Starting phenix.real_space_refine on Tue Jan 21 00:02:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l8w_23238/01_2025/7l8w_23238.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l8w_23238/01_2025/7l8w_23238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l8w_23238/01_2025/7l8w_23238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l8w_23238/01_2025/7l8w_23238.map" model { file = "/net/cci-nas-00/data/ceres_data/7l8w_23238/01_2025/7l8w_23238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l8w_23238/01_2025/7l8w_23238.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 9845 2.51 5 N 2677 2.21 5 O 3176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 15803 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3485 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain breaks: 3 Chain: "B" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1055 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain breaks: 1 Chain: "C" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3460 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 20, 'TRANS': 417} Chain breaks: 3 Chain: "D" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1060 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain breaks: 1 Chain: "E" Number of atoms: 3466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3466 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 20, 'TRANS': 418} Chain breaks: 3 Chain: "F" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1052 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain breaks: 1 Chain: "H" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 545 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'TRANS': 108} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 109 Planarities with less than four sites: {'UNK:plan-1': 109} Unresolved non-hydrogen planarities: 109 Chain: "L" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 515 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'TRANS': 102} Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 103 Planarities with less than four sites: {'UNK:plan-1': 103} Unresolved non-hydrogen planarities: 103 Chain: "G" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "I" 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: "J" 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: "K" 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: "M" 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: "N" 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: "O" 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "B" 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: "C" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 10.78, per 1000 atoms: 0.68 Number of scatterers: 15803 At special positions: 0 Unit cell: (127.72, 136.99, 118.45, 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 105 16.00 O 3176 8.00 N 2677 7.00 C 9845 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.07 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.12 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 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 B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.02 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS D 561 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.06 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 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=2.10 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 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 54 " - pdb=" SG CYS E 73 " distance=2.04 Simple disulfide: pdb=" SG CYS E 74 " - pdb=" SG CYS F 561 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.05 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 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 ALPHA1-2 " MAN G 4 " - " MAN G 5 " " MAN G 5 " - " MAN G 6 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " MAN G 7 " - " MAN G 8 " " BMA K 3 " - " MAN K 4 " " BMA O 3 " - " MAN O 4 " ALPHA1-6 " BMA G 3 " - " MAN G 7 " " MAN G 7 " - " MAN G 9 " " BMA K 3 " - " MAN K 5 " " BMA O 3 " - " MAN O 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 241 " " NAG A 604 " - " ASN A 276 " " NAG A 605 " - " ASN A 392 " " NAG A 606 " - " ASN A 386 " " NAG A 607 " - " ASN A 339 " " NAG A 608 " - " ASN A 332 " " NAG A 609 " - " ASN A 295 " " NAG A 610 " - " ASN A 448 " " NAG A 611 " - " ASN A 301 " " NAG A 612 " - " ASN A 160 " " NAG A 613 " - " ASN A 197 " " NAG A 614 " - " ASN A 133 " " NAG A 615 " - " ASN A 289 " " NAG A 616 " - " ASN A 137 " " NAG A 617 " - " ASN A 363 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 241 " " NAG C 604 " - " ASN C 276 " " NAG C 605 " - " ASN C 392 " " NAG C 606 " - " ASN C 386 " " NAG C 607 " - " ASN C 339 " " NAG C 608 " - " ASN C 295 " " NAG C 609 " - " ASN C 448 " " NAG C 610 " - " ASN C 301 " " NAG C 611 " - " ASN C 160 " " NAG C 612 " - " ASN C 197 " " NAG C 613 " - " ASN C 133 " " NAG C 614 " - " ASN C 355 " " NAG C 615 " - " ASN C 289 " " NAG C 616 " - " ASN C 363 " " NAG D 701 " - " ASN D 618 " " NAG D 702 " - " ASN D 637 " " NAG D 703 " - " ASN D 611 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 234 " " NAG E 603 " - " ASN E 241 " " NAG E 604 " - " ASN E 276 " " NAG E 605 " - " ASN E 392 " " NAG E 606 " - " ASN E 386 " " NAG E 607 " - " ASN E 339 " " NAG E 608 " - " ASN E 295 " " NAG E 609 " - " ASN E 448 " " NAG E 610 " - " ASN E 301 " " NAG E 611 " - " ASN E 160 " " NAG E 612 " - " ASN E 197 " " NAG E 613 " - " ASN E 133 " " NAG E 614 " - " ASN E 355 " " NAG E 615 " - " ASN E 289 " " NAG E 616 " - " ASN E 363 " " NAG F 701 " - " ASN F 618 " " NAG F 702 " - " ASN F 637 " " NAG F 703 " - " ASN F 611 " " NAG G 1 " - " ASN A 262 " " NAG I 1 " - " ASN A 156 " " NAG J 1 " - " ASN C 332 " " NAG K 1 " - " ASN C 262 " " NAG M 1 " - " ASN C 156 " " NAG N 1 " - " ASN E 332 " " NAG O 1 " - " ASN E 262 " " NAG P 1 " - " ASN E 156 " Time building additional restraints: 4.86 Conformation dependent library (CDL) restraints added in 2.0 seconds 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3640 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 32 sheets defined 31.7% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 98 through 115 removed outlier: 3.525A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 334 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 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.534A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 543 Processing helix chain 'B' and resid 558 through 568 removed outlier: 3.744A pdb=" N GLN B 562 " --> pdb=" O ALA B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 596 Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 661 removed outlier: 3.631A pdb=" N TRP B 631 " --> pdb=" O THR B 627 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASN B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N TYR B 638 " --> pdb=" O GLU B 634 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLN B 640 " --> pdb=" O SER B 636 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ILE B 641 " --> pdb=" O ASN B 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.504A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 334 through 354 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 475 through 483 removed outlier: 3.783A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.345A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 544 removed outlier: 4.084A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 568 Processing helix chain 'D' and resid 568 through 596 Processing helix chain 'D' and resid 618 through 624 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 663 removed outlier: 3.965A pdb=" N LEU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.015A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 334 through 354 removed outlier: 3.762A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.500A pdb=" N ARG E 480 " --> pdb=" O ARG E 476 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.117A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 545 removed outlier: 4.027A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 568 Processing helix chain 'F' and resid 568 through 596 Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 663 Processing helix chain 'H' and resid 70 through 72 No H-bonds generated for 'chain 'H' and resid 70 through 72' Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.687A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 5.648A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.876A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.128A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 12.231A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.968A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.264A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 11.264A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.968A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.231A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 12.128A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.876A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 305 through 312 removed outlier: 6.445A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 494 through 499 Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB6, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.334A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.678A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 10.991A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.118A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.679A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.609A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.373A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.880A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.373A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.609A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.679A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.118A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 10.991A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 304 through 312 removed outlier: 3.753A pdb=" N ILE C 309 " --> pdb=" O GLN C 315 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.351A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC3, first strand: chain 'E' and resid 75 through 76 removed outlier: 3.704A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC6, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.236A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.698A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 10.992A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 9.986A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.361A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.516A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.370A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.128A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.522A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.128A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.370A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.516A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.361A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.986A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 10.992A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 304 through 312 removed outlier: 3.783A pdb=" N ILE E 309 " --> pdb=" O GLN E 315 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.778A pdb=" N UNK H 18 " --> pdb=" O UNK H 79 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 56 through 58 Processing sheet with id=AD3, first strand: chain 'L' and resid 6 through 8 Processing sheet with id=AD4, first strand: chain 'L' and resid 12 through 13 Processing sheet with id=AD5, first strand: chain 'L' and resid 55 through 56 removed outlier: 6.561A pdb=" N UNK L 37 " --> pdb=" O UNK L 49 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N UNK L 86 " --> pdb=" O UNK L 40 " (cutoff:3.500A) 668 hydrogen bonds defined for protein. 1797 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: 5.73 Time building geometry restraints manager: 5.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3102 1.32 - 1.46: 5297 1.46 - 1.60: 7510 1.60 - 1.74: 30 1.74 - 1.88: 133 Bond restraints: 16072 Sorted by residual: bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.414 -0.088 1.10e-02 8.26e+03 6.43e+01 bond pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " ideal model delta sigma weight residual 1.497 1.395 0.102 1.40e-02 5.10e+03 5.36e+01 bond pdb=" NE ARG E 503 " pdb=" CZ ARG E 503 " ideal model delta sigma weight residual 1.326 1.404 -0.078 1.10e-02 8.26e+03 4.98e+01 bond pdb=" NE ARG C 550 " pdb=" CZ ARG C 550 " ideal model delta sigma weight residual 1.326 1.393 -0.067 1.10e-02 8.26e+03 3.74e+01 bond pdb=" CB ILE A 396 " pdb=" CG1 ILE A 396 " ideal model delta sigma weight residual 1.530 1.651 -0.121 2.00e-02 2.50e+03 3.64e+01 ... (remaining 16067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 18523 2.29 - 4.58: 2814 4.58 - 6.87: 469 6.87 - 9.16: 44 9.16 - 11.44: 2 Bond angle restraints: 21852 Sorted by residual: angle pdb=" C PHE C 53 " pdb=" N CYS C 54 " pdb=" CA CYS C 54 " ideal model delta sigma weight residual 122.19 133.63 -11.44 1.41e+00 5.03e-01 6.59e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 127.67 -8.11 1.01e+00 9.80e-01 6.44e+01 angle pdb=" N PRO E 437 " pdb=" CA PRO E 437 " pdb=" C PRO E 437 " ideal model delta sigma weight residual 110.47 103.05 7.42 9.60e-01 1.09e+00 5.98e+01 angle pdb=" N THR A 464 " pdb=" CA THR A 464 " pdb=" C THR A 464 " ideal model delta sigma weight residual 113.23 122.33 -9.10 1.24e+00 6.50e-01 5.39e+01 angle pdb=" C CYS C 205 " pdb=" N PRO C 206 " pdb=" CA PRO C 206 " ideal model delta sigma weight residual 119.56 126.89 -7.33 1.02e+00 9.61e-01 5.16e+01 ... (remaining 21847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.43: 10478 21.43 - 42.86: 220 42.86 - 64.30: 74 64.30 - 85.73: 33 85.73 - 107.16: 13 Dihedral angle restraints: 10818 sinusoidal: 5229 harmonic: 5589 Sorted by residual: dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 166.12 -73.12 1 1.00e+01 1.00e-02 6.81e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 164.19 -71.19 1 1.00e+01 1.00e-02 6.51e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 159.81 -66.81 1 1.00e+01 1.00e-02 5.82e+01 ... (remaining 10815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.188: 2395 0.188 - 0.376: 311 0.376 - 0.565: 64 0.565 - 0.753: 1 0.753 - 0.941: 2 Chirality restraints: 2773 Sorted by residual: chirality pdb=" C1 MAN G 8 " pdb=" O3 MAN G 7 " pdb=" C2 MAN G 8 " pdb=" O5 MAN G 8 " both_signs ideal model delta sigma weight residual False 2.40 1.46 0.94 2.00e-02 2.50e+03 2.21e+03 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.07e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.53e+01 ... (remaining 2770 not shown) Planarity restraints: 2744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 602 " -0.339 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG E 602 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG E 602 " -0.153 2.00e-02 2.50e+03 pdb=" N2 NAG E 602 " 0.516 2.00e-02 2.50e+03 pdb=" O7 NAG E 602 " -0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 607 " -0.332 2.00e-02 2.50e+03 2.83e-01 9.99e+02 pdb=" C7 NAG A 607 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG A 607 " -0.174 2.00e-02 2.50e+03 pdb=" N2 NAG A 607 " 0.496 2.00e-02 2.50e+03 pdb=" O7 NAG A 607 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 612 " 0.322 2.00e-02 2.50e+03 2.74e-01 9.39e+02 pdb=" C7 NAG A 612 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG A 612 " 0.179 2.00e-02 2.50e+03 pdb=" N2 NAG A 612 " -0.479 2.00e-02 2.50e+03 pdb=" O7 NAG A 612 " 0.060 2.00e-02 2.50e+03 ... (remaining 2741 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 5748 2.88 - 3.39: 14373 3.39 - 3.89: 25518 3.89 - 4.40: 29106 4.40 - 4.90: 45961 Nonbonded interactions: 120706 Sorted by model distance: nonbonded pdb=" N ILE A 213 " pdb=" O ILE A 213 " model vdw 2.378 2.496 nonbonded pdb=" O3 NAG D 703 " pdb=" O7 NAG D 703 " model vdw 2.383 3.040 nonbonded pdb=" O ASN A 80 " pdb=" NE2 GLN A 82 " model vdw 2.436 3.120 nonbonded pdb=" OD1 ASN E 234 " pdb=" N GLY E 235 " model vdw 2.451 3.120 nonbonded pdb=" N ASP C 167 " pdb=" OD1 ASP C 167 " model vdw 2.488 3.120 ... (remaining 120701 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 57 or resid 64 through 503 or resid 601 through \ 616)) selection = (chain 'C' and (resid 33 through 185 or resid 189 through 457 or resid 461 throu \ gh 550 or resid 601 through 616)) selection = (chain 'E' and (resid 33 through 57 or resid 64 through 457 or resid 461 through \ 503 or resid 601 through 616)) } ncs_group { reference = (chain 'B' and (resid 521 through 546 or resid 558 through 662 or resid 701 thro \ ugh 702)) selection = (chain 'D' and (resid 521 through 662 or resid 702 through 703)) selection = (chain 'F' and (resid 521 through 662 or resid 702 through 703)) } ncs_group { reference = (chain 'H' and resid 8 through 110) selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'K' selection = chain 'O' } 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: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 39.430 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 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 : 0.021 0.121 16072 Z= 1.335 Angle : 1.709 11.444 21852 Z= 1.104 Chirality : 0.137 0.941 2773 Planarity : 0.018 0.291 2679 Dihedral : 11.366 107.162 7070 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.19), residues: 1678 helix: 0.58 (0.22), residues: 427 sheet: 1.21 (0.23), residues: 465 loop : 0.77 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.010 TRP C 35 HIS 0.013 0.002 HIS A 249 PHE 0.039 0.006 PHE A 383 TYR 0.071 0.008 TYR D 638 ARG 0.006 0.001 ARG F 542 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 512 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 SER cc_start: 0.9435 (p) cc_final: 0.8917 (t) REVERT: A 257 THR cc_start: 0.8957 (p) cc_final: 0.8655 (m) REVERT: B 591 GLN cc_start: 0.9098 (tt0) cc_final: 0.8843 (tt0) REVERT: B 599 SER cc_start: 0.9019 (p) cc_final: 0.8341 (t) REVERT: B 601 LYS cc_start: 0.8850 (ptpt) cc_final: 0.8597 (tptp) REVERT: B 603 ILE cc_start: 0.8779 (mt) cc_final: 0.8504 (mp) REVERT: C 38 VAL cc_start: 0.8541 (t) cc_final: 0.8184 (t) REVERT: C 69 TRP cc_start: 0.8141 (m-10) cc_final: 0.7916 (m-10) REVERT: C 102 GLU cc_start: 0.8251 (tp30) cc_final: 0.7744 (tm-30) REVERT: C 199 SER cc_start: 0.9546 (p) cc_final: 0.9297 (t) REVERT: D 585 ARG cc_start: 0.9197 (mmt180) cc_final: 0.8895 (ttm-80) REVERT: D 586 TYR cc_start: 0.9636 (t80) cc_final: 0.9361 (t80) REVERT: D 623 TRP cc_start: 0.8861 (m100) cc_final: 0.8397 (m-10) REVERT: E 45 TRP cc_start: 0.8802 (p90) cc_final: 0.8588 (p90) REVERT: E 57 ASP cc_start: 0.8224 (t0) cc_final: 0.7880 (p0) REVERT: E 103 GLN cc_start: 0.8566 (tt0) cc_final: 0.8209 (tm-30) REVERT: E 381 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7550 (tt0) REVERT: F 579 ARG cc_start: 0.9118 (mtp180) cc_final: 0.8779 (ttm170) REVERT: F 629 LEU cc_start: 0.9059 (tp) cc_final: 0.8768 (mp) REVERT: F 638 TYR cc_start: 0.8321 (m-80) cc_final: 0.8061 (m-10) REVERT: F 650 GLN cc_start: 0.8917 (tp40) cc_final: 0.7738 (tm-30) REVERT: F 654 GLU cc_start: 0.8592 (mt-10) cc_final: 0.7130 (mt-10) outliers start: 0 outliers final: 0 residues processed: 512 average time/residue: 0.3241 time to fit residues: 233.2793 Evaluate side-chains 249 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 171 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN A 422 GLN C 66 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 HIS C 302 ASN C 422 GLN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** 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 = 0.3505 r_free = 0.3505 target = 0.112964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.093741 restraints weight = 35210.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.096478 restraints weight = 20829.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.098301 restraints weight = 14611.752| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 16072 Z= 0.258 Angle : 0.781 11.415 21852 Z= 0.395 Chirality : 0.053 0.850 2773 Planarity : 0.004 0.043 2679 Dihedral : 9.761 91.741 3805 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.01 % Favored : 98.93 % Rotamer: Outliers : 0.33 % Allowed : 2.03 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.20), residues: 1678 helix: 1.87 (0.25), residues: 429 sheet: 1.10 (0.23), residues: 451 loop : 0.15 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 69 HIS 0.008 0.001 HIS A 249 PHE 0.018 0.002 PHE A 383 TYR 0.016 0.002 TYR A 191 ARG 0.007 0.001 ARG E 151 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 362 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8899 (mmm) cc_final: 0.8652 (mmm) REVERT: B 560 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8473 (mm-30) REVERT: B 599 SER cc_start: 0.9016 (p) cc_final: 0.8194 (t) REVERT: B 602 LEU cc_start: 0.8751 (mt) cc_final: 0.8351 (pt) REVERT: B 641 ILE cc_start: 0.7891 (mp) cc_final: 0.7343 (tp) REVERT: B 643 TYR cc_start: 0.9031 (m-10) cc_final: 0.8728 (m-10) REVERT: C 38 VAL cc_start: 0.8481 (t) cc_final: 0.7914 (t) REVERT: C 114 GLN cc_start: 0.8483 (tp40) cc_final: 0.7546 (tm-30) REVERT: C 199 SER cc_start: 0.9479 (p) cc_final: 0.9194 (t) REVERT: C 286 VAL cc_start: 0.9296 (t) cc_final: 0.9058 (m) REVERT: C 377 ASN cc_start: 0.9165 (t0) cc_final: 0.8871 (t0) REVERT: C 395 TRP cc_start: 0.7683 (m100) cc_final: 0.7446 (m100) REVERT: C 486 TYR cc_start: 0.9054 (m-80) cc_final: 0.8752 (m-80) REVERT: D 565 LEU cc_start: 0.7825 (tp) cc_final: 0.7351 (tp) REVERT: D 577 GLN cc_start: 0.8079 (tm-30) cc_final: 0.7725 (tm-30) REVERT: D 588 ARG cc_start: 0.8712 (tmm-80) cc_final: 0.8499 (tmm-80) REVERT: D 643 TYR cc_start: 0.8984 (m-10) cc_final: 0.8609 (m-80) REVERT: E 51 THR cc_start: 0.9068 (m) cc_final: 0.8632 (p) REVERT: E 103 GLN cc_start: 0.8186 (tt0) cc_final: 0.7697 (tm-30) REVERT: F 543 ASN cc_start: 0.8515 (t0) cc_final: 0.8196 (t0) REVERT: F 590 GLN cc_start: 0.9179 (mm-40) cc_final: 0.8937 (tp40) REVERT: F 629 LEU cc_start: 0.8805 (tp) cc_final: 0.8499 (mp) REVERT: F 634 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8175 (mm-30) REVERT: F 648 GLU cc_start: 0.8352 (tp30) cc_final: 0.8092 (tp30) REVERT: F 650 GLN cc_start: 0.8978 (tp40) cc_final: 0.8350 (tm-30) REVERT: F 652 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8307 (tt0) REVERT: F 653 GLN cc_start: 0.8323 (tt0) cc_final: 0.8090 (tt0) outliers start: 5 outliers final: 2 residues processed: 365 average time/residue: 0.2944 time to fit residues: 156.7988 Evaluate side-chains 255 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 253 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 180 optimal weight: 20.0000 chunk 122 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 174 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS B 658 GLN C 422 GLN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN E 203 GLN E 300 ASN ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.110041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.090601 restraints weight = 35806.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.093215 restraints weight = 21620.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.094987 restraints weight = 15319.823| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 16072 Z= 0.278 Angle : 0.698 10.374 21852 Z= 0.353 Chirality : 0.049 0.505 2773 Planarity : 0.004 0.041 2679 Dihedral : 8.570 74.452 3805 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.67 % Favored : 98.27 % Rotamer: Outliers : 0.13 % Allowed : 3.14 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.20), residues: 1678 helix: 1.91 (0.25), residues: 429 sheet: 0.91 (0.23), residues: 437 loop : 0.02 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 69 HIS 0.006 0.001 HIS C 66 PHE 0.017 0.002 PHE A 383 TYR 0.015 0.002 TYR E 173 ARG 0.009 0.001 ARG D 617 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 313 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 SER cc_start: 0.8691 (t) cc_final: 0.8437 (p) REVERT: A 256 SER cc_start: 0.9519 (p) cc_final: 0.9101 (m) REVERT: A 318 TYR cc_start: 0.8793 (m-80) cc_final: 0.8581 (m-80) REVERT: A 475 MET cc_start: 0.8878 (mmm) cc_final: 0.8626 (mmm) REVERT: B 599 SER cc_start: 0.8890 (p) cc_final: 0.8542 (p) REVERT: B 602 LEU cc_start: 0.8746 (mt) cc_final: 0.8392 (pt) REVERT: B 641 ILE cc_start: 0.8024 (mp) cc_final: 0.7364 (tp) REVERT: B 643 TYR cc_start: 0.9094 (m-10) cc_final: 0.8820 (m-10) REVERT: C 38 VAL cc_start: 0.8304 (t) cc_final: 0.7885 (t) REVERT: C 199 SER cc_start: 0.9493 (p) cc_final: 0.9173 (t) REVERT: C 377 ASN cc_start: 0.9215 (t0) cc_final: 0.8788 (t0) REVERT: C 395 TRP cc_start: 0.7536 (m100) cc_final: 0.7298 (m100) REVERT: C 475 MET cc_start: 0.8464 (mmm) cc_final: 0.7942 (mmm) REVERT: D 577 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7842 (tm-30) REVERT: D 588 ARG cc_start: 0.8798 (tmm-80) cc_final: 0.8567 (tmm-80) REVERT: D 657 GLU cc_start: 0.8607 (tp30) cc_final: 0.8407 (tp30) REVERT: E 103 GLN cc_start: 0.8200 (tt0) cc_final: 0.7822 (tm-30) REVERT: E 486 TYR cc_start: 0.8908 (m-80) cc_final: 0.8407 (m-80) REVERT: F 607 ASN cc_start: 0.8827 (p0) cc_final: 0.8404 (p0) REVERT: F 610 TRP cc_start: 0.8445 (t-100) cc_final: 0.7317 (t-100) REVERT: F 629 LEU cc_start: 0.8622 (tp) cc_final: 0.8384 (tp) REVERT: F 631 TRP cc_start: 0.8160 (t60) cc_final: 0.7684 (t-100) REVERT: F 634 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8083 (mm-30) REVERT: F 648 GLU cc_start: 0.8380 (tp30) cc_final: 0.8097 (tp30) outliers start: 2 outliers final: 0 residues processed: 315 average time/residue: 0.2904 time to fit residues: 134.2330 Evaluate side-chains 233 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 47 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 125 optimal weight: 0.0970 chunk 174 optimal weight: 9.9990 chunk 13 optimal weight: 0.6980 chunk 127 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 143 optimal weight: 0.2980 chunk 93 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 ASN B 658 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN E 249 HIS E 428 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.112214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.092835 restraints weight = 35337.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.095517 restraints weight = 20933.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.097347 restraints weight = 14697.582| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 16072 Z= 0.186 Angle : 0.629 12.098 21852 Z= 0.314 Chirality : 0.047 0.429 2773 Planarity : 0.003 0.048 2679 Dihedral : 7.908 67.457 3805 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.31 % Favored : 98.63 % Rotamer: Outliers : 0.07 % Allowed : 2.29 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.20), residues: 1678 helix: 1.98 (0.25), residues: 436 sheet: 0.82 (0.23), residues: 439 loop : -0.06 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 69 HIS 0.005 0.001 HIS A 249 PHE 0.022 0.002 PHE C 210 TYR 0.026 0.001 TYR D 643 ARG 0.004 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 310 time to evaluate : 1.671 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 209 SER cc_start: 0.8762 (t) cc_final: 0.8455 (p) REVERT: A 256 SER cc_start: 0.9470 (p) cc_final: 0.8990 (m) REVERT: B 599 SER cc_start: 0.8853 (p) cc_final: 0.8160 (t) REVERT: B 603 ILE cc_start: 0.8596 (mt) cc_final: 0.8322 (mp) REVERT: B 641 ILE cc_start: 0.8069 (mp) cc_final: 0.7344 (tp) REVERT: B 643 TYR cc_start: 0.8921 (m-10) cc_final: 0.8693 (m-10) REVERT: C 38 VAL cc_start: 0.8092 (t) cc_final: 0.7548 (t) REVERT: C 114 GLN cc_start: 0.8590 (tp40) cc_final: 0.7633 (tm-30) REVERT: C 199 SER cc_start: 0.9502 (p) cc_final: 0.9198 (t) REVERT: C 377 ASN cc_start: 0.9228 (t0) cc_final: 0.8732 (t0) REVERT: D 567 LYS cc_start: 0.8870 (ttmm) cc_final: 0.8641 (tmtt) REVERT: D 650 GLN cc_start: 0.8725 (tp40) cc_final: 0.7834 (tm-30) REVERT: E 103 GLN cc_start: 0.8137 (tt0) cc_final: 0.7909 (tm-30) REVERT: E 150 MET cc_start: 0.8069 (mmm) cc_final: 0.7541 (mmt) REVERT: F 607 ASN cc_start: 0.8829 (p0) cc_final: 0.8342 (p0) REVERT: F 629 LEU cc_start: 0.8745 (tp) cc_final: 0.8496 (mp) REVERT: F 634 GLU cc_start: 0.8780 (mt-10) cc_final: 0.7982 (mm-30) REVERT: F 648 GLU cc_start: 0.8360 (tp30) cc_final: 0.8119 (tp30) outliers start: 1 outliers final: 0 residues processed: 311 average time/residue: 0.2878 time to fit residues: 132.3834 Evaluate side-chains 240 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 10 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 127 optimal weight: 0.6980 chunk 61 optimal weight: 0.0570 chunk 23 optimal weight: 0.7980 chunk 163 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN C 352 HIS D 630 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN E 249 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.112077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.092838 restraints weight = 36005.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.095508 restraints weight = 21174.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.097290 restraints weight = 14830.792| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 16072 Z= 0.189 Angle : 0.610 11.919 21852 Z= 0.307 Chirality : 0.047 0.412 2773 Planarity : 0.003 0.047 2679 Dihedral : 7.282 61.414 3805 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.73 % Favored : 98.21 % Rotamer: Outliers : 0.07 % Allowed : 2.03 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.20), residues: 1678 helix: 1.92 (0.25), residues: 434 sheet: 0.76 (0.24), residues: 432 loop : -0.14 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 69 HIS 0.004 0.001 HIS F 564 PHE 0.019 0.002 PHE C 210 TYR 0.015 0.001 TYR E 173 ARG 0.008 0.000 ARG D 617 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 304 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9075 (tpp) cc_final: 0.8690 (tpt) REVERT: A 209 SER cc_start: 0.8706 (t) cc_final: 0.8453 (p) REVERT: A 210 PHE cc_start: 0.7764 (m-80) cc_final: 0.7548 (m-10) REVERT: A 256 SER cc_start: 0.9373 (p) cc_final: 0.9015 (m) REVERT: B 599 SER cc_start: 0.8792 (p) cc_final: 0.8124 (t) REVERT: B 641 ILE cc_start: 0.8033 (mp) cc_final: 0.7321 (tp) REVERT: B 643 TYR cc_start: 0.8928 (m-10) cc_final: 0.8672 (m-10) REVERT: C 38 VAL cc_start: 0.8068 (t) cc_final: 0.7617 (t) REVERT: C 199 SER cc_start: 0.9467 (p) cc_final: 0.9148 (t) REVERT: C 377 ASN cc_start: 0.9282 (t0) cc_final: 0.8754 (t0) REVERT: C 414 ILE cc_start: 0.9294 (mm) cc_final: 0.9039 (tp) REVERT: D 542 ARG cc_start: 0.8429 (ttp80) cc_final: 0.7942 (tpt170) REVERT: D 565 LEU cc_start: 0.7809 (tp) cc_final: 0.7391 (tp) REVERT: D 571 TRP cc_start: 0.7253 (t60) cc_final: 0.6848 (t60) REVERT: D 650 GLN cc_start: 0.8675 (tp40) cc_final: 0.7882 (tm-30) REVERT: E 103 GLN cc_start: 0.8349 (tt0) cc_final: 0.7665 (tm-30) REVERT: E 150 MET cc_start: 0.8098 (mmm) cc_final: 0.7664 (mmt) REVERT: E 381 GLU cc_start: 0.7433 (mt-10) cc_final: 0.6915 (tt0) REVERT: F 536 THR cc_start: 0.8242 (p) cc_final: 0.8021 (p) REVERT: F 607 ASN cc_start: 0.8853 (p0) cc_final: 0.8317 (p0) REVERT: F 629 LEU cc_start: 0.8758 (tp) cc_final: 0.8310 (tp) REVERT: F 634 GLU cc_start: 0.8668 (mt-10) cc_final: 0.7917 (mm-30) outliers start: 1 outliers final: 0 residues processed: 305 average time/residue: 0.3002 time to fit residues: 134.4059 Evaluate side-chains 232 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 23 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 131 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS B 651 ASN B 658 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS E 287 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.100449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.082180 restraints weight = 36926.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.084545 restraints weight = 22385.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.086126 restraints weight = 15951.687| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.103 16072 Z= 0.515 Angle : 0.873 14.503 21852 Z= 0.434 Chirality : 0.054 0.443 2773 Planarity : 0.006 0.078 2679 Dihedral : 8.195 59.722 3805 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.68 % Favored : 97.26 % Rotamer: Outliers : 0.13 % Allowed : 2.49 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.20), residues: 1678 helix: 1.27 (0.25), residues: 429 sheet: 0.43 (0.24), residues: 444 loop : -0.56 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP C 69 HIS 0.008 0.002 HIS A 330 PHE 0.033 0.004 PHE A 93 TYR 0.026 0.003 TYR C 191 ARG 0.009 0.001 ARG D 585 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 267 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 VAL cc_start: 0.9424 (m) cc_final: 0.9174 (p) REVERT: A 104 MET cc_start: 0.8982 (tpp) cc_final: 0.8675 (tpp) REVERT: A 209 SER cc_start: 0.8956 (t) cc_final: 0.8700 (p) REVERT: A 210 PHE cc_start: 0.8137 (m-80) cc_final: 0.7882 (m-10) REVERT: A 256 SER cc_start: 0.9491 (p) cc_final: 0.9147 (m) REVERT: B 599 SER cc_start: 0.8966 (p) cc_final: 0.8441 (t) REVERT: B 641 ILE cc_start: 0.7965 (mp) cc_final: 0.7571 (tp) REVERT: B 643 TYR cc_start: 0.9120 (m-10) cc_final: 0.8850 (m-10) REVERT: C 98 ASN cc_start: 0.9258 (t0) cc_final: 0.9020 (t0) REVERT: C 150 MET cc_start: 0.8816 (ppp) cc_final: 0.8171 (ppp) REVERT: C 199 SER cc_start: 0.9417 (p) cc_final: 0.9196 (t) REVERT: C 414 ILE cc_start: 0.9495 (mm) cc_final: 0.9271 (tp) REVERT: C 475 MET cc_start: 0.8772 (mmm) cc_final: 0.8073 (mmm) REVERT: D 565 LEU cc_start: 0.8309 (tp) cc_final: 0.7536 (tp) REVERT: D 571 TRP cc_start: 0.7558 (t60) cc_final: 0.7071 (t60) REVERT: D 615 SER cc_start: 0.8115 (t) cc_final: 0.7906 (m) REVERT: E 150 MET cc_start: 0.8143 (mmm) cc_final: 0.7819 (mmt) REVERT: E 381 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7139 (tt0) REVERT: E 500 ARG cc_start: 0.5727 (mtt180) cc_final: 0.5021 (pmt170) REVERT: F 607 ASN cc_start: 0.9116 (p0) cc_final: 0.8543 (p0) REVERT: F 629 LEU cc_start: 0.8648 (tp) cc_final: 0.8312 (tp) REVERT: F 634 GLU cc_start: 0.8786 (mt-10) cc_final: 0.7992 (mm-30) outliers start: 2 outliers final: 0 residues processed: 267 average time/residue: 0.3054 time to fit residues: 119.1571 Evaluate side-chains 213 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.2407 > 50: distance: 41 - 43: 6.482 distance: 43 - 44: 21.604 distance: 44 - 45: 25.044 distance: 44 - 47: 6.813 distance: 45 - 46: 7.516 distance: 45 - 54: 22.963 distance: 47 - 48: 6.948 distance: 48 - 49: 8.289 distance: 48 - 50: 5.371 distance: 49 - 51: 9.483 distance: 50 - 52: 4.466 distance: 51 - 53: 15.708 distance: 52 - 53: 3.500 distance: 54 - 55: 24.640 distance: 54 - 228: 12.831 distance: 55 - 56: 22.454 distance: 55 - 58: 20.820 distance: 56 - 57: 13.550 distance: 56 - 59: 17.266 distance: 57 - 225: 14.035 distance: 59 - 60: 14.138 distance: 59 - 171: 13.224 distance: 60 - 61: 19.092 distance: 60 - 63: 15.880 distance: 61 - 62: 4.183 distance: 61 - 67: 6.155 distance: 62 - 168: 24.189 distance: 63 - 65: 6.892 distance: 64 - 66: 12.686 distance: 67 - 68: 6.537 distance: 67 - 217: 24.059 distance: 68 - 69: 7.522 distance: 68 - 71: 12.943 distance: 69 - 70: 15.379 distance: 69 - 75: 7.912 distance: 70 - 214: 34.417 distance: 71 - 72: 19.059 distance: 72 - 73: 14.932 distance: 72 - 74: 41.451 distance: 75 - 76: 8.373 distance: 75 - 158: 23.410 distance: 76 - 77: 9.782 distance: 76 - 79: 11.516 distance: 77 - 78: 23.170 distance: 77 - 84: 12.594 distance: 78 - 155: 25.364 distance: 79 - 80: 14.011 distance: 80 - 81: 8.477 distance: 81 - 82: 6.494 distance: 82 - 83: 22.598 distance: 84 - 85: 11.237 distance: 85 - 86: 12.792 distance: 85 - 88: 6.464 distance: 86 - 87: 18.192 distance: 86 - 90: 20.468 distance: 88 - 89: 11.072 distance: 89 - 141: 9.614 distance: 90 - 91: 11.542 distance: 91 - 92: 5.139 distance: 91 - 94: 6.079 distance: 92 - 93: 8.348 distance: 92 - 99: 3.762 distance: 94 - 95: 17.439 distance: 95 - 96: 9.292 distance: 96 - 97: 7.020 distance: 97 - 98: 13.669 distance: 99 - 100: 8.517 distance: 100 - 101: 34.799 distance: 100 - 103: 24.481 distance: 101 - 102: 14.451 distance: 101 - 107: 13.508 distance: 103 - 104: 12.131 distance: 104 - 105: 14.491 distance: 104 - 106: 6.879 distance: 107 - 108: 6.427 distance: 108 - 109: 7.531 distance: 108 - 111: 15.289 distance: 109 - 110: 8.912 distance: 109 - 116: 3.132 distance: 111 - 112: 14.227 distance: 112 - 113: 19.075 distance: 113 - 114: 13.783 distance: 114 - 115: 22.725 distance: 116 - 117: 9.921 distance: 117 - 118: 10.611 distance: 117 - 120: 5.506 distance: 118 - 119: 3.528 distance: 118 - 125: 5.502 distance: 120 - 121: 11.516 distance: 121 - 122: 20.373 distance: 122 - 123: 21.595