Starting phenix.real_space_refine on Fri Sep 19 04:14:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d8y_46653/09_2025/9d8y_46653.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d8y_46653/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9d8y_46653/09_2025/9d8y_46653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d8y_46653/09_2025/9d8y_46653.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d8y_46653/09_2025/9d8y_46653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d8y_46653/09_2025/9d8y_46653.map" } resolution = 4.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'GLU:plan': 10, 'ASP:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 2} 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: 4.33, per 1000 atoms: 0.23 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: 1.52 Conformation dependent library (CDL) restraints added in 881.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 66 through 72 removed outlier: 3.761A pdb=" N HIS A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.810A pdb=" N GLN A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.762A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 480 Processing helix chain 'B' and resid 100 through 115 removed outlier: 3.643A pdb=" N SER B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 353 Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.853A pdb=" N THR B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 481 removed outlier: 3.709A pdb=" N ASN B 478 " --> pdb=" O ASP B 474 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 74 removed outlier: 3.685A pdb=" N ALA C 73 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS C 74 " --> pdb=" O THR C 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 70 through 74' Processing helix chain 'C' and resid 100 through 114 removed outlier: 3.548A pdb=" N GLN C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 354 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 476 through 480 Processing helix chain 'D' and resid 536 through 543 removed outlier: 3.890A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG D 542 " --> pdb=" O THR D 538 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 596 removed outlier: 3.689A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 removed outlier: 3.518A pdb=" N ASN D 625 " --> pdb=" O GLU D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.603A pdb=" N TRP D 631 " --> pdb=" O THR D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 650 removed outlier: 3.835A pdb=" N ILE D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 662 Processing helix chain 'E' and resid 567 through 596 removed outlier: 3.689A pdb=" N GLY E 572 " --> pdb=" O LEU E 568 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ILE E 573 " --> pdb=" O THR E 569 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP E 589 " --> pdb=" O ARG E 585 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU E 592 " --> pdb=" O ARG E 588 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU E 593 " --> pdb=" O ASP E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 623 Processing helix chain 'E' and resid 627 through 636 Processing helix chain 'E' and resid 638 through 649 removed outlier: 3.514A pdb=" N ILE E 642 " --> pdb=" O TYR E 638 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 655 removed outlier: 3.538A pdb=" N LYS E 655 " --> pdb=" O ASN E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 657 through 662 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.919A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 596 removed outlier: 3.748A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 654 removed outlier: 3.589A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLN F 650 " --> pdb=" O LEU F 646 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) Processing helix chain 'F' and resid 656 through 662 removed outlier: 3.523A pdb=" N LEU F 660 " --> pdb=" O ASN F 656 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.711A pdb=" N GLY G 31 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 28 through 32' Processing helix chain 'I' and resid 28 through 32 removed outlier: 4.070A pdb=" N ASN I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 removed outlier: 4.173A pdb=" N GLN I 64 " --> pdb=" O GLN I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.854A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 4.128A pdb=" N ASN K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.859A pdb=" N THR K 87 " --> pdb=" O SER K 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 64 removed outlier: 3.812A pdb=" N ASP M 63 " --> pdb=" O SER M 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 51 through 53 No H-bonds generated for 'chain 'N' and resid 51 through 53' Processing helix chain 'O' and resid 59 through 64 removed outlier: 4.034A pdb=" N ASP O 63 " --> pdb=" O SER O 60 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 79 removed outlier: 3.509A pdb=" N ASP O 78 " --> pdb=" O LYS O 75 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER O 79 " --> pdb=" O ILE O 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 75 through 79' Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.132A pdb=" N VAL A 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N CYS D 604 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.012A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.744A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 202 Processing sheet with id=AA5, first strand: chain 'A' and resid 260 through 261 removed outlier: 6.743A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.594A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.058A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 12.064A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.745A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.647A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.154A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 12.848A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR A 384 " --> pdb=" O ARG A 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273 removed outlier: 12.848A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 11.154A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 10.647A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.745A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.064A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 12.058A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.594A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 494 through 499 removed outlier: 3.930A pdb=" N VAL B 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 45 through 47 removed outlier: 4.066A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 86 " --> pdb=" O VAL B 242 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 75 through 76 removed outlier: 6.694A pdb=" N CYS B 54 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 91 through 93 removed outlier: 3.752A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 259 through 261 removed outlier: 3.736A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS B 296 " --> pdb=" O CYS B 445 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER B 447 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N GLY B 451 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 11.269A pdb=" N THR B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 12.205A pdb=" N ILE B 453 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 11.715A pdb=" N PHE B 288 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 10.869A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 11.082A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 259 through 261 removed outlier: 3.736A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 374 through 378 Processing sheet with id=AB5, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.400A pdb=" N VAL F 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL C 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N THR F 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N TYR C 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N CYS F 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.790A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.905A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB9, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.737A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.847A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.928A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 11.921A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.659A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.101A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE C 376 " --> pdb=" O PHE C 383 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 271 through 273 removed outlier: 11.101A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.659A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.921A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.928A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.847A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 423 through 424 Processing sheet with id=AC3, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AC4, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.463A pdb=" N LEU G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N TRP G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 10 through 11 removed outlier: 4.182A pdb=" N VAL G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AC7, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.716A pdb=" N THR H 102 " --> pdb=" O TYR H 86 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.485A pdb=" N LEU I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N TRP I 50 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.934A pdb=" N VAL I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.693A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'J' and resid 53 through 54 removed outlier: 6.383A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AD6, first strand: chain 'K' and resid 10 through 11 removed outlier: 7.204A pdb=" N GLU K 10 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TRP K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 10 through 11 removed outlier: 7.204A pdb=" N GLU K 10 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD9, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.586A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 2 through 5 removed outlier: 4.184A pdb=" N LYS M 2 " --> pdb=" O GLU M 92 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N TRP M 28 " --> pdb=" O ILE M 36 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 11 through 17 removed outlier: 3.750A pdb=" N CYS M 16 " --> pdb=" O PHE M 67 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 2 through 3 removed outlier: 6.741A pdb=" N LYS N 2 " --> pdb=" O GLN N 94 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 12 through 14 Processing sheet with id=AE5, first strand: chain 'N' and resid 37 through 39 Processing sheet with id=AE6, first strand: chain 'O' and resid 2 through 5 removed outlier: 6.655A pdb=" N LYS O 2 " --> pdb=" O GLN O 94 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N LEU O 96 " --> pdb=" O LYS O 2 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL O 4 " --> pdb=" O LEU O 96 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N PHE O 26 " --> pdb=" O GLY O 38 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLY O 38 " --> pdb=" O PHE O 26 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TRP O 28 " --> pdb=" O ILE O 36 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 12 through 17 666 hydrogen bonds defined for protein. 1749 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.12 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 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: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.620 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.010 ------------------------------------------------------------------------------- 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 : 4.25 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.022 0.001 ARG J 30 TYR 0.039 0.002 TYR C 484 PHE 0.052 0.002 PHE N 67 TRP 0.089 0.003 TRP K 50 HIS 0.014 0.001 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00487 (19192) covalent geometry : angle 0.97152 (26038) SS BOND : bond 0.00779 ( 37) SS BOND : angle 2.72756 ( 74) hydrogen bonds : bond 0.13862 ( 638) hydrogen bonds : angle 7.00250 ( 1749) link_ALPHA1-3 : bond 0.01109 ( 3) link_ALPHA1-3 : angle 2.98107 ( 9) 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_NAG-ASN : bond 0.00861 ( 6) link_NAG-ASN : angle 4.65430 ( 18) *********************** 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 : 0.503 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: 0.6921 (tt) REVERT: A 486 TYR cc_start: 0.8562 (m-80) cc_final: 0.8160 (m-80) REVERT: C 95 MET cc_start: 0.8084 (ppp) cc_final: 0.7595 (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: 0.6012 (mtt) REVERT: H 53 THR cc_start: 0.8387 (m) cc_final: 0.8143 (p) REVERT: I 86 ASP cc_start: 0.6180 (p0) cc_final: 0.5842 (m-30) REVERT: I 100 MET cc_start: 0.7591 (mtm) cc_final: 0.7182 (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: 0.7725 (tp) outliers start: 2 outliers final: 1 residues processed: 428 average time/residue: 0.1151 time to fit residues: 77.5474 Evaluate side-chains 352 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 351 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS B 348 GLN D 607 ASN D 650 GLN H 90 HIS J 6 GLN ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.180044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.147436 restraints weight = 27434.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.147260 restraints weight = 48932.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.148152 restraints weight = 46500.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.148478 restraints weight = 30657.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.149766 restraints weight = 26585.038| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 19248 Z= 0.305 Angle : 0.811 13.325 26169 Z= 0.413 Chirality : 0.050 0.238 2975 Planarity : 0.006 0.087 3293 Dihedral : 9.448 84.213 2894 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.80 % Favored : 93.15 % Rotamer: Outliers : 0.25 % Allowed : 7.65 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.17), residues: 2322 helix: -1.12 (0.25), residues: 362 sheet: 0.22 (0.19), residues: 679 loop : -1.72 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG H 24 TYR 0.022 0.002 TYR I 91 PHE 0.032 0.003 PHE B 53 TRP 0.039 0.003 TRP K 50 HIS 0.012 0.003 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00720 (19192) covalent geometry : angle 0.78481 (26038) SS BOND : bond 0.00640 ( 37) SS BOND : angle 2.32451 ( 74) hydrogen bonds : bond 0.05274 ( 638) hydrogen bonds : angle 5.94610 ( 1749) link_ALPHA1-3 : bond 0.02451 ( 3) link_ALPHA1-3 : angle 2.59548 ( 9) link_ALPHA1-6 : bond 0.00353 ( 3) link_ALPHA1-6 : angle 1.82359 ( 9) link_BETA1-4 : bond 0.01397 ( 7) link_BETA1-4 : angle 3.82943 ( 21) link_NAG-ASN : bond 0.00709 ( 6) link_NAG-ASN : angle 4.44177 ( 18) *********************** 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 415 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 410 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8794 (tpp) cc_final: 0.8514 (tpp) REVERT: B 100 MET cc_start: 0.8096 (mtp) cc_final: 0.7782 (mtp) REVERT: B 377 ASN cc_start: 0.7514 (t0) cc_final: 0.7293 (t0) REVERT: C 49 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7502 (mm-30) REVERT: C 95 MET cc_start: 0.8145 (ppp) cc_final: 0.7919 (ppp) REVERT: D 647 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7704 (tm-30) REVERT: E 543 ASN cc_start: 0.8124 (p0) cc_final: 0.7899 (p0) REVERT: F 543 ASN cc_start: 0.8737 (t0) cc_final: 0.8493 (t0) REVERT: H 33 LEU cc_start: 0.8250 (tp) cc_final: 0.7910 (tt) REVERT: H 94 TYR cc_start: 0.8499 (m-80) cc_final: 0.8249 (m-10) REVERT: I 100 MET cc_start: 0.8576 (mtm) cc_final: 0.7312 (mtt) REVERT: L 33 LEU cc_start: 0.8181 (tp) cc_final: 0.7955 (tp) REVERT: L 45 ASN cc_start: 0.8303 (t0) cc_final: 0.8003 (t0) REVERT: M 26 PHE cc_start: 0.6771 (p90) cc_final: 0.6327 (p90) outliers start: 5 outliers final: 3 residues processed: 415 average time/residue: 0.1294 time to fit residues: 84.5115 Evaluate side-chains 340 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 337 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 216 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 204 optimal weight: 20.0000 chunk 114 optimal weight: 0.0070 chunk 228 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 210 optimal weight: 8.9990 chunk 119 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 158 optimal weight: 6.9990 overall best weight: 1.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS G 39 GLN K 6 GLN ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.184757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.148345 restraints weight = 27335.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.146833 restraints weight = 37478.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.148229 restraints weight = 37926.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.149949 restraints weight = 23930.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.150293 restraints weight = 21003.887| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19248 Z= 0.158 Angle : 0.673 11.825 26169 Z= 0.337 Chirality : 0.046 0.224 2975 Planarity : 0.004 0.050 3293 Dihedral : 8.198 71.179 2894 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.86 % Favored : 94.10 % Rotamer: Outliers : 0.05 % Allowed : 3.48 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.17), residues: 2322 helix: -0.54 (0.27), residues: 362 sheet: 0.30 (0.20), residues: 669 loop : -1.54 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 579 TYR 0.017 0.002 TYR A 484 PHE 0.023 0.002 PHE F 522 TRP 0.041 0.002 TRP G 50 HIS 0.007 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00359 (19192) covalent geometry : angle 0.64317 (26038) SS BOND : bond 0.00625 ( 37) SS BOND : angle 2.22421 ( 74) hydrogen bonds : bond 0.04087 ( 638) hydrogen bonds : angle 5.58753 ( 1749) link_ALPHA1-3 : bond 0.02656 ( 3) link_ALPHA1-3 : angle 3.63348 ( 9) link_ALPHA1-6 : bond 0.00565 ( 3) link_ALPHA1-6 : angle 1.83046 ( 9) link_BETA1-4 : bond 0.01424 ( 7) link_BETA1-4 : angle 3.78070 ( 21) link_NAG-ASN : bond 0.00693 ( 6) link_NAG-ASN : angle 3.88828 ( 18) *********************** 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 444 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 443 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8728 (tpp) cc_final: 0.8124 (tpt) REVERT: B 100 MET cc_start: 0.7963 (mtp) cc_final: 0.7645 (mtp) REVERT: B 104 MET cc_start: 0.7777 (ttt) cc_final: 0.7093 (ttm) REVERT: C 244 THR cc_start: 0.8490 (OUTLIER) cc_final: 0.7964 (m) REVERT: D 647 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7617 (tm-30) REVERT: E 543 ASN cc_start: 0.8003 (p0) cc_final: 0.7726 (p0) REVERT: F 543 ASN cc_start: 0.8710 (t0) cc_final: 0.8386 (t0) REVERT: I 47 TRP cc_start: 0.8600 (t60) cc_final: 0.8257 (t60) REVERT: K 45 LEU cc_start: 0.8714 (mt) cc_final: 0.8484 (mt) REVERT: L 33 LEU cc_start: 0.8121 (tp) cc_final: 0.7901 (tp) REVERT: L 45 ASN cc_start: 0.8234 (t0) cc_final: 0.7899 (t0) REVERT: L 52 SER cc_start: 0.8465 (p) cc_final: 0.8245 (t) outliers start: 1 outliers final: 0 residues processed: 444 average time/residue: 0.1245 time to fit residues: 86.7316 Evaluate side-chains 350 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 349 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 9 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 220 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 190 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 330 HIS B 352 HIS B 422 GLN D 651 ASN H 37 GLN H 90 HIS J 90 HIS L 90 HIS ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.176134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.147241 restraints weight = 28335.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.148358 restraints weight = 54437.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.147792 restraints weight = 41987.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.147310 restraints weight = 34839.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.147837 restraints weight = 28839.810| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 19248 Z= 0.336 Angle : 0.854 13.530 26169 Z= 0.431 Chirality : 0.052 0.287 2975 Planarity : 0.005 0.073 3293 Dihedral : 8.102 63.178 2894 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.44 % Favored : 91.52 % Rotamer: Outliers : 0.15 % Allowed : 5.69 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.17), residues: 2322 helix: -0.81 (0.26), residues: 370 sheet: 0.20 (0.20), residues: 631 loop : -1.79 (0.16), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 30 TYR 0.023 0.003 TYR I 91 PHE 0.033 0.003 PHE C 53 TRP 0.038 0.003 TRP C 45 HIS 0.015 0.002 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00797 (19192) covalent geometry : angle 0.82451 (26038) SS BOND : bond 0.00843 ( 37) SS BOND : angle 2.68799 ( 74) hydrogen bonds : bond 0.05349 ( 638) hydrogen bonds : angle 5.89285 ( 1749) link_ALPHA1-3 : bond 0.02689 ( 3) link_ALPHA1-3 : angle 3.65531 ( 9) link_ALPHA1-6 : bond 0.00607 ( 3) link_ALPHA1-6 : angle 1.73858 ( 9) link_BETA1-4 : bond 0.01401 ( 7) link_BETA1-4 : angle 4.13418 ( 21) link_NAG-ASN : bond 0.00802 ( 6) link_NAG-ASN : angle 4.30215 ( 18) *********************** 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 404 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 401 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8753 (tpp) cc_final: 0.8087 (tpt) REVERT: B 49 GLU cc_start: 0.7758 (tp30) cc_final: 0.7388 (mm-30) REVERT: B 99 ASN cc_start: 0.7807 (t0) cc_final: 0.7154 (t0) REVERT: B 100 MET cc_start: 0.8103 (mtp) cc_final: 0.7713 (mtp) REVERT: C 49 GLU cc_start: 0.7598 (tp30) cc_final: 0.7260 (mm-30) REVERT: C 95 MET cc_start: 0.8384 (ppp) cc_final: 0.7925 (ppp) REVERT: C 99 ASN cc_start: 0.8025 (t0) cc_final: 0.7498 (t0) REVERT: D 530 MET cc_start: 0.8001 (tpt) cc_final: 0.7517 (tpt) REVERT: D 595 ILE cc_start: 0.8662 (tt) cc_final: 0.8305 (tt) REVERT: D 647 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7839 (tm-30) REVERT: F 515 ILE cc_start: 0.8860 (tt) cc_final: 0.8582 (tt) REVERT: F 543 ASN cc_start: 0.8788 (t0) cc_final: 0.8552 (t0) REVERT: H 33 LEU cc_start: 0.7963 (tp) cc_final: 0.7710 (tt) REVERT: I 47 TRP cc_start: 0.8770 (t60) cc_final: 0.8531 (t60) REVERT: J 91 MET cc_start: 0.5314 (mtp) cc_final: 0.5105 (mtp) REVERT: K 47 TRP cc_start: 0.8344 (t60) cc_final: 0.7839 (t60) REVERT: L 33 LEU cc_start: 0.7973 (tp) cc_final: 0.7721 (tp) REVERT: L 45 ASN cc_start: 0.8472 (t0) cc_final: 0.8171 (t0) REVERT: M 30 ASN cc_start: 0.6879 (p0) cc_final: 0.6623 (p0) REVERT: M 56 ASP cc_start: 0.6021 (t0) cc_final: 0.5729 (t0) outliers start: 3 outliers final: 2 residues processed: 404 average time/residue: 0.1196 time to fit residues: 76.8396 Evaluate side-chains 342 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 340 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 87 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 229 optimal weight: 8.9990 chunk 202 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN B 105 HIS B 246 GLN B 330 HIS B 352 HIS C 330 HIS H 90 HIS J 6 GLN ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.181061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.148700 restraints weight = 28117.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.147436 restraints weight = 44578.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.148465 restraints weight = 46675.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.148937 restraints weight = 29199.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.149792 restraints weight = 25767.392| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 19248 Z= 0.208 Angle : 0.720 12.440 26169 Z= 0.361 Chirality : 0.048 0.291 2975 Planarity : 0.005 0.070 3293 Dihedral : 7.305 55.826 2894 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.68 % Favored : 93.28 % Rotamer: Outliers : 0.05 % Allowed : 3.63 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.17), residues: 2322 helix: -0.51 (0.27), residues: 373 sheet: 0.22 (0.20), residues: 635 loop : -1.66 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 30 TYR 0.017 0.002 TYR A 484 PHE 0.023 0.002 PHE C 376 TRP 0.060 0.002 TRP K 50 HIS 0.007 0.001 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00488 (19192) covalent geometry : angle 0.69135 (26038) SS BOND : bond 0.00624 ( 37) SS BOND : angle 2.27688 ( 74) hydrogen bonds : bond 0.04321 ( 638) hydrogen bonds : angle 5.61942 ( 1749) link_ALPHA1-3 : bond 0.02995 ( 3) link_ALPHA1-3 : angle 4.01012 ( 9) link_ALPHA1-6 : bond 0.00588 ( 3) link_ALPHA1-6 : angle 1.59554 ( 9) link_BETA1-4 : bond 0.01454 ( 7) link_BETA1-4 : angle 3.90530 ( 21) link_NAG-ASN : bond 0.00604 ( 6) link_NAG-ASN : angle 3.64395 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 410 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8507 (tpp) cc_final: 0.7878 (tpp) REVERT: B 100 MET cc_start: 0.8115 (mtp) cc_final: 0.7765 (mtp) REVERT: B 384 TYR cc_start: 0.7826 (m-10) cc_final: 0.7621 (m-10) REVERT: C 95 MET cc_start: 0.8528 (ppp) cc_final: 0.8099 (ppp) REVERT: D 530 MET cc_start: 0.7843 (tpt) cc_final: 0.7329 (tpt) REVERT: F 543 ASN cc_start: 0.8692 (t0) cc_final: 0.8376 (t0) REVERT: I 100 MET cc_start: 0.8579 (mtm) cc_final: 0.8162 (mtt) REVERT: K 45 LEU cc_start: 0.8715 (mt) cc_final: 0.8476 (mt) REVERT: L 45 ASN cc_start: 0.8401 (t0) cc_final: 0.8082 (t0) REVERT: L 52 SER cc_start: 0.8437 (p) cc_final: 0.8194 (t) REVERT: M 46 LYS cc_start: 0.6228 (mtmt) cc_final: 0.5844 (tttt) REVERT: M 52 ASN cc_start: 0.7591 (p0) cc_final: 0.7293 (p0) REVERT: N 30 ASN cc_start: 0.7653 (p0) cc_final: 0.6782 (p0) outliers start: 1 outliers final: 0 residues processed: 411 average time/residue: 0.1248 time to fit residues: 79.6757 Evaluate side-chains 339 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 170 optimal weight: 9.9990 chunk 169 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 HIS ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 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 = 0.4010 r_free = 0.4010 target = 0.180458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.145806 restraints weight = 28083.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.142401 restraints weight = 42785.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.143902 restraints weight = 43729.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.144902 restraints weight = 28111.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.145281 restraints weight = 26152.406| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 19248 Z= 0.192 Angle : 0.703 12.416 26169 Z= 0.352 Chirality : 0.047 0.258 2975 Planarity : 0.004 0.070 3293 Dihedral : 6.898 54.789 2894 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.75 % Favored : 92.20 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.17), residues: 2322 helix: -0.20 (0.28), residues: 354 sheet: 0.26 (0.21), residues: 621 loop : -1.52 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 61 TYR 0.020 0.002 TYR A 484 PHE 0.021 0.002 PHE B 53 TRP 0.044 0.002 TRP G 50 HIS 0.007 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00457 (19192) covalent geometry : angle 0.67548 (26038) SS BOND : bond 0.00642 ( 37) SS BOND : angle 2.32185 ( 74) hydrogen bonds : bond 0.04153 ( 638) hydrogen bonds : angle 5.50962 ( 1749) link_ALPHA1-3 : bond 0.02733 ( 3) link_ALPHA1-3 : angle 3.77344 ( 9) link_ALPHA1-6 : bond 0.00626 ( 3) link_ALPHA1-6 : angle 1.49303 ( 9) link_BETA1-4 : bond 0.01357 ( 7) link_BETA1-4 : angle 3.82235 ( 21) link_NAG-ASN : bond 0.00568 ( 6) link_NAG-ASN : angle 3.43206 ( 18) *********************** 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 396 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8424 (tpp) cc_final: 0.7965 (tpp) REVERT: B 100 MET cc_start: 0.8074 (mtp) cc_final: 0.7718 (mtp) REVERT: C 95 MET cc_start: 0.8454 (ppp) cc_final: 0.8034 (ppp) REVERT: D 647 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7886 (tm-30) REVERT: F 543 ASN cc_start: 0.8630 (t0) cc_final: 0.8322 (t0) REVERT: I 47 TRP cc_start: 0.8788 (t60) cc_final: 0.8420 (t60) REVERT: I 100 MET cc_start: 0.8713 (mtm) cc_final: 0.8414 (mtt) REVERT: K 45 LEU cc_start: 0.8751 (mt) cc_final: 0.8519 (mt) REVERT: L 45 ASN cc_start: 0.8371 (t0) cc_final: 0.8097 (t0) REVERT: M 46 LYS cc_start: 0.6197 (mtmt) cc_final: 0.5868 (tttt) REVERT: M 52 ASN cc_start: 0.7709 (p0) cc_final: 0.7374 (p0) outliers start: 0 outliers final: 0 residues processed: 396 average time/residue: 0.1211 time to fit residues: 75.7988 Evaluate side-chains 340 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 179 optimal weight: 9.9990 chunk 157 optimal weight: 0.0770 chunk 95 optimal weight: 20.0000 chunk 63 optimal weight: 0.7980 chunk 218 optimal weight: 10.0000 chunk 212 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 170 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 219 optimal weight: 5.9990 overall best weight: 1.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS B 330 HIS ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS C 330 HIS D 651 ASN H 90 HIS J 90 HIS ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.181856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.144838 restraints weight = 28307.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.142455 restraints weight = 42588.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.144280 restraints weight = 43203.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.144791 restraints weight = 27444.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.145836 restraints weight = 24809.647| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 19248 Z= 0.197 Angle : 0.724 14.168 26169 Z= 0.361 Chirality : 0.048 0.324 2975 Planarity : 0.005 0.069 3293 Dihedral : 6.788 54.937 2894 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.62 % Favored : 92.33 % Rotamer: Outliers : 0.05 % Allowed : 1.86 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.17), residues: 2322 helix: -0.21 (0.28), residues: 362 sheet: 0.19 (0.20), residues: 627 loop : -1.51 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 71 TYR 0.019 0.002 TYR C 484 PHE 0.025 0.002 PHE C 376 TRP 0.036 0.002 TRP A 112 HIS 0.006 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00467 (19192) covalent geometry : angle 0.69168 (26038) SS BOND : bond 0.00617 ( 37) SS BOND : angle 2.42741 ( 74) hydrogen bonds : bond 0.04148 ( 638) hydrogen bonds : angle 5.44122 ( 1749) link_ALPHA1-3 : bond 0.02703 ( 3) link_ALPHA1-3 : angle 3.77168 ( 9) link_ALPHA1-6 : bond 0.00636 ( 3) link_ALPHA1-6 : angle 1.45630 ( 9) link_BETA1-4 : bond 0.01452 ( 7) link_BETA1-4 : angle 3.87207 ( 21) link_NAG-ASN : bond 0.00498 ( 6) link_NAG-ASN : angle 4.55864 ( 18) *********************** 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 403 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 402 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8383 (tpp) cc_final: 0.7700 (tpp) REVERT: B 99 ASN cc_start: 0.7916 (t0) cc_final: 0.7679 (t0) REVERT: B 384 TYR cc_start: 0.7871 (m-10) cc_final: 0.7618 (m-10) REVERT: C 95 MET cc_start: 0.8405 (ppp) cc_final: 0.7936 (ppp) REVERT: D 647 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7837 (tm-30) REVERT: F 543 ASN cc_start: 0.8698 (t0) cc_final: 0.8381 (t0) REVERT: H 24 ARG cc_start: 0.7362 (tpp80) cc_final: 0.7132 (tpp80) REVERT: I 100 MET cc_start: 0.8805 (mtm) cc_final: 0.8549 (mtt) REVERT: K 45 LEU cc_start: 0.8766 (mt) cc_final: 0.8513 (mt) REVERT: L 45 ASN cc_start: 0.8333 (t0) cc_final: 0.8102 (t0) REVERT: M 46 LYS cc_start: 0.6137 (mtmt) cc_final: 0.5751 (tttt) REVERT: M 52 ASN cc_start: 0.7776 (p0) cc_final: 0.7384 (p0) outliers start: 1 outliers final: 0 residues processed: 403 average time/residue: 0.1178 time to fit residues: 75.3237 Evaluate side-chains 339 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 214 optimal weight: 8.9990 chunk 227 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 chunk 200 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 201 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 205 optimal weight: 7.9990 chunk 116 optimal weight: 0.9980 chunk 146 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.178320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.143913 restraints weight = 28286.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.142558 restraints weight = 46883.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.143958 restraints weight = 45231.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.144615 restraints weight = 27510.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.146003 restraints weight = 23605.572| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 19248 Z= 0.266 Angle : 0.796 15.389 26169 Z= 0.400 Chirality : 0.050 0.371 2975 Planarity : 0.005 0.080 3293 Dihedral : 6.998 57.559 2894 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.87 % Favored : 91.09 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.17), residues: 2322 helix: -0.55 (0.27), residues: 375 sheet: -0.09 (0.19), residues: 704 loop : -1.72 (0.17), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 71 TYR 0.019 0.002 TYR C 484 PHE 0.024 0.002 PHE B 53 TRP 0.049 0.003 TRP I 47 HIS 0.009 0.002 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00636 (19192) covalent geometry : angle 0.76543 (26038) SS BOND : bond 0.00700 ( 37) SS BOND : angle 2.55148 ( 74) hydrogen bonds : bond 0.04677 ( 638) hydrogen bonds : angle 5.59919 ( 1749) link_ALPHA1-3 : bond 0.02672 ( 3) link_ALPHA1-3 : angle 3.81190 ( 9) link_ALPHA1-6 : bond 0.00633 ( 3) link_ALPHA1-6 : angle 1.47514 ( 9) link_BETA1-4 : bond 0.01484 ( 7) link_BETA1-4 : angle 4.11810 ( 21) link_NAG-ASN : bond 0.00481 ( 6) link_NAG-ASN : angle 4.24746 ( 18) *********************** 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 396 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8597 (tpp) cc_final: 0.7891 (tpp) REVERT: B 49 GLU cc_start: 0.7740 (tp30) cc_final: 0.7331 (mm-30) REVERT: B 99 ASN cc_start: 0.7875 (t0) cc_final: 0.7089 (t0) REVERT: B 104 MET cc_start: 0.7944 (ttt) cc_final: 0.7269 (ttm) REVERT: D 530 MET cc_start: 0.7876 (tpt) cc_final: 0.7227 (tpt) REVERT: F 543 ASN cc_start: 0.8650 (t0) cc_final: 0.8321 (t0) REVERT: G 86 ASP cc_start: 0.6919 (m-30) cc_final: 0.6650 (m-30) REVERT: K 45 LEU cc_start: 0.8819 (mt) cc_final: 0.8611 (mt) REVERT: K 47 TRP cc_start: 0.8358 (t60) cc_final: 0.7782 (t60) REVERT: L 45 ASN cc_start: 0.8403 (t0) cc_final: 0.8188 (t0) REVERT: M 26 PHE cc_start: 0.6819 (p90) cc_final: 0.6315 (p90) REVERT: M 46 LYS cc_start: 0.6183 (mtmt) cc_final: 0.5847 (tttt) REVERT: M 52 ASN cc_start: 0.7793 (p0) cc_final: 0.7415 (p0) outliers start: 0 outliers final: 0 residues processed: 396 average time/residue: 0.1142 time to fit residues: 72.3938 Evaluate side-chains 334 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 334 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 36 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 9 optimal weight: 0.2980 chunk 212 optimal weight: 9.9990 chunk 78 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 219 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 HIS ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 GLN ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 GLN O 52 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.181266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.152026 restraints weight = 27923.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.151973 restraints weight = 48174.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.152469 restraints weight = 41349.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.151951 restraints weight = 31378.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.152483 restraints weight = 29246.600| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19248 Z= 0.175 Angle : 0.719 12.310 26169 Z= 0.360 Chirality : 0.047 0.290 2975 Planarity : 0.004 0.074 3293 Dihedral : 6.605 55.279 2894 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.85 % Favored : 93.11 % Rotamer: Outliers : 0.05 % Allowed : 0.98 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.17), residues: 2322 helix: -0.24 (0.28), residues: 364 sheet: 0.01 (0.20), residues: 686 loop : -1.53 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 30 TYR 0.021 0.002 TYR A 484 PHE 0.017 0.002 PHE C 53 TRP 0.047 0.002 TRP A 112 HIS 0.005 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00413 (19192) covalent geometry : angle 0.68864 (26038) SS BOND : bond 0.00624 ( 37) SS BOND : angle 2.37489 ( 74) hydrogen bonds : bond 0.04038 ( 638) hydrogen bonds : angle 5.44121 ( 1749) link_ALPHA1-3 : bond 0.02719 ( 3) link_ALPHA1-3 : angle 3.76601 ( 9) link_ALPHA1-6 : bond 0.00647 ( 3) link_ALPHA1-6 : angle 1.41412 ( 9) link_BETA1-4 : bond 0.01425 ( 7) link_BETA1-4 : angle 3.92674 ( 21) link_NAG-ASN : bond 0.00503 ( 6) link_NAG-ASN : angle 3.94678 ( 18) *********************** 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 397 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 396 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8482 (tpp) cc_final: 0.7651 (tpp) REVERT: B 434 MET cc_start: 0.5415 (mtp) cc_final: 0.4050 (tpt) REVERT: D 530 MET cc_start: 0.7615 (tpt) cc_final: 0.7003 (tpt) REVERT: F 543 ASN cc_start: 0.8747 (t0) cc_final: 0.8340 (t0) REVERT: I 47 TRP cc_start: 0.8576 (t60) cc_final: 0.8318 (t60) REVERT: J 91 MET cc_start: 0.7044 (mtm) cc_final: 0.6763 (mtp) REVERT: K 13 LYS cc_start: 0.6295 (mmmt) cc_final: 0.5654 (mmtt) REVERT: K 47 TRP cc_start: 0.8267 (t60) cc_final: 0.7648 (t60) REVERT: M 26 PHE cc_start: 0.6560 (p90) cc_final: 0.6340 (p90) REVERT: M 52 ASN cc_start: 0.7531 (p0) cc_final: 0.7257 (p0) REVERT: N 30 ASN cc_start: 0.7612 (p0) cc_final: 0.6716 (p0) outliers start: 1 outliers final: 1 residues processed: 397 average time/residue: 0.1176 time to fit residues: 74.7712 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 : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 112 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 135 optimal weight: 0.0040 chunk 15 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 166 optimal weight: 0.1980 chunk 224 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 218 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 overall best weight: 1.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN B 330 HIS ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS ** C 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 HIS ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.182793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.148996 restraints weight = 27995.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.146953 restraints weight = 42688.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.148055 restraints weight = 39313.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.150230 restraints weight = 27860.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.150250 restraints weight = 21877.573| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 19248 Z= 0.149 Angle : 0.702 11.870 26169 Z= 0.350 Chirality : 0.046 0.266 2975 Planarity : 0.004 0.067 3293 Dihedral : 6.352 54.833 2894 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.24 % Favored : 92.68 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.18), residues: 2322 helix: -0.09 (0.28), residues: 364 sheet: 0.07 (0.20), residues: 698 loop : -1.46 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 542 TYR 0.026 0.002 TYR K 97 PHE 0.027 0.002 PHE C 376 TRP 0.036 0.002 TRP G 50 HIS 0.014 0.002 HIS C 352 Details of bonding type rmsd covalent geometry : bond 0.00349 (19192) covalent geometry : angle 0.67311 (26038) SS BOND : bond 0.00562 ( 37) SS BOND : angle 2.32997 ( 74) hydrogen bonds : bond 0.03763 ( 638) hydrogen bonds : angle 5.33892 ( 1749) link_ALPHA1-3 : bond 0.02627 ( 3) link_ALPHA1-3 : angle 3.64059 ( 9) link_ALPHA1-6 : bond 0.00664 ( 3) link_ALPHA1-6 : angle 1.39678 ( 9) link_BETA1-4 : bond 0.01410 ( 7) link_BETA1-4 : angle 3.76814 ( 21) link_NAG-ASN : bond 0.00500 ( 6) link_NAG-ASN : angle 3.74323 ( 18) ********************** 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 399 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 399 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8440 (tpp) cc_final: 0.7769 (tpp) REVERT: B 104 MET cc_start: 0.8044 (ttt) cc_final: 0.7237 (ttt) REVERT: B 395 TRP cc_start: 0.7220 (m100) cc_final: 0.6972 (m100) REVERT: B 434 MET cc_start: 0.5386 (mtp) cc_final: 0.4041 (tpt) REVERT: C 277 ILE cc_start: 0.7785 (mm) cc_final: 0.7462 (mm) REVERT: C 298 ARG cc_start: 0.6918 (ttt-90) cc_final: 0.6557 (tmt170) REVERT: F 543 ASN cc_start: 0.8653 (t0) cc_final: 0.8364 (t0) REVERT: F 635 ILE cc_start: 0.7750 (tp) cc_final: 0.7388 (tp) REVERT: K 45 LEU cc_start: 0.8738 (mt) cc_final: 0.8477 (mt) REVERT: K 47 TRP cc_start: 0.8211 (t60) cc_final: 0.7673 (t60) REVERT: L 33 LEU cc_start: 0.8261 (tp) cc_final: 0.7969 (tp) REVERT: L 45 ASN cc_start: 0.8221 (t0) cc_final: 0.7903 (t0) REVERT: M 26 PHE cc_start: 0.6525 (p90) cc_final: 0.6320 (p90) REVERT: M 52 ASN cc_start: 0.7882 (p0) cc_final: 0.7644 (p0) REVERT: N 30 ASN cc_start: 0.7628 (p0) cc_final: 0.6761 (p0) outliers start: 0 outliers final: 0 residues processed: 399 average time/residue: 0.1237 time to fit residues: 78.7635 Evaluate side-chains 345 residues out of total 2066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 182 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 chunk 162 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 146 optimal weight: 9.9990 chunk 138 optimal weight: 1.9990 chunk 222 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 104 optimal weight: 0.0270 chunk 171 optimal weight: 5.9990 chunk 221 optimal weight: 1.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN B 330 HIS ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS C 352 HIS I 6 GLN ** 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 = 0.4053 r_free = 0.4053 target = 0.184440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.155387 restraints weight = 27919.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.154677 restraints weight = 47461.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.155435 restraints weight = 42796.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.156568 restraints weight = 28702.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.156609 restraints weight = 24528.159| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19248 Z= 0.128 Angle : 0.681 11.545 26169 Z= 0.339 Chirality : 0.046 0.243 2975 Planarity : 0.004 0.059 3293 Dihedral : 6.076 54.863 2894 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.37 % Favored : 93.54 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.18), residues: 2322 helix: 0.24 (0.29), residues: 358 sheet: 0.12 (0.20), residues: 691 loop : -1.40 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 30 TYR 0.023 0.002 TYR K 97 PHE 0.028 0.001 PHE H 87 TRP 0.052 0.002 TRP I 47 HIS 0.009 0.001 HIS C 352 Details of bonding type rmsd covalent geometry : bond 0.00294 (19192) covalent geometry : angle 0.65328 (26038) SS BOND : bond 0.00566 ( 37) SS BOND : angle 2.33464 ( 74) hydrogen bonds : bond 0.03505 ( 638) hydrogen bonds : angle 5.20404 ( 1749) link_ALPHA1-3 : bond 0.02548 ( 3) link_ALPHA1-3 : angle 3.52946 ( 9) link_ALPHA1-6 : bond 0.00678 ( 3) link_ALPHA1-6 : angle 1.38999 ( 9) link_BETA1-4 : bond 0.01459 ( 7) link_BETA1-4 : angle 3.64299 ( 21) link_NAG-ASN : bond 0.00477 ( 6) link_NAG-ASN : angle 3.54670 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2601.03 seconds wall clock time: 46 minutes 6.45 seconds (2766.45 seconds total)