resi \ d 87 and (name N or name CA or name C or name O or name CB )) or resid 88 throug \ h 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or re \ sid 98 through 115 or resid 207 or (resid 208 and (name N or name CA or name C o \ r name O or name CB )) or resid 209 through 210 or (resid 211 and (name N or nam \ e CA or name C or name O or name CB )) or resid 212 through 230 or (resid 231 th \ rough 232 and (name N or name CA or name C or name O or name CB )) or resid 233 \ through 266 or (resid 267 through 269 and (name N or name CA or name C or name O \ or name CB )) or resid 270 through 274 or (resid 275 and (name N or name CA or \ name C or name O or name CB )) or resid 276 through 299 or resid 329 through 357 \ or (resid 358 and (name N or name CA or name C or name O or name CB )) or resid \ 359 through 369 or (resid 370 and (name N or name CA or name C or name O or nam \ e CB )) or resid 371 through 380 or (resid 381 and (name N or name CA or name C \ or name O or name CB )) or resid 382 through 395 or (resid 396 and (name N or na \ me CA or name C or name O or name CB )) or resid 397 or resid 413 through 439 or \ (resid 440 and (name N or name CA or name C or name O or name CB )) or resid 44 \ 1 through 456 or (resid 457 and (name N or name CA or name C or name O or name C \ B )) or resid 460 through 461 or (resid 465 and (name N or name CA or name C or \ name O or name CB or name OG1)) or (resid 466 and (name N or name CA or name C o \ r name O or name CB or name CG )) or (resid 467 and (name N or name CA or name C \ or name O or name CB )) or resid 468 through 473 or (resid 474 and (name N or n \ ame CA or name C or name O or name CB )) or resid 475 through 501 or (resid 502 \ and (name N or name CA or name C or name O or name CB )) or resid 503)) } ncs_group { reference = (chain 'D' and resid 512 through 662) selection = (chain 'E' and (resid 512 through 547 or resid 569 through 662)) selection = (chain 'F' and (resid 512 through 547 or resid 569 through 662)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = (chain 'M' and resid 1 through 95) selection = chain 'N' selection = (chain 'O' and resid 1 through 95) } ncs_group { reference = chain 'P' selection = chain 'U' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 3.170 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: 0.000 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.200 Process input model: 43.910 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 19248 Z= 0.232 Angle : 0.999 20.657 26169 Z= 0.500 Chirality : 0.058 0.333 2975 Planarity : 0.007 0.082 3293 Dihedral : 15.184 115.124 7192 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.16 % Favored : 93.76 % Rotamer: Outliers : 0.10 % Allowed : 0.39 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.95 (0.16), residues: 2322 helix: -2.31 (0.21), residues: 371 sheet: 0.28 (0.20), residues: 611 loop : -1.82 (0.15), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.089 0.003 TRP K 50 HIS 0.014 0.001 HIS B 85 PHE 0.052 0.002 PHE N 67 TYR 0.039 0.002 TYR C 484 ARG 0.022 0.001 ARG J 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00861 ( 6) link_NAG-ASN : angle 4.65430 ( 18) link_ALPHA1-6 : bond 0.00525 ( 3) link_ALPHA1-6 : angle 1.40162 ( 9) link_BETA1-4 : bond 0.01601 ( 7) link_BETA1-4 : angle 4.80731 ( 21) link_ALPHA1-3 : bond 0.01109 ( 3) link_ALPHA1-3 : angle 2.98107 ( 9) hydrogen bonds : bond 0.13862 ( 638) hydrogen bonds : angle 7.00250 ( 1749) SS BOND : bond 0.00779 ( 37) SS BOND : angle 2.72756 ( 74) covalent geometry : bond 0.00487 (19192) covalent geometry : angle 0.97152 (26038) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 428 time to evaluate : 2.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 LEU cc_start: 0.7129 (tt) cc_final: 0.6919 (tt) REVERT: A 486 TYR cc_start: 0.8562 (m-80) cc_final: 0.8162 (m-80) REVERT: C 95 MET cc_start: 0.8084 (ppp) cc_final: 0.7596 (ppp) REVERT: C 357 THR cc_start: 0.7916 (m) cc_final: 0.7659 (m) REVERT: D 530 MET cc_start: 0.7035 (tpt) cc_final: 0.6694 (tpt) REVERT: G 100 MET cc_start: 0.6253 (mtt) cc_final: 0.6025 (mtt) REVERT: H 53 THR cc_start: 0.8387 (m) cc_final: 0.8136 (p) REVERT: I 86 ASP cc_start: 0.6180 (p0) cc_final: 0.5845 (m-30) REVERT: I 100 MET cc_start: 0.7591 (mtm) cc_final: 0.7185 (mtt) REVERT: K 45 LEU cc_start: 0.8419 (mt) cc_final: 0.8215 (mt) REVERT: K 82 LEU cc_start: 0.6423 (mt) cc_final: 0.6069 (mt) REVERT: L 33 LEU cc_start: 0.7985 (tp) cc_final: 0.7726 (tp) outliers start: 2 outliers final: 1 residues processed: 428 average time/residue: 0.2801 time to fit residues: 187.8464 Evaluate side-chains 351 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 350 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 180 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 208 optimal weight: 9.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 HIS D 607 ASN D 650 GLN J 6 GLN ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.187560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.158765 restraints weight = 27845.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.157384 restraints weight = 45088.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.158225 restraints weight = 48319.066| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19248 Z= 0.161 Angle : 0.654 12.958 26169 Z= 0.329 Chirality : 0.045 0.248 2975 Planarity : 0.004 0.058 3293 Dihedral : 9.225 86.627 2894 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.56 % Favored : 94.40 % Rotamer: Outliers : 0.10 % Allowed : 5.15 % Favored : 94.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.31 (0.17), residues: 2322 helix: -0.95 (0.26), residues: 372 sheet: 0.42 (0.20), residues: 652 loop : -1.57 (0.16), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP K 50 HIS 0.008 0.001 HIS K 35 PHE 0.020 0.002 PHE B 53 TYR 0.015 0.002 TYR C 484 ARG 0.005 0.000 ARG H 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00673 ( 6) link_NAG-ASN : angle 4.45339 ( 18) link_ALPHA1-6 : bond 0.00590 ( 3) link_ALPHA1-6 : angle 1.71214 ( 9) link_BETA1-4 : bond 0.01289 ( 7) link_BETA1-4 : angle 3.54551 ( 21) link_ALPHA1-3 : bond 0.02161 ( 3) link_ALPHA1-3 : angle 2.16572 ( 9) hydrogen bonds : bond 0.04172 ( 638) hydrogen bonds : angle 5.67818 ( 1749) SS BOND : bond 0.00519 ( 37) SS BOND : angle 2.00279 ( 74) covalent geometry : bond 0.00370 (19192) covalent geometry : angle 0.62612 (26038) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 423 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8728 (tpp) cc_final: 0.8439 (tpp) REVERT: C 99 ASN cc_start: 0.8052 (t0) cc_final: 0.7789 (t0) REVERT: C 357 THR cc_start: 0.8010 (m) cc_final: 0.7758 (m) REVERT: D 530 MET cc_start: 0.7582 (tpt) cc_final: 0.7048 (tpt) REVERT: D 543 ASN cc_start: 0.8336 (t0) cc_final: 0.7908 (t0) REVERT: E 543 ASN cc_start: 0.8090 (p0) cc_final: 0.7785 (p0) REVERT: G 62 LYS cc_start: 0.7771 (mtpt) cc_final: 0.7300 (tptp) REVERT: G 98 TYR cc_start: 0.7632 (m-80) cc_final: 0.7409 (m-80) REVERT: K 45 LEU cc_start: 0.8639 (mt) cc_final: 0.8401 (mt) REVERT: K 75 ILE cc_start: 0.8190 (tp) cc_final: 0.7712 (mm) REVERT: L 45 ASN cc_start: 0.8207 (t0) cc_final: 0.7907 (t0) outliers start: 2 outliers final: 1 residues processed: 425 average time/residue: 0.2745 time to fit residues: 181.6682 Evaluate side-chains 347 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 346 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 1 optimal weight: 0.9990 chunk 209 optimal weight: 8.9990 chunk 214 optimal weight: 8.9990 chunk 146 optimal weight: 9.9990 chunk 171 optimal weight: 0.0970 chunk 121 optimal weight: 0.0000 chunk 113 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS B 348 GLN G 39 GLN ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 HIS ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.185670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.153187 restraints weight = 28035.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.151770 restraints weight = 43372.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.153014 restraints weight = 42586.943| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19248 Z= 0.185 Angle : 0.680 12.075 26169 Z= 0.342 Chirality : 0.046 0.215 2975 Planarity : 0.004 0.063 3293 Dihedral : 8.176 73.123 2894 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.29 % Favored : 93.67 % Rotamer: Outliers : 0.05 % Allowed : 4.56 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.11 (0.17), residues: 2322 helix: -0.35 (0.27), residues: 359 sheet: 0.38 (0.19), residues: 675 loop : -1.51 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP K 50 HIS 0.007 0.001 HIS B 105 PHE 0.023 0.002 PHE B 53 TYR 0.017 0.002 TYR C 484 ARG 0.006 0.000 ARG J 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00608 ( 6) link_NAG-ASN : angle 3.91245 ( 18) link_ALPHA1-6 : bond 0.00500 ( 3) link_ALPHA1-6 : angle 1.82163 ( 9) link_BETA1-4 : bond 0.01302 ( 7) link_BETA1-4 : angle 3.63063 ( 21) link_ALPHA1-3 : bond 0.02546 ( 3) link_ALPHA1-3 : angle 3.44734 ( 9) hydrogen bonds : bond 0.04124 ( 638) hydrogen bonds : angle 5.53288 ( 1749) SS BOND : bond 0.00628 ( 37) SS BOND : angle 2.48617 ( 74) covalent geometry : bond 0.00434 (19192) covalent geometry : angle 0.64868 (26038) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 425 time to evaluate : 1.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8551 (tpp) cc_final: 0.8165 (tpp) REVERT: A 486 TYR cc_start: 0.8997 (m-80) cc_final: 0.8389 (m-80) REVERT: D 530 MET cc_start: 0.7270 (tpt) cc_final: 0.7050 (tpt) REVERT: E 543 ASN cc_start: 0.8166 (p0) cc_final: 0.7874 (p0) REVERT: H 94 TYR cc_start: 0.8341 (m-80) cc_final: 0.8062 (m-10) REVERT: I 47 TRP cc_start: 0.8583 (t60) cc_final: 0.8297 (t60) REVERT: I 100 MET cc_start: 0.7882 (mtm) cc_final: 0.7164 (mtt) REVERT: L 45 ASN cc_start: 0.8241 (t0) cc_final: 0.7925 (t0) REVERT: M 56 ASP cc_start: 0.6065 (t70) cc_final: 0.5515 (t0) outliers start: 1 outliers final: 1 residues processed: 426 average time/residue: 0.2643 time to fit residues: 176.3444 Evaluate side-chains 344 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 343 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 144 optimal weight: 0.3980 chunk 102 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 174 optimal weight: 20.0000 chunk 106 optimal weight: 0.9990 chunk 69 optimal weight: 0.0270 chunk 65 optimal weight: 2.9990 overall best weight: 0.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 276 ASN D 650 GLN J 90 HIS ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.189323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.152670 restraints weight = 27935.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.151707 restraints weight = 40494.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.152994 restraints weight = 38227.803| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19248 Z= 0.126 Angle : 0.625 11.556 26169 Z= 0.311 Chirality : 0.045 0.227 2975 Planarity : 0.004 0.064 3293 Dihedral : 7.244 59.691 2894 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.64 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.95 (0.17), residues: 2322 helix: -0.05 (0.28), residues: 365 sheet: 0.45 (0.20), residues: 661 loop : -1.43 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP G 50 HIS 0.006 0.001 HIS A 374 PHE 0.025 0.001 PHE F 522 TYR 0.017 0.001 TYR C 484 ARG 0.008 0.000 ARG D 579 Details of bonding type rmsd link_NAG-ASN : bond 0.00602 ( 6) link_NAG-ASN : angle 4.26231 ( 18) link_ALPHA1-6 : bond 0.00561 ( 3) link_ALPHA1-6 : angle 1.77255 ( 9) link_BETA1-4 : bond 0.01288 ( 7) link_BETA1-4 : angle 3.42611 ( 21) link_ALPHA1-3 : bond 0.02317 ( 3) link_ALPHA1-3 : angle 3.01691 ( 9) hydrogen bonds : bond 0.03534 ( 638) hydrogen bonds : angle 5.26982 ( 1749) SS BOND : bond 0.00633 ( 37) SS BOND : angle 2.12377 ( 74) covalent geometry : bond 0.00283 (19192) covalent geometry : angle 0.59474 (26038) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 427 time to evaluate : 2.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8672 (tpp) cc_final: 0.8166 (tpp) REVERT: D 530 MET cc_start: 0.7471 (tpt) cc_final: 0.7198 (tpt) REVERT: D 543 ASN cc_start: 0.8322 (t0) cc_final: 0.7971 (t0) REVERT: D 599 SER cc_start: 0.3775 (t) cc_final: 0.3268 (p) REVERT: D 647 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7292 (tm-30) REVERT: E 543 ASN cc_start: 0.8115 (p0) cc_final: 0.7819 (p0) REVERT: F 543 ASN cc_start: 0.8681 (t0) cc_final: 0.8401 (t0) REVERT: H 24 ARG cc_start: 0.7285 (tpp80) cc_final: 0.6810 (tpp80) REVERT: I 47 TRP cc_start: 0.8571 (t60) cc_final: 0.8280 (t60) REVERT: K 45 LEU cc_start: 0.8657 (mt) cc_final: 0.8413 (mt) REVERT: L 45 ASN cc_start: 0.8214 (t0) cc_final: 0.7878 (t0) REVERT: M 56 ASP cc_start: 0.6365 (t70) cc_final: 0.5763 (t0) outliers start: 0 outliers final: 0 residues processed: 427 average time/residue: 0.2768 time to fit residues: 184.8696 Evaluate side-chains 351 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 60 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 205 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 188 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 160 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 199 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 330 HIS B 422 GLN D 651 ASN ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 HIS I 35 HIS J 90 HIS ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.178892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.146971 restraints weight = 27718.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.145464 restraints weight = 48167.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.146385 restraints weight = 45043.399| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 19248 Z= 0.307 Angle : 0.794 13.227 26169 Z= 0.402 Chirality : 0.051 0.227 2975 Planarity : 0.005 0.066 3293 Dihedral : 7.433 59.248 2894 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.84 % Favored : 92.12 % Rotamer: Outliers : 0.05 % Allowed : 3.73 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 (0.17), residues: 2322 helix: -0.50 (0.27), residues: 374 sheet: 0.25 (0.19), residues: 699 loop : -1.67 (0.17), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP G 50 HIS 0.012 0.002 HIS C 216 PHE 0.030 0.003 PHE C 53 TYR 0.023 0.002 TYR I 91 ARG 0.006 0.001 ARG J 30 Details of bonding type rmsd link_NAG-ASN : bond 0.01468 ( 6) link_NAG-ASN : angle 3.90737 ( 18) link_ALPHA1-6 : bond 0.00606 ( 3) link_ALPHA1-6 : angle 1.65619 ( 9) link_BETA1-4 : bond 0.01269 ( 7) link_BETA1-4 : angle 3.88560 ( 21) link_ALPHA1-3 : bond 0.02686 ( 3) link_ALPHA1-3 : angle 3.64514 ( 9) hydrogen bonds : bond 0.04877 ( 638) hydrogen bonds : angle 5.59989 ( 1749) SS BOND : bond 0.00754 ( 37) SS BOND : angle 2.50087 ( 74) covalent geometry : bond 0.00734 (19192) covalent geometry : angle 0.76700 (26038) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 410 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8647 (tpp) cc_final: 0.7726 (tpp) REVERT: B 49 GLU cc_start: 0.7713 (tp30) cc_final: 0.7332 (mm-30) REVERT: B 99 ASN cc_start: 0.7838 (t0) cc_final: 0.7061 (t0) REVERT: C 261 LEU cc_start: 0.8819 (mm) cc_final: 0.8612 (mp) REVERT: D 647 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7784 (tm-30) REVERT: E 543 ASN cc_start: 0.8207 (p0) cc_final: 0.7979 (p0) REVERT: F 515 ILE cc_start: 0.8778 (tt) cc_final: 0.8535 (tt) REVERT: F 543 ASN cc_start: 0.8757 (t0) cc_final: 0.8510 (t0) REVERT: G 50 TRP cc_start: 0.7754 (p-90) cc_final: 0.7523 (p-90) REVERT: H 24 ARG cc_start: 0.7173 (tpp80) cc_final: 0.6847 (tpp80) REVERT: I 47 TRP cc_start: 0.8768 (t60) cc_final: 0.8456 (t60) REVERT: I 100 MET cc_start: 0.8984 (mtm) cc_final: 0.7502 (mtt) REVERT: K 45 LEU cc_start: 0.8675 (mt) cc_final: 0.8471 (mt) REVERT: L 11 LEU cc_start: 0.8364 (tp) cc_final: 0.8011 (tt) REVERT: L 33 LEU cc_start: 0.8202 (tp) cc_final: 0.7941 (tp) REVERT: L 45 ASN cc_start: 0.8326 (t0) cc_final: 0.8083 (t0) REVERT: L 52 SER cc_start: 0.8486 (p) cc_final: 0.8248 (t) REVERT: M 56 ASP cc_start: 0.6272 (t70) cc_final: 0.5744 (t0) outliers start: 1 outliers final: 0 residues processed: 411 average time/residue: 0.2780 time to fit residues: 178.7906 Evaluate side-chains 335 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 23 optimal weight: 8.9990 chunk 156 optimal weight: 0.9990 chunk 215 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 187 optimal weight: 0.8980 chunk 168 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 213 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN B 422 GLN D 651 ASN H 79 GLN H 90 HIS I 35 HIS J 6 GLN ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.182670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.148469 restraints weight = 28208.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.146984 restraints weight = 45355.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.148449 restraints weight = 43385.605| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19248 Z= 0.191 Angle : 0.696 12.158 26169 Z= 0.349 Chirality : 0.047 0.229 2975 Planarity : 0.004 0.054 3293 Dihedral : 6.900 55.019 2894 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.33 % Favored : 93.63 % Rotamer: Outliers : 0.05 % Allowed : 2.21 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.11 (0.17), residues: 2322 helix: -0.16 (0.28), residues: 361 sheet: 0.24 (0.19), residues: 703 loop : -1.53 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP K 50 HIS 0.007 0.001 HIS L 90 PHE 0.022 0.002 PHE B 53 TYR 0.016 0.002 TYR D 638 ARG 0.007 0.000 ARG G 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00517 ( 6) link_NAG-ASN : angle 3.62257 ( 18) link_ALPHA1-6 : bond 0.00607 ( 3) link_ALPHA1-6 : angle 1.52691 ( 9) link_BETA1-4 : bond 0.01306 ( 7) link_BETA1-4 : angle 3.76740 ( 21) link_ALPHA1-3 : bond 0.02688 ( 3) link_ALPHA1-3 : angle 3.74821 ( 9) hydrogen bonds : bond 0.04078 ( 638) hydrogen bonds : angle 5.41821 ( 1749) SS BOND : bond 0.00614 ( 37) SS BOND : angle 2.43159 ( 74) covalent geometry : bond 0.00447 (19192) covalent geometry : angle 0.66643 (26038) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 414 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8725 (tpp) cc_final: 0.7864 (tpp) REVERT: C 95 MET cc_start: 0.8250 (ppp) cc_final: 0.8020 (ppp) REVERT: C 261 LEU cc_start: 0.8689 (mm) cc_final: 0.8468 (mp) REVERT: D 530 MET cc_start: 0.7921 (tpp) cc_final: 0.7444 (tpt) REVERT: D 647 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7715 (tm-30) REVERT: E 543 ASN cc_start: 0.8128 (p0) cc_final: 0.7875 (p0) REVERT: F 543 ASN cc_start: 0.8735 (t0) cc_final: 0.8433 (t0) REVERT: H 24 ARG cc_start: 0.7213 (tpp80) cc_final: 0.6844 (tpp80) REVERT: K 45 LEU cc_start: 0.8756 (mt) cc_final: 0.8497 (mt) REVERT: L 11 LEU cc_start: 0.8292 (tp) cc_final: 0.7936 (tt) REVERT: L 33 LEU cc_start: 0.8175 (tp) cc_final: 0.7935 (tp) REVERT: L 45 ASN cc_start: 0.8295 (t0) cc_final: 0.8002 (t0) REVERT: L 52 SER cc_start: 0.8457 (p) cc_final: 0.8257 (t) REVERT: M 56 ASP cc_start: 0.6270 (t70) cc_final: 0.5926 (t0) outliers start: 1 outliers final: 0 residues processed: 415 average time/residue: 0.2728 time to fit residues: 176.5384 Evaluate side-chains 336 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 120 optimal weight: 0.9990 chunk 217 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 chunk 218 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 179 optimal weight: 10.0000 chunk 90 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 178 optimal weight: 0.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS B 246 GLN B 422 GLN H 90 HIS J 90 HIS ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.185844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.149639 restraints weight = 27811.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.147864 restraints weight = 43407.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.148852 restraints weight = 40734.774| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19248 Z= 0.136 Angle : 0.654 11.344 26169 Z= 0.326 Chirality : 0.045 0.204 2975 Planarity : 0.004 0.048 3293 Dihedral : 6.399 54.260 2894 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.12 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.96 (0.17), residues: 2322 helix: 0.03 (0.28), residues: 364 sheet: 0.27 (0.19), residues: 700 loop : -1.41 (0.18), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP I 50 HIS 0.005 0.001 HIS A 374 PHE 0.016 0.001 PHE F 522 TYR 0.014 0.001 TYR C 484 ARG 0.007 0.000 ARG J 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00661 ( 6) link_NAG-ASN : angle 4.66915 ( 18) link_ALPHA1-6 : bond 0.00653 ( 3) link_ALPHA1-6 : angle 1.45801 ( 9) link_BETA1-4 : bond 0.01424 ( 7) link_BETA1-4 : angle 3.59043 ( 21) link_ALPHA1-3 : bond 0.02648 ( 3) link_ALPHA1-3 : angle 3.56897 ( 9) hydrogen bonds : bond 0.03656 ( 638) hydrogen bonds : angle 5.24756 ( 1749) SS BOND : bond 0.00558 ( 37) SS BOND : angle 2.04797 ( 74) covalent geometry : bond 0.00312 (19192) covalent geometry : angle 0.62263 (26038) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 419 time to evaluate : 1.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8595 (tpp) cc_final: 0.7783 (tpp) REVERT: C 95 MET cc_start: 0.8190 (ppp) cc_final: 0.7824 (ppp) REVERT: D 530 MET cc_start: 0.7796 (tpp) cc_final: 0.7398 (tpt) REVERT: D 543 ASN cc_start: 0.8473 (t0) cc_final: 0.8202 (t0) REVERT: D 647 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7666 (tm-30) REVERT: E 543 ASN cc_start: 0.8106 (p0) cc_final: 0.7834 (p0) REVERT: F 543 ASN cc_start: 0.8846 (t0) cc_final: 0.8515 (t0) REVERT: H 87 PHE cc_start: 0.7877 (m-80) cc_final: 0.7389 (m-10) REVERT: K 45 LEU cc_start: 0.8735 (mt) cc_final: 0.8523 (mt) REVERT: L 11 LEU cc_start: 0.8265 (tp) cc_final: 0.7983 (tt) REVERT: L 33 LEU cc_start: 0.8070 (tp) cc_final: 0.7842 (tp) REVERT: L 52 SER cc_start: 0.8306 (p) cc_final: 0.8104 (t) REVERT: M 52 ASN cc_start: 0.7747 (p0) cc_final: 0.7495 (p0) REVERT: M 56 ASP cc_start: 0.6257 (t70) cc_final: 0.5955 (t0) outliers start: 0 outliers final: 0 residues processed: 419 average time/residue: 0.2662 time to fit residues: 175.9611 Evaluate side-chains 345 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 140 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 207 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 170 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 186 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 46 optimal weight: 0.3980 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN B 422 GLN H 90 HIS ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.181670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.146299 restraints weight = 27532.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.144544 restraints weight = 40193.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.145921 restraints weight = 42438.202| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 19248 Z= 0.209 Angle : 0.727 11.846 26169 Z= 0.365 Chirality : 0.048 0.242 2975 Planarity : 0.005 0.065 3293 Dihedral : 6.504 56.051 2894 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.88 % Favored : 92.03 % Rotamer: Outliers : 0.05 % Allowed : 1.47 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.06 (0.17), residues: 2322 helix: -0.07 (0.28), residues: 361 sheet: 0.15 (0.19), residues: 710 loop : -1.42 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP G 50 HIS 0.012 0.002 HIS H 70 PHE 0.024 0.002 PHE C 376 TYR 0.018 0.002 TYR C 484 ARG 0.009 0.001 ARG J 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00596 ( 6) link_NAG-ASN : angle 4.27988 ( 18) link_ALPHA1-6 : bond 0.00638 ( 3) link_ALPHA1-6 : angle 1.39292 ( 9) link_BETA1-4 : bond 0.01369 ( 7) link_BETA1-4 : angle 3.76666 ( 21) link_ALPHA1-3 : bond 0.02612 ( 3) link_ALPHA1-3 : angle 3.58925 ( 9) hydrogen bonds : bond 0.04195 ( 638) hydrogen bonds : angle 5.35394 ( 1749) SS BOND : bond 0.00627 ( 37) SS BOND : angle 2.51683 ( 74) covalent geometry : bond 0.00496 (19192) covalent geometry : angle 0.69560 (26038) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 411 time to evaluate : 1.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8815 (tpp) cc_final: 0.8010 (tpp) REVERT: C 95 MET cc_start: 0.8319 (ppp) cc_final: 0.7987 (ppp) REVERT: D 647 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7803 (tm-30) REVERT: E 543 ASN cc_start: 0.8149 (p0) cc_final: 0.7900 (p0) REVERT: F 543 ASN cc_start: 0.9095 (t0) cc_final: 0.8758 (t0) REVERT: G 89 ILE cc_start: 0.7588 (mt) cc_final: 0.7250 (mt) REVERT: I 47 TRP cc_start: 0.8797 (t60) cc_final: 0.8427 (t60) REVERT: K 45 LEU cc_start: 0.8755 (mt) cc_final: 0.8533 (mt) REVERT: L 11 LEU cc_start: 0.8205 (tp) cc_final: 0.7939 (tt) REVERT: L 33 LEU cc_start: 0.8143 (tp) cc_final: 0.7817 (tp) REVERT: L 45 ASN cc_start: 0.8379 (t0) cc_final: 0.8073 (t0) REVERT: M 52 ASN cc_start: 0.7996 (p0) cc_final: 0.7738 (p0) REVERT: M 56 ASP cc_start: 0.6141 (t70) cc_final: 0.5868 (t0) outliers start: 1 outliers final: 0 residues processed: 412 average time/residue: 0.2616 time to fit residues: 169.0358 Evaluate side-chains 334 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 334 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 99 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 195 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 96 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 61 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 HIS J 90 HIS ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.185545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.151958 restraints weight = 27975.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.149042 restraints weight = 45551.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.150887 restraints weight = 42963.810| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19248 Z= 0.129 Angle : 0.669 11.708 26169 Z= 0.334 Chirality : 0.045 0.203 2975 Planarity : 0.004 0.058 3293 Dihedral : 6.158 54.497 2894 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.99 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.18), residues: 2322 helix: 0.17 (0.28), residues: 362 sheet: 0.17 (0.19), residues: 716 loop : -1.32 (0.18), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP G 50 HIS 0.005 0.001 HIS K 35 PHE 0.024 0.001 PHE C 376 TYR 0.019 0.001 TYR C 217 ARG 0.014 0.000 ARG K 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00511 ( 6) link_NAG-ASN : angle 3.94108 ( 18) link_ALPHA1-6 : bond 0.00650 ( 3) link_ALPHA1-6 : angle 1.35559 ( 9) link_BETA1-4 : bond 0.01415 ( 7) link_BETA1-4 : angle 3.60703 ( 21) link_ALPHA1-3 : bond 0.02564 ( 3) link_ALPHA1-3 : angle 3.41476 ( 9) hydrogen bonds : bond 0.03543 ( 638) hydrogen bonds : angle 5.18969 ( 1749) SS BOND : bond 0.00497 ( 37) SS BOND : angle 2.41469 ( 74) covalent geometry : bond 0.00294 (19192) covalent geometry : angle 0.63830 (26038) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 2.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8681 (tpp) cc_final: 0.7838 (tpp) REVERT: A 289 ASN cc_start: 0.6249 (p0) cc_final: 0.5827 (t0) REVERT: B 384 TYR cc_start: 0.7754 (m-10) cc_final: 0.7483 (m-10) REVERT: C 95 MET cc_start: 0.8202 (ppp) cc_final: 0.7812 (ppp) REVERT: C 104 MET cc_start: 0.8375 (ttm) cc_final: 0.7672 (tpp) REVERT: D 530 MET cc_start: 0.7575 (tpp) cc_final: 0.7076 (tpt) REVERT: D 543 ASN cc_start: 0.8453 (t0) cc_final: 0.8203 (t0) REVERT: D 647 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7698 (tm-30) REVERT: E 543 ASN cc_start: 0.8083 (p0) cc_final: 0.7816 (p0) REVERT: F 543 ASN cc_start: 0.8881 (t0) cc_final: 0.8525 (t0) REVERT: H 79 GLN cc_start: 0.7593 (mp10) cc_final: 0.7379 (mp-120) REVERT: H 87 PHE cc_start: 0.7856 (m-80) cc_final: 0.7527 (m-10) REVERT: I 47 TRP cc_start: 0.8648 (t60) cc_final: 0.8409 (t60) REVERT: J 91 MET cc_start: 0.6309 (mtm) cc_final: 0.6007 (mtp) REVERT: K 45 LEU cc_start: 0.8740 (mt) cc_final: 0.8498 (mt) REVERT: L 11 LEU cc_start: 0.8212 (tp) cc_final: 0.7947 (tt) REVERT: L 33 LEU cc_start: 0.8059 (tp) cc_final: 0.7816 (tp) REVERT: M 52 ASN cc_start: 0.8090 (p0) cc_final: 0.7669 (p0) outliers start: 0 outliers final: 0 residues processed: 415 average time/residue: 0.2739 time to fit residues: 178.3853 Evaluate side-chains 344 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 2.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 216 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 202 optimal weight: 0.6980 chunk 43 optimal weight: 0.0670 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN H 89 GLN I 35 HIS ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.186397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.151027 restraints weight = 27802.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.149471 restraints weight = 40735.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.150945 restraints weight = 41105.461| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19248 Z= 0.131 Angle : 0.656 11.294 26169 Z= 0.327 Chirality : 0.045 0.196 2975 Planarity : 0.004 0.047 3293 Dihedral : 5.986 54.604 2894 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.46 % Favored : 93.45 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.87 (0.18), residues: 2322 helix: 0.27 (0.29), residues: 365 sheet: 0.14 (0.19), residues: 720 loop : -1.30 (0.18), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP G 50 HIS 0.010 0.001 HIS H 90 PHE 0.016 0.001 PHE L 10 TYR 0.017 0.001 TYR C 484 ARG 0.007 0.000 ARG J 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00490 ( 6) link_NAG-ASN : angle 3.79802 ( 18) link_ALPHA1-6 : bond 0.00690 ( 3) link_ALPHA1-6 : angle 1.32724 ( 9) link_BETA1-4 : bond 0.01369 ( 7) link_BETA1-4 : angle 3.49969 ( 21) link_ALPHA1-3 : bond 0.02502 ( 3) link_ALPHA1-3 : angle 3.33409 ( 9) hydrogen bonds : bond 0.03490 ( 638) hydrogen bonds : angle 5.09408 ( 1749) SS BOND : bond 0.00505 ( 37) SS BOND : angle 2.37917 ( 74) covalent geometry : bond 0.00303 (19192) covalent geometry : angle 0.62574 (26038) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 409 time to evaluate : 2.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8013 (ppp) cc_final: 0.7776 (ppp) REVERT: A 104 MET cc_start: 0.8814 (tpp) cc_final: 0.7952 (tpp) REVERT: A 289 ASN cc_start: 0.6176 (p0) cc_final: 0.5853 (t0) REVERT: B 100 MET cc_start: 0.7565 (mtp) cc_final: 0.7342 (ttm) REVERT: B 384 TYR cc_start: 0.7775 (m-10) cc_final: 0.7517 (m-10) REVERT: B 434 MET cc_start: 0.5269 (mtp) cc_final: 0.4054 (tpt) REVERT: C 95 MET cc_start: 0.8194 (ppp) cc_final: 0.7828 (ppp) REVERT: C 104 MET cc_start: 0.8672 (ttm) cc_final: 0.8102 (tpp) REVERT: D 530 MET cc_start: 0.7729 (tpp) cc_final: 0.7307 (tpt) REVERT: D 543 ASN cc_start: 0.8425 (t0) cc_final: 0.8190 (t0) REVERT: D 647 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7670 (tm-30) REVERT: E 543 ASN cc_start: 0.8105 (p0) cc_final: 0.7842 (p0) REVERT: F 543 ASN cc_start: 0.8968 (t0) cc_final: 0.8538 (t0) REVERT: H 79 GLN cc_start: 0.7607 (mp10) cc_final: 0.7365 (mp-120) REVERT: K 45 LEU cc_start: 0.8743 (mt) cc_final: 0.8524 (mt) REVERT: L 11 LEU cc_start: 0.8264 (tp) cc_final: 0.7956 (tt) REVERT: L 33 LEU cc_start: 0.8135 (tp) cc_final: 0.7873 (tp) outliers start: 0 outliers final: 0 residues processed: 409 average time/residue: 0.2791 time to fit residues: 179.6849 Evaluate side-chains 342 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 70 optimal weight: 5.9990 chunk 189 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 227 optimal weight: 0.0070 chunk 78 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 213 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN H 90 HIS I 35 HIS J 90 HIS ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.183217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.147532 restraints weight = 27540.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.144833 restraints weight = 41477.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.146861 restraints weight = 40781.552| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19248 Z= 0.182 Angle : 0.700 11.644 26169 Z= 0.350 Chirality : 0.046 0.213 2975 Planarity : 0.004 0.053 3293 Dihedral : 6.138 55.283 2894 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.41 % Favored : 92.51 % Rotamer: Outliers : 0.05 % Allowed : 0.34 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.95 (0.18), residues: 2322 helix: 0.17 (0.28), residues: 367 sheet: 0.08 (0.19), residues: 722 loop : -1.32 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP I 47 HIS 0.007 0.001 HIS K 35 PHE 0.020 0.002 PHE B 53 TYR 0.017 0.002 TYR C 484 ARG 0.007 0.000 ARG K 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00475 ( 6) link_NAG-ASN : angle 3.74765 ( 18) link_ALPHA1-6 : bond 0.00689 ( 3) link_ALPHA1-6 : angle 1.32518 ( 9) link_BETA1-4 : bond 0.01388 ( 7) link_BETA1-4 : angle 3.69032 ( 21) link_ALPHA1-3 : bond 0.02483 ( 3) link_ALPHA1-3 : angle 3.32585 ( 9) hydrogen bonds : bond 0.03908 ( 638) hydrogen bonds : angle 5.18324 ( 1749) SS BOND : bond 0.00546 ( 37) SS BOND : angle 2.46155 ( 74) covalent geometry : bond 0.00431 (19192) covalent geometry : angle 0.67041 (26038) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5331.05 seconds wall clock time: 94 minutes 54.13 seconds (5694.13 seconds total)