Starting phenix.real_space_refine on Thu Jun 19 22:29:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d8y_46653/06_2025/9d8y_46653.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d8y_46653/06_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_46653/06_2025/9d8y_46653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d8y_46653/06_2025/9d8y_46653.map" model { file = "/net/cci-nas-00/data/ceres_data/9d8y_46653/06_2025/9d8y_46653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d8y_46653/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 11.89, per 1000 atoms: 0.63 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: 5.14 Conformation dependent library (CDL) restraints added in 2.5 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: 2.77 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: 6.95 Time building geometry restraints manager: 5.95 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: 0.000 Normalize map: mean=0, sd=1: 2.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 46.330 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.870 ------------------------------------------------------------------------------- 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 : 2.092 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: 0.2922 time to fit residues: 196.4726 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 : 2.178 ------------------------------------------------------------------------------- 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 = 0.187561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.158696 restraints weight = 27846.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.157314 restraints weight = 45271.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.158231 restraints weight = 47776.679| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 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 : 9.226 86.639 2894 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.62 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 0.00670 ( 6) link_NAG-ASN : angle 4.45290 ( 18) link_ALPHA1-6 : bond 0.00588 ( 3) link_ALPHA1-6 : angle 1.71080 ( 9) link_BETA1-4 : bond 0.01291 ( 7) link_BETA1-4 : angle 3.54707 ( 21) link_ALPHA1-3 : bond 0.02165 ( 3) link_ALPHA1-3 : angle 2.16835 ( 9) hydrogen bonds : bond 0.04172 ( 638) hydrogen bonds : angle 5.67839 ( 1749) SS BOND : bond 0.00518 ( 37) SS BOND : angle 2.00290 ( 74) covalent geometry : bond 0.00370 (19192) covalent geometry : angle 0.62610 (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 : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8730 (tpp) cc_final: 0.8448 (tpp) REVERT: C 95 MET cc_start: 0.7960 (ppp) cc_final: 0.7750 (ppp) REVERT: C 99 ASN cc_start: 0.8025 (t0) cc_final: 0.7751 (t0) REVERT: C 357 THR cc_start: 0.8006 (m) cc_final: 0.7749 (m) REVERT: D 530 MET cc_start: 0.7520 (tpt) cc_final: 0.7030 (tpt) REVERT: D 543 ASN cc_start: 0.8303 (t0) cc_final: 0.7901 (t0) REVERT: E 543 ASN cc_start: 0.8035 (p0) cc_final: 0.7721 (p0) REVERT: G 62 LYS cc_start: 0.7680 (mtpt) cc_final: 0.7289 (tptp) REVERT: K 45 LEU cc_start: 0.8572 (mt) cc_final: 0.8315 (mt) REVERT: K 75 ILE cc_start: 0.8077 (tp) cc_final: 0.7581 (mm) REVERT: L 45 ASN cc_start: 0.8201 (t0) cc_final: 0.7932 (t0) outliers start: 2 outliers final: 1 residues processed: 425 average time/residue: 0.2770 time to fit residues: 184.7564 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 : 2.293 ------------------------------------------------------------------------------- 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: 7.9990 chunk 214 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 chunk 171 optimal weight: 0.9980 chunk 121 optimal weight: 0.2980 chunk 113 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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 B 422 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.181000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.153603 restraints weight = 27981.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.153211 restraints weight = 56571.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.154090 restraints weight = 49452.095| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 19248 Z= 0.256 Angle : 0.772 12.777 26169 Z= 0.391 Chirality : 0.050 0.230 2975 Planarity : 0.005 0.064 3293 Dihedral : 8.284 69.811 2894 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.06 % Favored : 92.89 % Rotamer: Outliers : 0.15 % Allowed : 5.83 % Favored : 94.02 % 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: -1.31 (0.17), residues: 2322 helix: -0.59 (0.27), residues: 360 sheet: 0.30 (0.20), residues: 634 loop : -1.59 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP K 50 HIS 0.012 0.002 HIS B 105 PHE 0.031 0.002 PHE B 53 TYR 0.021 0.002 TYR I 91 ARG 0.007 0.001 ARG J 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00599 ( 6) link_NAG-ASN : angle 3.85832 ( 18) link_ALPHA1-6 : bond 0.00491 ( 3) link_ALPHA1-6 : angle 1.79858 ( 9) link_BETA1-4 : bond 0.01279 ( 7) link_BETA1-4 : angle 3.92336 ( 21) link_ALPHA1-3 : bond 0.02806 ( 3) link_ALPHA1-3 : angle 3.91132 ( 9) hydrogen bonds : bond 0.04838 ( 638) hydrogen bonds : angle 5.72519 ( 1749) SS BOND : bond 0.00680 ( 37) SS BOND : angle 2.71867 ( 74) covalent geometry : bond 0.00603 (19192) covalent geometry : angle 0.74108 (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 421 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 418 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8603 (tpp) cc_final: 0.8223 (tpp) REVERT: B 99 ASN cc_start: 0.8015 (t0) cc_final: 0.7793 (t0) REVERT: B 257 THR cc_start: 0.9078 (m) cc_final: 0.8867 (p) REVERT: B 368 ASP cc_start: 0.8633 (m-30) cc_final: 0.8421 (m-30) REVERT: C 428 GLN cc_start: 0.7742 (pm20) cc_final: 0.7510 (pm20) REVERT: D 530 MET cc_start: 0.7738 (tpt) cc_final: 0.7344 (tpt) REVERT: D 647 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7700 (tm-30) REVERT: E 543 ASN cc_start: 0.8083 (p0) cc_final: 0.7838 (p0) REVERT: F 543 ASN cc_start: 0.8773 (t0) cc_final: 0.8544 (t0) REVERT: H 24 ARG cc_start: 0.7168 (tpp80) cc_final: 0.6801 (tpp80) REVERT: I 47 TRP cc_start: 0.8745 (t60) cc_final: 0.8308 (t60) REVERT: I 100 MET cc_start: 0.8450 (mtm) cc_final: 0.7971 (mtt) REVERT: L 33 LEU cc_start: 0.8257 (tp) cc_final: 0.8044 (tp) REVERT: L 45 ASN cc_start: 0.8293 (t0) cc_final: 0.7992 (t0) REVERT: M 56 ASP cc_start: 0.6266 (t70) cc_final: 0.5708 (t0) outliers start: 3 outliers final: 2 residues processed: 421 average time/residue: 0.2838 time to fit residues: 187.0497 Evaluate side-chains 351 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 349 time to evaluate : 2.536 ------------------------------------------------------------------------------- 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: 5.9990 chunk 102 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 128 optimal weight: 0.6980 chunk 174 optimal weight: 20.0000 chunk 106 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 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 = 0.4074 r_free = 0.4074 target = 0.187396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.151876 restraints weight = 27233.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.149366 restraints weight = 41240.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.151093 restraints weight = 35753.027| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19248 Z= 0.123 Angle : 0.642 11.095 26169 Z= 0.319 Chirality : 0.045 0.231 2975 Planarity : 0.004 0.069 3293 Dihedral : 7.317 58.783 2894 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.60 % Favored : 94.36 % 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 : 0.09 % 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: -1.02 (0.17), residues: 2322 helix: -0.16 (0.28), residues: 365 sheet: 0.37 (0.19), residues: 673 loop : -1.46 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP G 50 HIS 0.007 0.001 HIS A 374 PHE 0.024 0.001 PHE F 522 TYR 0.018 0.001 TYR A 217 ARG 0.008 0.000 ARG D 579 Details of bonding type rmsd link_NAG-ASN : bond 0.00540 ( 6) link_NAG-ASN : angle 4.27939 ( 18) link_ALPHA1-6 : bond 0.00569 ( 3) link_ALPHA1-6 : angle 1.74730 ( 9) link_BETA1-4 : bond 0.01311 ( 7) link_BETA1-4 : angle 3.52656 ( 21) link_ALPHA1-3 : bond 0.02561 ( 3) link_ALPHA1-3 : angle 3.11922 ( 9) hydrogen bonds : bond 0.03642 ( 638) hydrogen bonds : angle 5.36637 ( 1749) SS BOND : bond 0.00487 ( 37) SS BOND : angle 2.23909 ( 74) covalent geometry : bond 0.00275 (19192) covalent geometry : angle 0.61047 (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 428 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 428 time to evaluate : 2.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8611 (tpp) cc_final: 0.8238 (tpp) REVERT: D 530 MET cc_start: 0.7370 (tpt) cc_final: 0.7088 (tpt) REVERT: D 543 ASN cc_start: 0.8378 (t0) cc_final: 0.8056 (t0) REVERT: E 543 ASN cc_start: 0.8143 (p0) cc_final: 0.7861 (p0) REVERT: F 543 ASN cc_start: 0.8717 (t0) cc_final: 0.8433 (t0) REVERT: F 647 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7816 (tm-30) REVERT: H 24 ARG cc_start: 0.7211 (tpp80) cc_final: 0.6971 (tpp80) REVERT: H 61 ARG cc_start: 0.7056 (ptp90) cc_final: 0.6846 (ptp90) REVERT: I 47 TRP cc_start: 0.8616 (t60) cc_final: 0.8395 (t60) REVERT: I 100 MET cc_start: 0.8278 (mtm) cc_final: 0.7500 (mtt) REVERT: K 45 LEU cc_start: 0.8678 (mt) cc_final: 0.8439 (mt) REVERT: L 33 LEU cc_start: 0.8083 (tp) cc_final: 0.7870 (tp) REVERT: L 45 ASN cc_start: 0.8226 (t0) cc_final: 0.7908 (t0) REVERT: M 56 ASP cc_start: 0.6404 (t70) cc_final: 0.5753 (t0) outliers start: 0 outliers final: 0 residues processed: 428 average time/residue: 0.3080 time to fit residues: 207.3491 Evaluate side-chains 349 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 2.327 ------------------------------------------------------------------------------- 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: 0.8980 chunk 18 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 205 optimal weight: 0.0980 chunk 57 optimal weight: 0.8980 chunk 188 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 160 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 199 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS H 38 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 = 0.4088 r_free = 0.4088 target = 0.189086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.152356 restraints weight = 28213.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.150756 restraints weight = 42926.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.152526 restraints weight = 37449.567| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19248 Z= 0.117 Angle : 0.617 10.987 26169 Z= 0.306 Chirality : 0.044 0.209 2975 Planarity : 0.004 0.055 3293 Dihedral : 6.607 55.038 2894 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.73 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % 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: -0.82 (0.17), residues: 2322 helix: 0.12 (0.28), residues: 371 sheet: 0.44 (0.19), residues: 682 loop : -1.34 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP G 50 HIS 0.006 0.001 HIS A 374 PHE 0.023 0.001 PHE C 376 TYR 0.016 0.001 TYR C 484 ARG 0.006 0.000 ARG J 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00526 ( 6) link_NAG-ASN : angle 3.78877 ( 18) link_ALPHA1-6 : bond 0.00583 ( 3) link_ALPHA1-6 : angle 1.74568 ( 9) link_BETA1-4 : bond 0.01405 ( 7) link_BETA1-4 : angle 3.39959 ( 21) link_ALPHA1-3 : bond 0.02571 ( 3) link_ALPHA1-3 : angle 3.21051 ( 9) hydrogen bonds : bond 0.03380 ( 638) hydrogen bonds : angle 5.20182 ( 1749) SS BOND : bond 0.00520 ( 37) SS BOND : angle 2.14142 ( 74) covalent geometry : bond 0.00263 (19192) covalent geometry : angle 0.58791 (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 425 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 425 time to evaluate : 3.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8390 (tpp) cc_final: 0.7638 (tpt) REVERT: C 95 MET cc_start: 0.8152 (ppp) cc_final: 0.7945 (ppp) REVERT: D 530 MET cc_start: 0.7391 (tpt) cc_final: 0.7152 (tpt) REVERT: D 543 ASN cc_start: 0.8416 (t0) cc_final: 0.8115 (t0) REVERT: D 599 SER cc_start: 0.3686 (t) cc_final: 0.3108 (p) REVERT: E 543 ASN cc_start: 0.8169 (p0) cc_final: 0.7855 (p0) REVERT: F 543 ASN cc_start: 0.8843 (t0) cc_final: 0.8510 (t0) REVERT: I 47 TRP cc_start: 0.8475 (t60) cc_final: 0.8265 (t60) REVERT: K 45 LEU cc_start: 0.8675 (mt) cc_final: 0.8447 (mt) REVERT: L 11 LEU cc_start: 0.8183 (tp) cc_final: 0.7943 (tt) REVERT: L 33 LEU cc_start: 0.8111 (tp) cc_final: 0.7822 (tp) REVERT: M 56 ASP cc_start: 0.6233 (t70) cc_final: 0.5686 (t0) outliers start: 0 outliers final: 0 residues processed: 425 average time/residue: 0.3520 time to fit residues: 235.7424 Evaluate side-chains 343 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 2.415 ------------------------------------------------------------------------------- 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: 10.0000 chunk 156 optimal weight: 8.9990 chunk 215 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 187 optimal weight: 0.0570 chunk 168 optimal weight: 1.9990 chunk 126 optimal weight: 0.4980 chunk 50 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 213 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN A 352 HIS ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS D 651 ASN H 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 = 0.4072 r_free = 0.4072 target = 0.187094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.151053 restraints weight = 28218.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.148790 restraints weight = 42418.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.150726 restraints weight = 41966.241| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2334 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= 0.143 Angle : 0.634 10.732 26169 Z= 0.316 Chirality : 0.045 0.194 2975 Planarity : 0.004 0.050 3293 Dihedral : 6.353 54.534 2894 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.81 % Favored : 94.14 % Rotamer: Outliers : 0.10 % Allowed : 2.01 % Favored : 97.89 % 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: -0.81 (0.17), residues: 2322 helix: 0.26 (0.29), residues: 362 sheet: 0.40 (0.19), residues: 685 loop : -1.35 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP K 50 HIS 0.005 0.001 HIS A 374 PHE 0.017 0.001 PHE B 53 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 0.00508 ( 6) link_NAG-ASN : angle 3.55763 ( 18) link_ALPHA1-6 : bond 0.00599 ( 3) link_ALPHA1-6 : angle 1.58057 ( 9) link_BETA1-4 : bond 0.01302 ( 7) link_BETA1-4 : angle 3.43582 ( 21) link_ALPHA1-3 : bond 0.02587 ( 3) link_ALPHA1-3 : angle 3.29335 ( 9) hydrogen bonds : bond 0.03571 ( 638) hydrogen bonds : angle 5.16586 ( 1749) SS BOND : bond 0.00506 ( 37) SS BOND : angle 2.12084 ( 74) covalent geometry : bond 0.00332 (19192) covalent geometry : angle 0.60689 (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: 2 poor density : 413 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8483 (tpp) cc_final: 0.7686 (tpp) REVERT: C 95 MET cc_start: 0.8144 (ppp) cc_final: 0.7943 (ppp) REVERT: D 543 ASN cc_start: 0.8474 (t0) cc_final: 0.8127 (t0) REVERT: D 647 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7548 (tm-30) REVERT: E 543 ASN cc_start: 0.8053 (p0) cc_final: 0.7784 (p0) REVERT: F 543 ASN cc_start: 0.8914 (t0) cc_final: 0.8598 (t0) REVERT: K 45 LEU cc_start: 0.8692 (mt) cc_final: 0.8490 (mt) REVERT: L 11 LEU cc_start: 0.8185 (tp) cc_final: 0.7942 (tt) REVERT: L 33 LEU cc_start: 0.8209 (tp) cc_final: 0.7922 (tp) REVERT: M 56 ASP cc_start: 0.6231 (t70) cc_final: 0.5722 (t0) outliers start: 2 outliers final: 1 residues processed: 415 average time/residue: 0.2739 time to fit residues: 179.2421 Evaluate side-chains 338 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 337 time to evaluate : 2.052 ------------------------------------------------------------------------------- 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: 2.9990 chunk 217 optimal weight: 20.0000 chunk 171 optimal weight: 0.9980 chunk 218 optimal weight: 0.0000 chunk 55 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 179 optimal weight: 9.9990 chunk 90 optimal weight: 0.0000 chunk 96 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS C 330 HIS D 651 ASN H 89 GLN ** J 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 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 = 0.4089 r_free = 0.4089 target = 0.188425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.154247 restraints weight = 27320.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.152217 restraints weight = 40477.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.154100 restraints weight = 39238.004| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19248 Z= 0.112 Angle : 0.621 10.989 26169 Z= 0.305 Chirality : 0.044 0.217 2975 Planarity : 0.004 0.051 3293 Dihedral : 6.022 53.956 2894 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.94 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: -0.72 (0.18), residues: 2322 helix: 0.41 (0.29), residues: 362 sheet: 0.43 (0.20), residues: 673 loop : -1.27 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP I 47 HIS 0.005 0.001 HIS H 90 PHE 0.022 0.001 PHE C 376 TYR 0.015 0.001 TYR C 484 ARG 0.008 0.000 ARG J 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00517 ( 6) link_NAG-ASN : angle 4.66299 ( 18) link_ALPHA1-6 : bond 0.00648 ( 3) link_ALPHA1-6 : angle 1.51841 ( 9) link_BETA1-4 : bond 0.01381 ( 7) link_BETA1-4 : angle 3.43169 ( 21) link_ALPHA1-3 : bond 0.02570 ( 3) link_ALPHA1-3 : angle 3.44315 ( 9) hydrogen bonds : bond 0.03260 ( 638) hydrogen bonds : angle 5.05021 ( 1749) SS BOND : bond 0.00469 ( 37) SS BOND : angle 2.02902 ( 74) covalent geometry : bond 0.00250 (19192) covalent geometry : angle 0.58825 (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 421 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 421 time to evaluate : 2.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8357 (tpp) cc_final: 0.7469 (tpp) REVERT: C 95 MET cc_start: 0.8128 (ppp) cc_final: 0.7860 (ppp) REVERT: D 530 MET cc_start: 0.6766 (tpt) cc_final: 0.6444 (tpt) REVERT: D 543 ASN cc_start: 0.8371 (t0) cc_final: 0.8062 (t0) REVERT: E 543 ASN cc_start: 0.8114 (p0) cc_final: 0.7785 (p0) REVERT: F 543 ASN cc_start: 0.9037 (t0) cc_final: 0.8634 (t0) REVERT: G 86 ASP cc_start: 0.6631 (m-30) cc_final: 0.6429 (m-30) REVERT: K 45 LEU cc_start: 0.8629 (mt) cc_final: 0.8286 (mt) REVERT: L 33 LEU cc_start: 0.8236 (tp) cc_final: 0.7929 (tp) REVERT: M 56 ASP cc_start: 0.6077 (t70) cc_final: 0.5548 (t0) outliers start: 0 outliers final: 0 residues processed: 421 average time/residue: 0.2765 time to fit residues: 186.4880 Evaluate side-chains 350 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 2.178 ------------------------------------------------------------------------------- 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: 8.9990 chunk 207 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 14 optimal weight: 0.0980 chunk 170 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 chunk 186 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS C 330 HIS H 38 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 = 0.4075 r_free = 0.4075 target = 0.186964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.150899 restraints weight = 27514.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.149752 restraints weight = 38271.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.151177 restraints weight = 38913.771| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19248 Z= 0.146 Angle : 0.646 11.242 26169 Z= 0.322 Chirality : 0.045 0.197 2975 Planarity : 0.004 0.046 3293 Dihedral : 5.947 54.366 2894 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.99 % Favored : 93.97 % Rotamer: Outliers : 0.05 % Allowed : 1.13 % Favored : 98.82 % 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: -0.73 (0.18), residues: 2322 helix: 0.45 (0.29), residues: 361 sheet: 0.40 (0.19), residues: 685 loop : -1.29 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP K 50 HIS 0.005 0.001 HIS L 90 PHE 0.018 0.001 PHE F 522 TYR 0.015 0.001 TYR C 484 ARG 0.007 0.000 ARG J 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00496 ( 6) link_NAG-ASN : angle 4.12286 ( 18) link_ALPHA1-6 : bond 0.00655 ( 3) link_ALPHA1-6 : angle 1.37254 ( 9) link_BETA1-4 : bond 0.01348 ( 7) link_BETA1-4 : angle 3.47741 ( 21) link_ALPHA1-3 : bond 0.02519 ( 3) link_ALPHA1-3 : angle 3.31769 ( 9) hydrogen bonds : bond 0.03513 ( 638) hydrogen bonds : angle 5.07195 ( 1749) SS BOND : bond 0.00522 ( 37) SS BOND : angle 2.37493 ( 74) covalent geometry : bond 0.00341 (19192) covalent geometry : angle 0.61388 (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 414 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 413 time to evaluate : 2.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8657 (tpp) cc_final: 0.7805 (tpp) REVERT: B 434 MET cc_start: 0.4814 (mtp) cc_final: 0.3885 (tpt) REVERT: C 95 MET cc_start: 0.8190 (ppp) cc_final: 0.7879 (ppp) REVERT: D 543 ASN cc_start: 0.8453 (t0) cc_final: 0.8113 (t0) REVERT: E 543 ASN cc_start: 0.8114 (p0) cc_final: 0.7820 (p0) REVERT: F 543 ASN cc_start: 0.9048 (t0) cc_final: 0.8651 (t0) REVERT: H 3 GLN cc_start: 0.8280 (tp-100) cc_final: 0.8043 (mm-40) REVERT: I 47 TRP cc_start: 0.8721 (t60) cc_final: 0.8362 (t60) REVERT: K 100 MET cc_start: 0.7969 (mmt) cc_final: 0.6970 (mmt) REVERT: K 101 ASP cc_start: 0.8333 (t70) cc_final: 0.8050 (t70) REVERT: M 56 ASP cc_start: 0.6141 (t70) cc_final: 0.5682 (t0) outliers start: 1 outliers final: 0 residues processed: 414 average time/residue: 0.2801 time to fit residues: 183.8991 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 : 2.112 ------------------------------------------------------------------------------- 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: 1.9990 chunk 100 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 195 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 153 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 61 optimal weight: 0.0770 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 330 HIS J 90 HIS ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.186820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.150423 restraints weight = 27762.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.148861 restraints weight = 39480.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.150338 restraints weight = 38463.430| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19248 Z= 0.145 Angle : 0.652 11.480 26169 Z= 0.325 Chirality : 0.045 0.199 2975 Planarity : 0.004 0.047 3293 Dihedral : 5.919 55.633 2894 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.20 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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: -0.71 (0.18), residues: 2322 helix: 0.47 (0.29), residues: 362 sheet: 0.41 (0.20), residues: 675 loop : -1.28 (0.17), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP G 103 HIS 0.010 0.001 HIS H 90 PHE 0.025 0.002 PHE C 376 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 0.00471 ( 6) link_NAG-ASN : angle 3.97810 ( 18) link_ALPHA1-6 : bond 0.00675 ( 3) link_ALPHA1-6 : angle 1.32279 ( 9) link_BETA1-4 : bond 0.01370 ( 7) link_BETA1-4 : angle 3.54990 ( 21) link_ALPHA1-3 : bond 0.02442 ( 3) link_ALPHA1-3 : angle 3.27474 ( 9) hydrogen bonds : bond 0.03547 ( 638) hydrogen bonds : angle 5.06238 ( 1749) SS BOND : bond 0.00550 ( 37) SS BOND : angle 2.34209 ( 74) covalent geometry : bond 0.00338 (19192) covalent geometry : angle 0.62133 (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 407 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 1.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8572 (tpp) cc_final: 0.7731 (tpp) REVERT: B 100 MET cc_start: 0.7698 (mtp) cc_final: 0.7314 (ttm) REVERT: B 434 MET cc_start: 0.5164 (mtp) cc_final: 0.4046 (tpt) REVERT: C 95 MET cc_start: 0.8132 (ppp) cc_final: 0.7924 (ppp) REVERT: D 543 ASN cc_start: 0.8382 (t0) cc_final: 0.8077 (t0) REVERT: E 543 ASN cc_start: 0.8103 (p0) cc_final: 0.7815 (p0) REVERT: F 543 ASN cc_start: 0.9021 (t0) cc_final: 0.8618 (t0) REVERT: G 100 MET cc_start: 0.7172 (mtt) cc_final: 0.6828 (mtt) REVERT: I 47 TRP cc_start: 0.8699 (t60) cc_final: 0.8366 (t60) REVERT: K 101 ASP cc_start: 0.8468 (t70) cc_final: 0.8237 (t70) REVERT: L 11 LEU cc_start: 0.8281 (tp) cc_final: 0.8049 (tt) REVERT: M 56 ASP cc_start: 0.5983 (t70) cc_final: 0.5740 (t0) outliers start: 0 outliers final: 0 residues processed: 407 average time/residue: 0.2684 time to fit residues: 171.5194 Evaluate side-chains 343 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 1.992 ------------------------------------------------------------------------------- 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: 7.9990 chunk 55 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 71 optimal weight: 0.0000 chunk 202 optimal weight: 3.9990 chunk 43 optimal weight: 0.0170 overall best weight: 0.9826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 330 HIS H 90 HIS J 90 HIS ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4069 r_free = 0.4069 target = 0.186400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.154649 restraints weight = 27477.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.151253 restraints weight = 44036.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.153123 restraints weight = 43945.026| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19248 Z= 0.137 Angle : 0.649 11.394 26169 Z= 0.323 Chirality : 0.045 0.222 2975 Planarity : 0.004 0.046 3293 Dihedral : 5.806 54.831 2894 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.77 % Favored : 94.14 % Rotamer: Outliers : 0.05 % Allowed : 0.69 % Favored : 99.26 % 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: -0.71 (0.18), residues: 2322 helix: 0.50 (0.29), residues: 365 sheet: 0.40 (0.20), residues: 678 loop : -1.28 (0.18), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP G 50 HIS 0.004 0.001 HIS K 35 PHE 0.024 0.001 PHE C 376 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 0.00473 ( 6) link_NAG-ASN : angle 3.88504 ( 18) link_ALPHA1-6 : bond 0.00687 ( 3) link_ALPHA1-6 : angle 1.29917 ( 9) link_BETA1-4 : bond 0.01368 ( 7) link_BETA1-4 : angle 3.49365 ( 21) link_ALPHA1-3 : bond 0.02402 ( 3) link_ALPHA1-3 : angle 3.17198 ( 9) hydrogen bonds : bond 0.03457 ( 638) hydrogen bonds : angle 5.07401 ( 1749) SS BOND : bond 0.00557 ( 37) SS BOND : angle 2.25474 ( 74) covalent geometry : bond 0.00317 (19192) covalent geometry : angle 0.62046 (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 406 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 405 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8480 (tpp) cc_final: 0.7666 (tpp) REVERT: A 482 GLU cc_start: 0.8906 (mp0) cc_final: 0.8651 (mp0) REVERT: B 100 MET cc_start: 0.7642 (mtp) cc_final: 0.7276 (ttm) REVERT: B 395 TRP cc_start: 0.7181 (m100) cc_final: 0.6933 (m100) REVERT: B 426 MET cc_start: 0.5526 (tpt) cc_final: 0.5324 (mmm) REVERT: B 434 MET cc_start: 0.5182 (mtp) cc_final: 0.4066 (tpt) REVERT: B 484 TYR cc_start: 0.8666 (p90) cc_final: 0.8100 (p90) REVERT: C 78 ASP cc_start: 0.8768 (t0) cc_final: 0.8486 (t0) REVERT: C 95 MET cc_start: 0.8157 (ppp) cc_final: 0.7833 (ppp) REVERT: D 543 ASN cc_start: 0.8386 (t0) cc_final: 0.8094 (t0) REVERT: D 640 GLN cc_start: 0.8054 (mp10) cc_final: 0.7814 (mp10) REVERT: E 543 ASN cc_start: 0.8034 (p0) cc_final: 0.7730 (p0) REVERT: F 543 ASN cc_start: 0.9261 (t0) cc_final: 0.8828 (t0) REVERT: H 87 PHE cc_start: 0.8055 (m-80) cc_final: 0.7656 (m-10) REVERT: I 47 TRP cc_start: 0.8654 (t60) cc_final: 0.8356 (t60) REVERT: K 101 ASP cc_start: 0.8430 (t70) cc_final: 0.8217 (t70) REVERT: L 11 LEU cc_start: 0.8286 (tp) cc_final: 0.8065 (tt) outliers start: 1 outliers final: 0 residues processed: 406 average time/residue: 0.2639 time to fit residues: 168.7971 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 : 2.170 ------------------------------------------------------------------------------- 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: 5.9990 chunk 123 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 227 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 213 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN C 330 HIS D 650 GLN J 90 HIS ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.179871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.142617 restraints weight = 28203.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.140337 restraints weight = 42482.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.142225 restraints weight = 42759.927| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 19248 Z= 0.278 Angle : 0.806 16.563 26169 Z= 0.405 Chirality : 0.050 0.259 2975 Planarity : 0.005 0.069 3293 Dihedral : 6.545 56.840 2894 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.27 % Favored : 91.65 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: -1.13 (0.17), residues: 2322 helix: -0.11 (0.28), residues: 362 sheet: 0.05 (0.19), residues: 710 loop : -1.44 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP K 50 HIS 0.009 0.002 HIS B 105 PHE 0.028 0.003 PHE B 53 TYR 0.021 0.002 TYR I 91 ARG 0.007 0.001 ARG J 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00552 ( 6) link_NAG-ASN : angle 3.97203 ( 18) link_ALPHA1-6 : bond 0.00697 ( 3) link_ALPHA1-6 : angle 1.41290 ( 9) link_BETA1-4 : bond 0.01455 ( 7) link_BETA1-4 : angle 4.02485 ( 21) link_ALPHA1-3 : bond 0.02587 ( 3) link_ALPHA1-3 : angle 3.36040 ( 9) hydrogen bonds : bond 0.04729 ( 638) hydrogen bonds : angle 5.39640 ( 1749) SS BOND : bond 0.00833 ( 37) SS BOND : angle 2.65992 ( 74) covalent geometry : bond 0.00666 (19192) covalent geometry : angle 0.77748 (26038) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5792.38 seconds wall clock time: 102 minutes 56.58 seconds (6176.58 seconds total)