Starting phenix.real_space_refine on Fri Jul 3 19:13:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l8u_23237/07_2026/7l8u_23237.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l8u_23237/07_2026/7l8u_23237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7l8u_23237/07_2026/7l8u_23237.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l8u_23237/07_2026/7l8u_23237.cif" model { file = "/net/cci-nas-00/data/ceres_data/7l8u_23237/07_2026/7l8u_23237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l8u_23237/07_2026/7l8u_23237.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l8u_23237/07_2026/7l8u_23237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l8u_23237/07_2026/7l8u_23237.map" } resolution = 4.5 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= 0.002 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 104 5.16 5 C 9639 2.51 5 N 2626 2.21 5 O 3106 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15475 Number of models: 1 Model: "" Number of chains: 25 Chain: "C" Number of atoms: 3401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3401 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 20, 'TRANS': 409} Chain breaks: 4 Chain: "D" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1052 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "A" Number of atoms: 3459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3459 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 20, 'TRANS': 417} Chain breaks: 3 Chain: "B" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1006 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "E" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3410 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 20, 'TRANS': 410} Chain breaks: 4 Chain: "F" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 942 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "H" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 565 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'TRANS': 112} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 113 Planarities with less than four sites: {'UNK:plan-1': 113} Unresolved non-hydrogen planarities: 113 Chain: "L" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 525 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'TRANS': 104} Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 105 Planarities with less than four sites: {'UNK:plan-1': 105} Unresolved non-hydrogen planarities: 105 Chain: "G" 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 chiralities: 2 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 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 chiralities: 2 Chain: "K" 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 chiralities: 2 Chain: "M" 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 chiralities: 5 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 chiralities: 2 Chain: "O" 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 chiralities: 2 Chain: "P" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "Q" 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 chiralities: 2 Chain: "R" 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 chiralities: 2 Chain: "S" 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 chiralities: 5 Chain: "T" 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 chiralities: 2 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 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 chiralities: 2 Chain: "E" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 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 chiralities: 3 Time building chain proxies: 3.55, per 1000 atoms: 0.23 Number of scatterers: 15475 At special positions: 0 Unit cell: (128.75, 134.93, 133.9, 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 104 16.00 O 3106 8.00 N 2626 7.00 C 9639 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.13 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS D 561 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.05 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 228 " - pdb=" SG CYS C 239 " distance=2.09 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 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 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 A 54 " - pdb=" SG CYS A 73 " distance=2.04 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.18 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.12 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 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 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.02 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.15 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=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 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 M 4 " - " MAN M 5 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA P 3 " - " MAN P 7 " " MAN P 4 " - " MAN P 5 " " BMA S 3 " - " MAN S 4 " ALPHA1-6 " BMA P 3 " - " MAN P 4 " " MAN P 4 " - " MAN P 6 " " BMA S 3 " - " MAN S 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 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 339 " " NAG A 607 " - " ASN A 332 " " NAG A 608 " - " ASN A 295 " " NAG A 609 " - " ASN A 448 " " NAG A 610 " - " ASN A 301 " " NAG A 611 " - " ASN A 160 " " NAG A 612 " - " ASN A 197 " " NAG A 613 " - " ASN A 133 " " NAG A 614 " - " ASN A 355 " " NAG A 615 " - " ASN A 289 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 625 " " 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 339 " " NAG C 607 " - " ASN C 332 " " 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 E 601 " - " ASN E 234 " " NAG E 602 " - " ASN E 241 " " NAG E 603 " - " ASN E 276 " " NAG E 604 " - " ASN E 392 " " NAG E 605 " - " ASN E 332 " " NAG E 606 " - " ASN E 295 " " NAG E 607 " - " ASN E 448 " " NAG E 608 " - " ASN E 301 " " NAG E 609 " - " ASN E 160 " " NAG E 610 " - " ASN E 197 " " NAG E 611 " - " ASN E 133 " " NAG E 612 " - " ASN E 289 " " NAG F 701 " - " ASN F 618 " " NAG F 702 " - " ASN F 637 " " NAG F 703 " - " ASN F 611 " " NAG G 1 " - " ASN C 386 " " NAG I 1 " - " ASN C 262 " " NAG J 1 " - " ASN C 156 " " NAG K 1 " - " ASN A 386 " " NAG M 1 " - " ASN A 262 " " NAG N 1 " - " ASN A 156 " " NAG O 1 " - " ASN B 618 " " NAG P 1 " - " ASN B 611 " " NAG Q 1 " - " ASN E 88 " " NAG R 1 " - " ASN E 386 " " NAG S 1 " - " ASN E 262 " " NAG T 1 " - " ASN E 156 " Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 591.1 milliseconds 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3574 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 35 sheets defined 28.4% alpha, 36.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.503A 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 removed outlier: 3.864A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 531 through 536 removed outlier: 4.278A pdb=" N MET D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR D 536 " --> pdb=" O ALA D 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 531 through 536' Processing helix chain 'D' and resid 536 through 543 Processing helix chain 'D' and resid 544 through 546 No H-bonds generated for 'chain 'D' and resid 544 through 546' Processing helix chain 'D' and resid 561 through 566 removed outlier: 4.144A pdb=" N HIS D 564 " --> pdb=" O CYS D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 596 Processing helix chain 'D' and resid 628 through 635 removed outlier: 3.672A pdb=" N ILE D 635 " --> pdb=" O TRP D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 639 through 663 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.061A 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 334 through 342 Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.760A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 475 through 483 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 563 through 568 Processing helix chain 'B' and resid 570 through 596 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 639 through 658 Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 139 through 151 Processing helix chain 'E' and resid 334 through 350 removed outlier: 4.960A pdb=" N GLU E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.721A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 removed outlier: 4.101A pdb=" N MET F 535 " --> pdb=" O ALA F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.951A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG F 542 " --> pdb=" O THR F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 571 No H-bonds generated for 'chain 'F' and resid 569 through 571' Processing helix chain 'F' and resid 572 through 596 Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 662 removed outlier: 3.519A pdb=" N GLN F 653 " --> pdb=" O SER F 649 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA F 662 " --> pdb=" O GLN F 658 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.228A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.698A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 91 through 92 Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.337A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 260 through 261 removed outlier: 6.675A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.502A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.986A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 12.110A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.383A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.903A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 271 through 273 removed outlier: 10.903A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 11.383A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.110A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.986A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.502A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 301 through 312 removed outlier: 6.748A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 35 through 40 Processing sheet with id=AB2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.764A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AB6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.771A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 259 through 261 removed outlier: 5.644A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.804A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.935A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.982A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.983A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.776A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 271 through 274 removed outlier: 10.776A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.983A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.982A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.935A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.804A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE A 359 " --> pdb=" O TRP A 395 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TRP A 395 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AC1, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.442A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.277A 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 removed outlier: 3.692A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 53 through 55 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 201 through 203 removed outlier: 6.685A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET E 434 " --> pdb=" O ILE E 424 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 394 through 395 removed outlier: 6.047A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.501A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.634A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.807A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.766A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.748A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 271 through 273 Processing sheet with id=AD1, first strand: chain 'E' and resid 315 through 323A removed outlier: 7.088A pdb=" N TRP E 316 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ILE E 309 " --> pdb=" O TRP E 316 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP E 322 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.537A pdb=" N UNK H 79 " --> pdb=" O UNK H 19 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N UNK H 74 " --> pdb=" O UNK H 70 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 35 through 36 removed outlier: 3.586A pdb=" N UNK H 103 " --> pdb=" O UNK H 96 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 88 through 89 Processing sheet with id=AD5, first strand: chain 'L' and resid 17 through 20 removed outlier: 6.938A pdb=" N UNK L 19 " --> pdb=" O UNK L 76 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N UNK L 76 " --> pdb=" O UNK L 19 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 23 through 24 Processing sheet with id=AD7, first strand: chain 'L' and resid 35 through 36 removed outlier: 6.880A pdb=" N UNK L 35 " --> pdb=" O UNK L 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 88 through 89 574 hydrogen bonds defined for protein. 1533 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: 2.65 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 4538 1.34 - 1.48: 4593 1.48 - 1.63: 6463 1.63 - 1.78: 44 1.78 - 1.93: 99 Bond restraints: 15737 Sorted by residual: 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 4.99e+01 bond pdb=" NE ARG A 30 " pdb=" CZ ARG A 30 " ideal model delta sigma weight residual 1.326 1.401 -0.075 1.10e-02 8.26e+03 4.63e+01 bond pdb=" CB ILE C 396 " pdb=" CG1 ILE C 396 " ideal model delta sigma weight residual 1.530 1.664 -0.134 2.00e-02 2.50e+03 4.50e+01 bond pdb=" CB LEU F 544 " pdb=" CG LEU F 544 " ideal model delta sigma weight residual 1.530 1.656 -0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" CB ILE E 396 " pdb=" CG1 ILE E 396 " ideal model delta sigma weight residual 1.530 1.656 -0.126 2.00e-02 2.50e+03 3.95e+01 ... (remaining 15732 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 17673 2.21 - 4.42: 3116 4.42 - 6.63: 528 6.63 - 8.83: 76 8.83 - 11.04: 8 Bond angle restraints: 21401 Sorted by residual: angle pdb=" C ASN A 80 " pdb=" N PRO A 81 " pdb=" CA PRO A 81 " ideal model delta sigma weight residual 119.78 127.75 -7.97 1.03e+00 9.43e-01 5.99e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 127.30 -7.74 1.01e+00 9.80e-01 5.88e+01 angle pdb=" N PRO E 437 " pdb=" CA PRO E 437 " pdb=" C PRO E 437 " ideal model delta sigma weight residual 110.47 103.31 7.16 9.60e-01 1.09e+00 5.57e+01 angle pdb=" N ALA B 525 " pdb=" CA ALA B 525 " pdb=" C ALA B 525 " ideal model delta sigma weight residual 114.39 103.79 10.60 1.45e+00 4.76e-01 5.34e+01 angle pdb=" C CYS E 205 " pdb=" N PRO E 206 " pdb=" CA PRO E 206 " ideal model delta sigma weight residual 119.56 126.75 -7.19 1.02e+00 9.61e-01 4.96e+01 ... (remaining 21396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 8466 17.96 - 35.91: 238 35.91 - 53.87: 88 53.87 - 71.82: 28 71.82 - 89.78: 16 Dihedral angle restraints: 8836 sinusoidal: 3349 harmonic: 5487 Sorted by residual: 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 93.00 167.30 -74.30 1 1.00e+01 1.00e-02 7.00e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 162.29 -69.29 1 1.00e+01 1.00e-02 6.20e+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 93.00 150.40 -57.40 1 1.00e+01 1.00e-02 4.43e+01 ... (remaining 8833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1800 0.105 - 0.209: 566 0.209 - 0.314: 207 0.314 - 0.418: 89 0.418 - 0.523: 48 Chirality restraints: 2710 Sorted by residual: chirality pdb=" C1 BMA P 3 " pdb=" O4 NAG P 2 " pdb=" C2 BMA P 3 " pdb=" O5 BMA P 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-02 2.50e+03 5.82e+02 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-02 2.50e+03 3.29e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.29e+02 ... (remaining 2707 not shown) Planarity restraints: 2689 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 601 " -0.351 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG C 601 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG C 601 " -0.127 2.00e-02 2.50e+03 pdb=" N2 NAG C 601 " 0.537 2.00e-02 2.50e+03 pdb=" O7 NAG C 601 " -0.146 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 601 " -0.340 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C7 NAG A 601 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG A 601 " -0.151 2.00e-02 2.50e+03 pdb=" N2 NAG A 601 " 0.518 2.00e-02 2.50e+03 pdb=" O7 NAG A 601 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 602 " -0.315 2.00e-02 2.50e+03 2.68e-01 8.95e+02 pdb=" C7 NAG C 602 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG C 602 " -0.179 2.00e-02 2.50e+03 pdb=" N2 NAG C 602 " 0.466 2.00e-02 2.50e+03 pdb=" O7 NAG C 602 " -0.052 2.00e-02 2.50e+03 ... (remaining 2686 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2026 2.74 - 3.28: 14945 3.28 - 3.82: 24458 3.82 - 4.36: 30937 4.36 - 4.90: 48084 Nonbonded interactions: 120450 Sorted by model distance: nonbonded pdb=" O3 NAG B 702 " pdb=" O7 NAG B 702 " model vdw 2.199 3.040 nonbonded pdb=" O ASN B 616 " pdb=" OD1 ASN B 616 " model vdw 2.325 3.040 nonbonded pdb=" CB TRP D 623 " pdb=" N ASP D 624 " model vdw 2.336 2.816 nonbonded pdb=" N ALA B 525 " pdb=" N ALA B 526 " model vdw 2.401 2.560 nonbonded pdb=" N ASP D 664 " pdb=" OD1 ASP D 664 " model vdw 2.407 3.120 ... (remaining 120445 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 34 through 185 or resid 189 through 396 or resid 414 throu \ gh 456 or resid 462 through 502 or resid 601 through 612)) selection = (chain 'C' and (resid 34 through 56 or resid 66 through 185 or resid 189 through \ 456 or resid 462 through 612)) selection = (chain 'E' and (resid 34 through 56 or resid 66 through 396 or resid 414 through \ 502 or resid 601 through 612)) } ncs_group { reference = (chain 'B' and (resid 521 through 544 or resid 569 through 658)) selection = (chain 'D' and (resid 521 through 544 or resid 569 through 658)) selection = (chain 'F' and resid 521 through 658) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'T' } ncs_group { reference = (chain 'H' and resid 10 through 114) selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'S' } 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: 3.470 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.220 Find NCS groups from input model: 0.410 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: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 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 : 0.022 0.148 15852 Z= 1.185 Angle : 1.797 11.043 21713 Z= 1.131 Chirality : 0.141 0.523 2710 Planarity : 0.015 0.302 2630 Dihedral : 11.104 89.777 5163 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 0.24 (0.20), residues: 1635 helix: -0.27 (0.25), residues: 388 sheet: 0.58 (0.24), residues: 407 loop : 0.32 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 308 TYR 0.079 0.009 TYR A 39 PHE 0.033 0.006 PHE E 93 TRP 0.069 0.009 TRP A 479 HIS 0.014 0.003 HIS B 564 Details of bonding type rmsd/Z covalent geometry : bond 0.02146 / 1.16 (15737) covalent geometry : angle 1.76859 / 1.13 (21401) SS BOND : bond 0.04266 / 2.97 ( 33) SS BOND : angle 3.20252 / 2.29 ( 66) hydrogen bonds : bond 0.17806 / 11.83 ( 560) hydrogen bonds : angle 8.21381 / 5.81 ( 1533) link_ALPHA1-2 : bond 0.08531 / 4.49 ( 1) link_ALPHA1-2 : angle 4.23687 / 2.22 ( 3) link_ALPHA1-3 : bond 0.04965 / 2.53 ( 4) link_ALPHA1-3 : angle 3.06554 / 1.41 ( 12) link_ALPHA1-6 : bond 0.03783 / 1.93 ( 3) link_ALPHA1-6 : angle 2.28305 / 0.95 ( 9) link_BETA1-4 : bond 0.05993 / 3.35 ( 15) link_BETA1-4 : angle 4.59942 / 3.25 ( 45) link_NAG-ASN : bond 0.07633 / 4.66 ( 59) link_NAG-ASN : angle 2.71802 / 1.84 ( 177) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 493 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8798 (m-80) cc_final: 0.8486 (m-10) REVERT: C 69 TRP cc_start: 0.8966 (m-90) cc_final: 0.8484 (m-90) REVERT: C 91 GLU cc_start: 0.8312 (tp30) cc_final: 0.7800 (tp30) REVERT: C 116 LEU cc_start: 0.9610 (mt) cc_final: 0.9358 (pp) REVERT: D 569 THR cc_start: 0.8825 (p) cc_final: 0.8426 (p) REVERT: D 584 GLU cc_start: 0.9555 (mt-10) cc_final: 0.9288 (mt-10) REVERT: D 585 ARG cc_start: 0.9285 (mtp180) cc_final: 0.9064 (ttm-80) REVERT: D 590 GLN cc_start: 0.9166 (mm-40) cc_final: 0.8909 (mm110) REVERT: D 593 LEU cc_start: 0.9596 (mt) cc_final: 0.9360 (tp) REVERT: D 598 CYS cc_start: 0.8568 (m) cc_final: 0.7598 (m) REVERT: D 656 ASN cc_start: 0.9282 (m-40) cc_final: 0.9068 (m-40) REVERT: A 95 MET cc_start: 0.9251 (ptm) cc_final: 0.9028 (ptm) REVERT: A 155 LYS cc_start: 0.9366 (mmtt) cc_final: 0.8932 (mtpt) REVERT: A 284 ILE cc_start: 0.9567 (mt) cc_final: 0.9337 (mp) REVERT: A 381 GLU cc_start: 0.9149 (tp30) cc_final: 0.8768 (tp30) REVERT: B 530 MET cc_start: 0.8897 (mtm) cc_final: 0.8344 (mtm) REVERT: B 599 SER cc_start: 0.8506 (p) cc_final: 0.8178 (t) REVERT: E 80 ASN cc_start: 0.8408 (t0) cc_final: 0.8040 (p0) REVERT: E 212 PRO cc_start: 0.9079 (Cg_endo) cc_final: 0.8644 (Cg_exo) REVERT: E 490 LYS cc_start: 0.9427 (pttt) cc_final: 0.9117 (ptmt) REVERT: E 491 ILE cc_start: 0.9793 (mm) cc_final: 0.9404 (mm) REVERT: F 629 LEU cc_start: 0.9275 (mt) cc_final: 0.9074 (tp) REVERT: F 630 GLN cc_start: 0.9239 (mt0) cc_final: 0.9018 (mt0) REVERT: F 631 TRP cc_start: 0.9063 (t60) cc_final: 0.8855 (t60) REVERT: F 651 ASN cc_start: 0.8480 (m-40) cc_final: 0.7266 (m110) REVERT: F 654 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8209 (mm-30) outliers start: 0 outliers final: 0 residues processed: 493 average time/residue: 0.1435 time to fit residues: 100.4696 Evaluate side-chains 252 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 103 GLN C 130 GLN D 630 GLN D 652 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 HIS ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN F 658 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.070596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.060277 restraints weight = 76302.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.062083 restraints weight = 43403.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.063355 restraints weight = 29040.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.064281 restraints weight = 21499.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.064963 restraints weight = 16999.152| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15852 Z= 0.198 Angle : 0.870 14.548 21713 Z= 0.428 Chirality : 0.049 0.356 2710 Planarity : 0.004 0.045 2630 Dihedral : 5.373 26.388 1988 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.26 % Favored : 97.68 % Rotamer: Outliers : 0.20 % Allowed : 2.88 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.20), residues: 1635 helix: 0.55 (0.26), residues: 394 sheet: 0.62 (0.24), residues: 433 loop : -0.12 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 327 TYR 0.038 0.003 TYR A 39 PHE 0.029 0.003 PHE E 376 TRP 0.050 0.003 TRP F 610 HIS 0.008 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.20 (15737) covalent geometry : angle 0.80928 / 0.42 (21401) SS BOND : bond 0.00802 / 0.39 ( 33) SS BOND : angle 1.58447 / 0.88 ( 66) hydrogen bonds : bond 0.06438 / 4.19 ( 560) hydrogen bonds : angle 6.36416 / 4.43 ( 1533) link_ALPHA1-2 : bond 0.00167 / 0.09 ( 1) link_ALPHA1-2 : angle 2.05215 / 1.15 ( 3) link_ALPHA1-3 : bond 0.00493 / 0.25 ( 4) link_ALPHA1-3 : angle 1.66339 / 0.87 ( 12) link_ALPHA1-6 : bond 0.00978 / 0.50 ( 3) link_ALPHA1-6 : angle 1.22476 / 0.59 ( 9) link_BETA1-4 : bond 0.00668 / 0.46 ( 15) link_BETA1-4 : angle 2.45429 / 1.69 ( 45) link_NAG-ASN : bond 0.00534 / 0.30 ( 59) link_NAG-ASN : angle 3.28566 / 2.10 ( 177) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 334 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 TRP cc_start: 0.8768 (m-90) cc_final: 0.8541 (m-90) REVERT: C 107 ASP cc_start: 0.9570 (m-30) cc_final: 0.9256 (m-30) REVERT: C 432 GLN cc_start: 0.9057 (mp10) cc_final: 0.8688 (mp10) REVERT: C 435 TYR cc_start: 0.8802 (t80) cc_final: 0.8498 (t80) REVERT: D 584 GLU cc_start: 0.9375 (mt-10) cc_final: 0.8867 (tm-30) REVERT: D 596 TRP cc_start: 0.9030 (m-10) cc_final: 0.8466 (m-10) REVERT: D 628 TRP cc_start: 0.6803 (m100) cc_final: 0.5795 (m100) REVERT: A 155 LYS cc_start: 0.9166 (mmtt) cc_final: 0.8747 (mmtm) REVERT: A 284 ILE cc_start: 0.9331 (mt) cc_final: 0.9111 (mp) REVERT: A 381 GLU cc_start: 0.9320 (tp30) cc_final: 0.8927 (tp30) REVERT: A 426 MET cc_start: 0.8776 (tpt) cc_final: 0.8415 (mmm) REVERT: A 487 LYS cc_start: 0.9245 (ttmm) cc_final: 0.8892 (ttmm) REVERT: B 530 MET cc_start: 0.8379 (mtm) cc_final: 0.8095 (mtm) REVERT: B 629 LEU cc_start: 0.9515 (mp) cc_final: 0.9174 (mm) REVERT: E 37 THR cc_start: 0.8895 (m) cc_final: 0.8551 (p) REVERT: E 45 TRP cc_start: 0.8895 (p90) cc_final: 0.8600 (p90) REVERT: E 80 ASN cc_start: 0.8494 (t0) cc_final: 0.8136 (p0) REVERT: E 91 GLU cc_start: 0.7617 (tp30) cc_final: 0.6422 (tp30) REVERT: E 150 MET cc_start: 0.9033 (mmp) cc_final: 0.8727 (mmm) REVERT: E 227 LYS cc_start: 0.8799 (ttpt) cc_final: 0.8442 (tmtt) REVERT: E 249 HIS cc_start: 0.8628 (p90) cc_final: 0.8340 (p90) REVERT: E 434 MET cc_start: 0.8078 (tmm) cc_final: 0.7735 (tmm) REVERT: E 474 ASP cc_start: 0.8517 (t0) cc_final: 0.8015 (t0) REVERT: F 586 TYR cc_start: 0.9064 (t80) cc_final: 0.8815 (t80) REVERT: F 593 LEU cc_start: 0.9713 (mp) cc_final: 0.9508 (tp) outliers start: 3 outliers final: 0 residues processed: 335 average time/residue: 0.1271 time to fit residues: 62.7245 Evaluate side-chains 217 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 146 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 148 optimal weight: 0.0970 chunk 162 optimal weight: 2.9990 chunk 177 optimal weight: 30.0000 chunk 2 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 141 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 170 optimal weight: 9.9990 chunk 135 optimal weight: 7.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 105 HIS D 575 GLN A 328 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS E 302 ASN E 352 HIS ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.067555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.057715 restraints weight = 78085.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.059413 restraints weight = 44979.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.060598 restraints weight = 30143.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.061495 restraints weight = 22384.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.062065 restraints weight = 17713.771| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 15852 Z= 0.200 Angle : 0.768 11.855 21713 Z= 0.378 Chirality : 0.047 0.475 2710 Planarity : 0.004 0.053 2630 Dihedral : 5.182 22.660 1988 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.13 % Allowed : 3.02 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 0.14 (0.20), residues: 1635 helix: 0.74 (0.26), residues: 391 sheet: 0.37 (0.24), residues: 426 loop : -0.29 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 166 TYR 0.025 0.002 TYR A 39 PHE 0.028 0.002 PHE C 382 TRP 0.036 0.002 TRP D 571 HIS 0.006 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.20 (15737) covalent geometry : angle 0.72267 / 0.37 (21401) SS BOND : bond 0.00319 / 0.20 ( 33) SS BOND : angle 1.27303 / 0.77 ( 66) hydrogen bonds : bond 0.05358 / 3.48 ( 560) hydrogen bonds : angle 5.83542 / 4.04 ( 1533) link_ALPHA1-2 : bond 0.00211 / 0.11 ( 1) link_ALPHA1-2 : angle 1.95298 / 1.12 ( 3) link_ALPHA1-3 : bond 0.00442 / 0.22 ( 4) link_ALPHA1-3 : angle 1.57369 / 0.79 ( 12) link_ALPHA1-6 : bond 0.00869 / 0.45 ( 3) link_ALPHA1-6 : angle 1.66436 / 0.87 ( 9) link_BETA1-4 : bond 0.00435 / 0.28 ( 15) link_BETA1-4 : angle 1.75248 / 1.19 ( 45) link_NAG-ASN : bond 0.00898 / 0.69 ( 59) link_NAG-ASN : angle 2.74072 / 1.78 ( 177) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 296 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 TRP cc_start: 0.8946 (m-90) cc_final: 0.8593 (m-90) REVERT: C 217 TYR cc_start: 0.8837 (m-10) cc_final: 0.8597 (m-80) REVERT: C 432 GLN cc_start: 0.9035 (mp10) cc_final: 0.8622 (mp10) REVERT: D 584 GLU cc_start: 0.9338 (mt-10) cc_final: 0.8886 (tm-30) REVERT: D 585 ARG cc_start: 0.9194 (tpp80) cc_final: 0.8943 (tpp80) REVERT: D 596 TRP cc_start: 0.8807 (m-10) cc_final: 0.8494 (m-10) REVERT: A 161 MET cc_start: 0.9170 (tpp) cc_final: 0.8321 (tmm) REVERT: A 217 TYR cc_start: 0.8926 (m-80) cc_final: 0.8630 (m-80) REVERT: A 284 ILE cc_start: 0.9327 (mt) cc_final: 0.8910 (mm) REVERT: A 285 LEU cc_start: 0.9470 (mp) cc_final: 0.9221 (mp) REVERT: A 294 ILE cc_start: 0.8872 (tt) cc_final: 0.8514 (tt) REVERT: A 381 GLU cc_start: 0.9291 (tp30) cc_final: 0.8472 (tp30) REVERT: A 487 LYS cc_start: 0.9222 (ttmm) cc_final: 0.8993 (ttmm) REVERT: B 530 MET cc_start: 0.8268 (mtm) cc_final: 0.7435 (mtm) REVERT: B 589 ASP cc_start: 0.8939 (m-30) cc_final: 0.8717 (m-30) REVERT: B 628 TRP cc_start: 0.8648 (m100) cc_final: 0.7521 (m100) REVERT: B 647 GLU cc_start: 0.8791 (pp20) cc_final: 0.8462 (pp20) REVERT: B 654 GLU cc_start: 0.9291 (tp30) cc_final: 0.9086 (tp30) REVERT: E 37 THR cc_start: 0.9061 (m) cc_final: 0.8601 (p) REVERT: E 80 ASN cc_start: 0.8595 (t0) cc_final: 0.8187 (p0) REVERT: E 91 GLU cc_start: 0.7861 (tp30) cc_final: 0.6597 (tp30) REVERT: E 104 MET cc_start: 0.9085 (tpp) cc_final: 0.8421 (tpp) REVERT: E 150 MET cc_start: 0.8939 (mmp) cc_final: 0.8697 (mmm) REVERT: E 211 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7842 (tm-30) REVERT: E 217 TYR cc_start: 0.8371 (m-80) cc_final: 0.7258 (m-80) REVERT: E 249 HIS cc_start: 0.8877 (p90) cc_final: 0.8518 (p90) REVERT: E 476 ARG cc_start: 0.9019 (mpt90) cc_final: 0.8801 (mmt90) REVERT: F 577 GLN cc_start: 0.9256 (tm-30) cc_final: 0.8858 (tm-30) REVERT: F 581 LEU cc_start: 0.9281 (tt) cc_final: 0.8837 (mm) REVERT: F 590 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8745 (tm-30) REVERT: F 603 ILE cc_start: 0.8887 (mp) cc_final: 0.8653 (mp) REVERT: F 622 ILE cc_start: 0.8812 (mm) cc_final: 0.8385 (mm) REVERT: F 646 LEU cc_start: 0.9570 (mt) cc_final: 0.8963 (mt) REVERT: F 647 GLU cc_start: 0.9060 (tm-30) cc_final: 0.8553 (tm-30) REVERT: F 651 ASN cc_start: 0.8343 (m-40) cc_final: 0.7510 (m110) outliers start: 2 outliers final: 1 residues processed: 297 average time/residue: 0.1278 time to fit residues: 56.6432 Evaluate side-chains 206 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 205 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 62 optimal weight: 0.9990 chunk 44 optimal weight: 0.0270 chunk 79 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 123 optimal weight: 0.7980 chunk 60 optimal weight: 9.9990 chunk 175 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 overall best weight: 2.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 HIS B 577 GLN E 352 HIS ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.067691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.057891 restraints weight = 78784.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.059513 restraints weight = 45538.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.060697 restraints weight = 30959.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.061578 restraints weight = 22958.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.062182 restraints weight = 18218.673| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 15852 Z= 0.175 Angle : 0.717 16.130 21713 Z= 0.351 Chirality : 0.046 0.486 2710 Planarity : 0.004 0.043 2630 Dihedral : 5.043 19.267 1988 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 0.10 (0.21), residues: 1635 helix: 0.77 (0.26), residues: 386 sheet: 0.35 (0.24), residues: 450 loop : -0.37 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 500 TYR 0.025 0.002 TYR A 39 PHE 0.028 0.002 PHE E 376 TRP 0.068 0.002 TRP F 610 HIS 0.005 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (15737) covalent geometry : angle 0.66613 / 0.34 (21401) SS BOND : bond 0.00311 / 0.20 ( 33) SS BOND : angle 1.18172 / 0.71 ( 66) hydrogen bonds : bond 0.04815 / 3.16 ( 560) hydrogen bonds : angle 5.59817 / 3.89 ( 1533) link_ALPHA1-2 : bond 0.00307 / 0.16 ( 1) link_ALPHA1-2 : angle 1.91984 / 1.08 ( 3) link_ALPHA1-3 : bond 0.00429 / 0.21 ( 4) link_ALPHA1-3 : angle 1.54999 / 0.79 ( 12) link_ALPHA1-6 : bond 0.00957 / 0.49 ( 3) link_ALPHA1-6 : angle 1.64247 / 0.84 ( 9) link_BETA1-4 : bond 0.00466 / 0.33 ( 15) link_BETA1-4 : angle 1.59549 / 1.07 ( 45) link_NAG-ASN : bond 0.00498 / 0.33 ( 59) link_NAG-ASN : angle 2.81903 / 1.80 ( 177) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 53 PHE cc_start: 0.8461 (m-80) cc_final: 0.8127 (m-80) REVERT: C 69 TRP cc_start: 0.8963 (m-90) cc_final: 0.8615 (m-90) REVERT: C 107 ASP cc_start: 0.9333 (m-30) cc_final: 0.8974 (m-30) REVERT: C 217 TYR cc_start: 0.8531 (m-10) cc_final: 0.8252 (m-80) REVERT: C 432 GLN cc_start: 0.8995 (mp10) cc_final: 0.8620 (mp10) REVERT: C 479 TRP cc_start: 0.8157 (m-10) cc_final: 0.7890 (m-90) REVERT: D 530 MET cc_start: 0.8299 (ppp) cc_final: 0.8001 (ppp) REVERT: D 584 GLU cc_start: 0.9327 (mt-10) cc_final: 0.8809 (tm-30) REVERT: D 596 TRP cc_start: 0.9044 (m-10) cc_final: 0.8336 (m-10) REVERT: D 652 GLN cc_start: 0.9196 (mm110) cc_final: 0.8858 (mm-40) REVERT: A 95 MET cc_start: 0.9321 (ptm) cc_final: 0.7676 (ppp) REVERT: A 114 GLN cc_start: 0.9314 (tp40) cc_final: 0.8652 (tm-30) REVERT: A 155 LYS cc_start: 0.9172 (mmtt) cc_final: 0.8696 (mmmm) REVERT: A 284 ILE cc_start: 0.9316 (mt) cc_final: 0.8874 (mm) REVERT: A 285 LEU cc_start: 0.9432 (mp) cc_final: 0.9143 (mp) REVERT: A 338 TRP cc_start: 0.8545 (t-100) cc_final: 0.8234 (t-100) REVERT: A 381 GLU cc_start: 0.9214 (tp30) cc_final: 0.8480 (tp30) REVERT: B 585 ARG cc_start: 0.8842 (mtm-85) cc_final: 0.8484 (mtm-85) REVERT: B 596 TRP cc_start: 0.9486 (m-10) cc_final: 0.8555 (m-90) REVERT: B 647 GLU cc_start: 0.8835 (pp20) cc_final: 0.8476 (pp20) REVERT: B 654 GLU cc_start: 0.9311 (tp30) cc_final: 0.9038 (tp30) REVERT: E 34 LEU cc_start: 0.8859 (mm) cc_final: 0.8542 (mt) REVERT: E 37 THR cc_start: 0.8700 (m) cc_final: 0.8176 (p) REVERT: E 80 ASN cc_start: 0.8630 (t0) cc_final: 0.8246 (p0) REVERT: E 104 MET cc_start: 0.9143 (tpp) cc_final: 0.8392 (tpp) REVERT: E 150 MET cc_start: 0.8968 (mmp) cc_final: 0.8702 (mmm) REVERT: E 155 LYS cc_start: 0.8819 (mmtt) cc_final: 0.8522 (mmtm) REVERT: E 166 ARG cc_start: 0.8666 (mtt180) cc_final: 0.8448 (mtm-85) REVERT: E 211 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7771 (tm-30) REVERT: E 217 TYR cc_start: 0.8398 (m-80) cc_final: 0.7260 (m-80) REVERT: E 249 HIS cc_start: 0.8927 (p90) cc_final: 0.8427 (p90) REVERT: F 536 THR cc_start: 0.8469 (p) cc_final: 0.7553 (t) REVERT: F 581 LEU cc_start: 0.9281 (tt) cc_final: 0.8950 (tt) REVERT: F 642 ILE cc_start: 0.9356 (mp) cc_final: 0.9148 (mp) REVERT: F 646 LEU cc_start: 0.9450 (mt) cc_final: 0.8719 (mt) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.1387 time to fit residues: 57.2812 Evaluate side-chains 207 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 52 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 chunk 105 optimal weight: 0.0980 chunk 18 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 114 optimal weight: 20.0000 chunk 170 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 543 ASN ** D 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN ** E 374 HIS ** 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 = 0.3183 r_free = 0.3183 target = 0.067460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.057786 restraints weight = 77881.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.059361 restraints weight = 45714.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.060514 restraints weight = 31205.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.061332 restraints weight = 23352.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.061852 restraints weight = 18786.272| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15852 Z= 0.170 Angle : 0.707 15.854 21713 Z= 0.346 Chirality : 0.045 0.510 2710 Planarity : 0.004 0.051 2630 Dihedral : 4.947 20.625 1988 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.13 % Allowed : 2.21 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -0.04 (0.21), residues: 1635 helix: 0.68 (0.27), residues: 392 sheet: 0.25 (0.25), residues: 452 loop : -0.47 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 178 TYR 0.032 0.002 TYR A 39 PHE 0.016 0.002 PHE A 233 TRP 0.043 0.002 TRP F 610 HIS 0.012 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (15737) covalent geometry : angle 0.66056 / 0.34 (21401) SS BOND : bond 0.00293 / 0.20 ( 33) SS BOND : angle 1.21240 / 0.78 ( 66) hydrogen bonds : bond 0.04611 / 3.02 ( 560) hydrogen bonds : angle 5.50514 / 3.80 ( 1533) link_ALPHA1-2 : bond 0.00367 / 0.19 ( 1) link_ALPHA1-2 : angle 1.87714 / 1.05 ( 3) link_ALPHA1-3 : bond 0.00453 / 0.22 ( 4) link_ALPHA1-3 : angle 1.57509 / 0.81 ( 12) link_ALPHA1-6 : bond 0.00926 / 0.48 ( 3) link_ALPHA1-6 : angle 1.65230 / 0.87 ( 9) link_BETA1-4 : bond 0.00411 / 0.29 ( 15) link_BETA1-4 : angle 1.54604 / 1.03 ( 45) link_NAG-ASN : bond 0.00401 / 0.29 ( 59) link_NAG-ASN : angle 2.65363 / 1.67 ( 177) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 273 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 51 THR cc_start: 0.9308 (m) cc_final: 0.9012 (t) REVERT: C 69 TRP cc_start: 0.9011 (m-90) cc_final: 0.8608 (m-90) REVERT: C 107 ASP cc_start: 0.9359 (m-30) cc_final: 0.8893 (m-30) REVERT: C 217 TYR cc_start: 0.8323 (m-10) cc_final: 0.8035 (m-80) REVERT: C 432 GLN cc_start: 0.9008 (mp10) cc_final: 0.8694 (mp10) REVERT: C 446 VAL cc_start: 0.8729 (t) cc_final: 0.8466 (t) REVERT: C 479 TRP cc_start: 0.8239 (m-10) cc_final: 0.7943 (m-90) REVERT: D 584 GLU cc_start: 0.9344 (mt-10) cc_final: 0.8794 (tm-30) REVERT: D 585 ARG cc_start: 0.9248 (tpp80) cc_final: 0.8987 (ttm-80) REVERT: D 596 TRP cc_start: 0.8986 (m-10) cc_final: 0.8310 (m-10) REVERT: D 652 GLN cc_start: 0.9242 (mm110) cc_final: 0.8913 (mm110) REVERT: D 654 GLU cc_start: 0.9204 (tt0) cc_final: 0.8960 (tp30) REVERT: A 155 LYS cc_start: 0.9166 (mmtt) cc_final: 0.8748 (mmmm) REVERT: A 161 MET cc_start: 0.9142 (tpp) cc_final: 0.8436 (tmm) REVERT: A 217 TYR cc_start: 0.8774 (m-80) cc_final: 0.8162 (m-80) REVERT: A 284 ILE cc_start: 0.9331 (mt) cc_final: 0.8915 (mm) REVERT: A 285 LEU cc_start: 0.9395 (mp) cc_final: 0.9153 (mp) REVERT: A 338 TRP cc_start: 0.8515 (t-100) cc_final: 0.8247 (t-100) REVERT: A 381 GLU cc_start: 0.9142 (tp30) cc_final: 0.8493 (tp30) REVERT: A 426 MET cc_start: 0.7948 (tmm) cc_final: 0.7159 (tmm) REVERT: B 530 MET cc_start: 0.8329 (mpp) cc_final: 0.7011 (mmp) REVERT: B 577 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8451 (tm-30) REVERT: B 585 ARG cc_start: 0.8766 (mtm-85) cc_final: 0.8359 (mtm-85) REVERT: B 628 TRP cc_start: 0.8428 (m100) cc_final: 0.8072 (m100) REVERT: B 647 GLU cc_start: 0.8824 (pp20) cc_final: 0.8406 (pp20) REVERT: B 654 GLU cc_start: 0.9259 (tp30) cc_final: 0.8967 (tp30) REVERT: E 34 LEU cc_start: 0.8784 (mm) cc_final: 0.8432 (mt) REVERT: E 37 THR cc_start: 0.8685 (m) cc_final: 0.8377 (p) REVERT: E 80 ASN cc_start: 0.8574 (t0) cc_final: 0.8220 (p0) REVERT: E 100 MET cc_start: 0.8994 (ptm) cc_final: 0.8646 (ptp) REVERT: E 104 MET cc_start: 0.9004 (tpp) cc_final: 0.8210 (tpp) REVERT: E 150 MET cc_start: 0.8900 (mmp) cc_final: 0.8607 (mmm) REVERT: E 155 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8443 (mmmt) REVERT: E 211 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7825 (tm-30) REVERT: E 217 TYR cc_start: 0.8313 (m-80) cc_final: 0.7338 (m-10) REVERT: E 285 LEU cc_start: 0.9022 (mt) cc_final: 0.7974 (pp) REVERT: E 286 VAL cc_start: 0.9553 (t) cc_final: 0.9232 (p) REVERT: E 492 GLU cc_start: 0.7930 (mp0) cc_final: 0.7713 (mp0) REVERT: F 577 GLN cc_start: 0.9116 (tm-30) cc_final: 0.8653 (tm-30) REVERT: F 581 LEU cc_start: 0.9200 (tt) cc_final: 0.8781 (mm) REVERT: F 591 GLN cc_start: 0.8943 (tt0) cc_final: 0.8683 (tt0) REVERT: F 631 TRP cc_start: 0.8976 (t60) cc_final: 0.8724 (t60) REVERT: F 646 LEU cc_start: 0.9423 (mt) cc_final: 0.8442 (mt) REVERT: F 652 GLN cc_start: 0.9323 (mm-40) cc_final: 0.9095 (mm-40) REVERT: F 653 GLN cc_start: 0.9082 (mt0) cc_final: 0.8779 (mt0) outliers start: 2 outliers final: 1 residues processed: 274 average time/residue: 0.1293 time to fit residues: 52.7901 Evaluate side-chains 208 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 207 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 173 optimal weight: 20.0000 chunk 75 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 178 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 258 GLN ** D 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** 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 = 0.3151 r_free = 0.3151 target = 0.066259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.056431 restraints weight = 80347.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.058000 restraints weight = 47151.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.059091 restraints weight = 32201.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.059903 restraints weight = 24281.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.060448 restraints weight = 19563.286| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 15852 Z= 0.206 Angle : 0.733 15.351 21713 Z= 0.356 Chirality : 0.046 0.535 2710 Planarity : 0.004 0.108 2630 Dihedral : 4.973 19.568 1988 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -0.21 (0.21), residues: 1635 helix: 0.66 (0.26), residues: 396 sheet: 0.11 (0.25), residues: 448 loop : -0.63 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 166 TYR 0.018 0.002 TYR A 484 PHE 0.017 0.002 PHE A 361 TRP 0.040 0.002 TRP F 610 HIS 0.007 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.21 (15737) covalent geometry : angle 0.69065 / 0.35 (21401) SS BOND : bond 0.00380 / 0.26 ( 33) SS BOND : angle 1.21567 / 0.81 ( 66) hydrogen bonds : bond 0.04553 / 2.98 ( 560) hydrogen bonds : angle 5.45366 / 3.75 ( 1533) link_ALPHA1-2 : bond 0.00397 / 0.21 ( 1) link_ALPHA1-2 : angle 2.04713 / 1.16 ( 3) link_ALPHA1-3 : bond 0.00391 / 0.19 ( 4) link_ALPHA1-3 : angle 1.68270 / 0.87 ( 12) link_ALPHA1-6 : bond 0.00831 / 0.43 ( 3) link_ALPHA1-6 : angle 1.80079 / 0.95 ( 9) link_BETA1-4 : bond 0.00383 / 0.27 ( 15) link_BETA1-4 : angle 1.56949 / 1.04 ( 45) link_NAG-ASN : bond 0.00450 / 0.32 ( 59) link_NAG-ASN : angle 2.58307 / 1.62 ( 177) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7497 (mm-30) REVERT: C 69 TRP cc_start: 0.9045 (m-90) cc_final: 0.8715 (m-90) REVERT: C 99 ASN cc_start: 0.8710 (m-40) cc_final: 0.8400 (m-40) REVERT: C 107 ASP cc_start: 0.9315 (m-30) cc_final: 0.8935 (m-30) REVERT: C 426 MET cc_start: 0.8044 (ttm) cc_final: 0.7566 (ttm) REVERT: C 432 GLN cc_start: 0.9023 (mp10) cc_final: 0.8742 (mp10) REVERT: C 446 VAL cc_start: 0.8806 (t) cc_final: 0.8551 (t) REVERT: D 522 PHE cc_start: 0.8781 (t80) cc_final: 0.8460 (t80) REVERT: D 584 GLU cc_start: 0.9275 (mt-10) cc_final: 0.8795 (tm-30) REVERT: D 585 ARG cc_start: 0.9306 (tpp80) cc_final: 0.8994 (ttm-80) REVERT: D 596 TRP cc_start: 0.9084 (m-10) cc_final: 0.8529 (m-10) REVERT: D 650 GLN cc_start: 0.8548 (mp10) cc_final: 0.8273 (mt0) REVERT: D 652 GLN cc_start: 0.9209 (mm110) cc_final: 0.8883 (mm-40) REVERT: D 655 LYS cc_start: 0.9043 (pttm) cc_final: 0.8775 (pttm) REVERT: A 104 MET cc_start: 0.9126 (mmp) cc_final: 0.8622 (mmp) REVERT: A 155 LYS cc_start: 0.9122 (mmtt) cc_final: 0.8753 (mmmm) REVERT: A 161 MET cc_start: 0.9083 (tpp) cc_final: 0.8375 (tmm) REVERT: A 217 TYR cc_start: 0.8777 (m-80) cc_final: 0.8182 (m-80) REVERT: A 284 ILE cc_start: 0.9340 (mt) cc_final: 0.8933 (mm) REVERT: A 285 LEU cc_start: 0.9387 (mp) cc_final: 0.9162 (mp) REVERT: A 338 TRP cc_start: 0.8640 (t-100) cc_final: 0.8405 (t-100) REVERT: A 381 GLU cc_start: 0.9181 (tp30) cc_final: 0.8487 (tp30) REVERT: B 530 MET cc_start: 0.8247 (mpp) cc_final: 0.6108 (mmp) REVERT: B 577 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8446 (tm-30) REVERT: B 622 ILE cc_start: 0.9751 (mm) cc_final: 0.9462 (mm) REVERT: B 628 TRP cc_start: 0.8482 (m100) cc_final: 0.8011 (m100) REVERT: B 647 GLU cc_start: 0.8892 (pp20) cc_final: 0.8502 (pp20) REVERT: B 654 GLU cc_start: 0.9262 (tp30) cc_final: 0.8981 (tp30) REVERT: E 34 LEU cc_start: 0.8872 (mm) cc_final: 0.8467 (mt) REVERT: E 37 THR cc_start: 0.8794 (m) cc_final: 0.8432 (p) REVERT: E 80 ASN cc_start: 0.8710 (t0) cc_final: 0.8314 (p0) REVERT: E 150 MET cc_start: 0.8914 (mmp) cc_final: 0.8659 (mmm) REVERT: E 155 LYS cc_start: 0.8934 (mmtt) cc_final: 0.8469 (mmmt) REVERT: E 195 ASN cc_start: 0.9394 (p0) cc_final: 0.9172 (p0) REVERT: E 217 TYR cc_start: 0.8513 (m-80) cc_final: 0.8182 (m-10) REVERT: E 285 LEU cc_start: 0.8995 (mt) cc_final: 0.8012 (pp) REVERT: E 286 VAL cc_start: 0.9548 (t) cc_final: 0.9228 (p) REVERT: E 492 GLU cc_start: 0.7905 (mp0) cc_final: 0.7695 (mp0) REVERT: F 577 GLN cc_start: 0.9216 (tm-30) cc_final: 0.9014 (tm-30) REVERT: F 590 GLN cc_start: 0.8954 (tm-30) cc_final: 0.8730 (tm-30) REVERT: F 595 ILE cc_start: 0.9527 (tt) cc_final: 0.9125 (tp) REVERT: F 646 LEU cc_start: 0.9410 (mt) cc_final: 0.8696 (mt) REVERT: F 652 GLN cc_start: 0.9329 (mm-40) cc_final: 0.9075 (mm-40) REVERT: F 653 GLN cc_start: 0.9093 (mt0) cc_final: 0.8817 (mt0) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.1311 time to fit residues: 53.4393 Evaluate side-chains 203 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 59 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 166 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 543 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN ** E 374 HIS ** 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 = 0.3162 r_free = 0.3162 target = 0.066344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.056780 restraints weight = 78878.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.058342 restraints weight = 46410.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.059441 restraints weight = 31645.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.060239 restraints weight = 23801.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.060818 restraints weight = 19146.353| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.5530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15852 Z= 0.159 Angle : 0.697 15.045 21713 Z= 0.338 Chirality : 0.046 0.507 2710 Planarity : 0.004 0.043 2630 Dihedral : 4.909 21.531 1988 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.07 % Allowed : 1.61 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -0.30 (0.21), residues: 1635 helix: 0.60 (0.26), residues: 402 sheet: 0.04 (0.25), residues: 447 loop : -0.70 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 166 TYR 0.018 0.002 TYR A 217 PHE 0.019 0.002 PHE C 382 TRP 0.057 0.002 TRP F 596 HIS 0.007 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (15737) covalent geometry : angle 0.65354 / 0.33 (21401) SS BOND : bond 0.00305 / 0.18 ( 33) SS BOND : angle 1.20466 / 0.79 ( 66) hydrogen bonds : bond 0.04318 / 2.81 ( 560) hydrogen bonds : angle 5.39196 / 3.69 ( 1533) link_ALPHA1-2 : bond 0.00493 / 0.26 ( 1) link_ALPHA1-2 : angle 1.86366 / 1.05 ( 3) link_ALPHA1-3 : bond 0.00392 / 0.19 ( 4) link_ALPHA1-3 : angle 1.55777 / 0.79 ( 12) link_ALPHA1-6 : bond 0.00840 / 0.43 ( 3) link_ALPHA1-6 : angle 1.65806 / 0.87 ( 9) link_BETA1-4 : bond 0.00383 / 0.26 ( 15) link_BETA1-4 : angle 1.47434 / 0.96 ( 45) link_NAG-ASN : bond 0.00392 / 0.28 ( 59) link_NAG-ASN : angle 2.54111 / 1.65 ( 177) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7388 (mm-30) REVERT: C 69 TRP cc_start: 0.9032 (m-90) cc_final: 0.8619 (m-90) REVERT: C 95 MET cc_start: 0.9178 (ptm) cc_final: 0.7250 (ppp) REVERT: C 99 ASN cc_start: 0.8692 (m-40) cc_final: 0.8284 (m-40) REVERT: C 107 ASP cc_start: 0.9324 (m-30) cc_final: 0.8944 (m-30) REVERT: C 426 MET cc_start: 0.8045 (ttm) cc_final: 0.7492 (ttm) REVERT: C 432 GLN cc_start: 0.8992 (mp10) cc_final: 0.8771 (mp10) REVERT: C 446 VAL cc_start: 0.8887 (t) cc_final: 0.8638 (t) REVERT: C 479 TRP cc_start: 0.8212 (m-10) cc_final: 0.7867 (m-90) REVERT: D 522 PHE cc_start: 0.8792 (t80) cc_final: 0.8478 (t80) REVERT: D 584 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8751 (tm-30) REVERT: D 585 ARG cc_start: 0.9292 (tpp80) cc_final: 0.9009 (ttm-80) REVERT: D 596 TRP cc_start: 0.9050 (m-10) cc_final: 0.8456 (m-90) REVERT: D 652 GLN cc_start: 0.9235 (mm110) cc_final: 0.8955 (mm-40) REVERT: D 655 LYS cc_start: 0.8966 (pttm) cc_final: 0.8707 (pttm) REVERT: A 69 TRP cc_start: 0.7553 (m100) cc_final: 0.7135 (m100) REVERT: A 95 MET cc_start: 0.9347 (ptm) cc_final: 0.7697 (ppp) REVERT: A 155 LYS cc_start: 0.9119 (mmtt) cc_final: 0.8745 (mmmm) REVERT: A 161 MET cc_start: 0.9156 (tpp) cc_final: 0.8344 (tmm) REVERT: A 284 ILE cc_start: 0.9335 (mt) cc_final: 0.8905 (mm) REVERT: A 285 LEU cc_start: 0.9350 (mp) cc_final: 0.9073 (mp) REVERT: A 338 TRP cc_start: 0.8639 (t-100) cc_final: 0.8414 (t-100) REVERT: A 381 GLU cc_start: 0.9155 (tp30) cc_final: 0.8503 (tp30) REVERT: B 530 MET cc_start: 0.8340 (mpp) cc_final: 0.7995 (mmp) REVERT: B 540 GLN cc_start: 0.9009 (mp10) cc_final: 0.8557 (mp10) REVERT: B 577 GLN cc_start: 0.8699 (tm-30) cc_final: 0.8373 (tm-30) REVERT: B 622 ILE cc_start: 0.9777 (mm) cc_final: 0.9560 (mm) REVERT: B 628 TRP cc_start: 0.8550 (m100) cc_final: 0.8333 (m100) REVERT: B 641 ILE cc_start: 0.8871 (mp) cc_final: 0.8531 (tp) REVERT: B 647 GLU cc_start: 0.8905 (pp20) cc_final: 0.8436 (pp20) REVERT: B 654 GLU cc_start: 0.9192 (tp30) cc_final: 0.8893 (tp30) REVERT: E 34 LEU cc_start: 0.8876 (mm) cc_final: 0.8535 (mt) REVERT: E 80 ASN cc_start: 0.8690 (t0) cc_final: 0.8306 (p0) REVERT: E 112 TRP cc_start: 0.8583 (t-100) cc_final: 0.8354 (t60) REVERT: E 150 MET cc_start: 0.8869 (mmp) cc_final: 0.8668 (mmm) REVERT: E 161 MET cc_start: 0.9320 (tpp) cc_final: 0.9112 (tpt) REVERT: E 217 TYR cc_start: 0.9212 (m-80) cc_final: 0.8669 (m-10) REVERT: E 285 LEU cc_start: 0.8996 (mt) cc_final: 0.8020 (pp) REVERT: E 286 VAL cc_start: 0.9535 (t) cc_final: 0.9231 (p) REVERT: E 426 MET cc_start: 0.7645 (ttt) cc_final: 0.6398 (ttt) REVERT: E 492 GLU cc_start: 0.7945 (mp0) cc_final: 0.7659 (mp0) REVERT: E 502 LYS cc_start: 0.8971 (tmmt) cc_final: 0.8690 (tptm) REVERT: F 590 GLN cc_start: 0.9025 (tm-30) cc_final: 0.8796 (tm-30) REVERT: F 631 TRP cc_start: 0.8879 (t60) cc_final: 0.8644 (t60) outliers start: 1 outliers final: 0 residues processed: 263 average time/residue: 0.1257 time to fit residues: 49.5590 Evaluate side-chains 200 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 62 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 32 optimal weight: 0.1980 chunk 41 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 543 ASN D 653 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.066019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.056360 restraints weight = 80221.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.057923 restraints weight = 46623.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.059034 restraints weight = 31628.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.059831 restraints weight = 23745.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.060407 restraints weight = 19146.017| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.5765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15852 Z= 0.174 Angle : 0.716 14.628 21713 Z= 0.345 Chirality : 0.046 0.507 2710 Planarity : 0.004 0.044 2630 Dihedral : 4.926 20.838 1988 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.07 % Allowed : 1.34 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -0.37 (0.21), residues: 1635 helix: 0.65 (0.26), residues: 402 sheet: -0.04 (0.25), residues: 455 loop : -0.78 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 542 TYR 0.024 0.002 TYR A 217 PHE 0.028 0.002 PHE E 376 TRP 0.058 0.002 TRP A 35 HIS 0.011 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (15737) covalent geometry : angle 0.66767 / 0.33 (21401) SS BOND : bond 0.00717 / 0.35 ( 33) SS BOND : angle 1.28282 / 0.86 ( 66) hydrogen bonds : bond 0.04260 / 2.77 ( 560) hydrogen bonds : angle 5.33935 / 3.65 ( 1533) link_ALPHA1-2 : bond 0.00498 / 0.26 ( 1) link_ALPHA1-2 : angle 1.91109 / 1.08 ( 3) link_ALPHA1-3 : bond 0.00379 / 0.19 ( 4) link_ALPHA1-3 : angle 1.58108 / 0.81 ( 12) link_ALPHA1-6 : bond 0.00798 / 0.41 ( 3) link_ALPHA1-6 : angle 1.71693 / 0.90 ( 9) link_BETA1-4 : bond 0.00375 / 0.26 ( 15) link_BETA1-4 : angle 1.50254 / 0.98 ( 45) link_NAG-ASN : bond 0.00448 / 0.33 ( 59) link_NAG-ASN : angle 2.70831 / 1.76 ( 177) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 254 time to evaluate : 0.562 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: C 69 TRP cc_start: 0.8864 (m-90) cc_final: 0.8477 (m-90) REVERT: C 95 MET cc_start: 0.9141 (ptm) cc_final: 0.7321 (ppp) REVERT: C 107 ASP cc_start: 0.9305 (m-30) cc_final: 0.8957 (m-30) REVERT: C 432 GLN cc_start: 0.8978 (mp10) cc_final: 0.8746 (mp10) REVERT: C 434 MET cc_start: 0.8849 (ptp) cc_final: 0.8579 (ptp) REVERT: C 446 VAL cc_start: 0.8858 (t) cc_final: 0.8613 (t) REVERT: C 484 TYR cc_start: 0.7348 (t80) cc_final: 0.7139 (t80) REVERT: D 522 PHE cc_start: 0.8813 (t80) cc_final: 0.8359 (t80) REVERT: D 584 GLU cc_start: 0.9249 (mt-10) cc_final: 0.8775 (tm-30) REVERT: D 585 ARG cc_start: 0.9317 (tpp80) cc_final: 0.8937 (ttm-80) REVERT: D 596 TRP cc_start: 0.9080 (m-10) cc_final: 0.8438 (m-90) REVERT: D 648 GLU cc_start: 0.9215 (tm-30) cc_final: 0.8445 (tm-30) REVERT: D 652 GLN cc_start: 0.9249 (mm110) cc_final: 0.8861 (mm110) REVERT: D 654 GLU cc_start: 0.9237 (tp30) cc_final: 0.8991 (tp30) REVERT: D 655 LYS cc_start: 0.8982 (pttm) cc_final: 0.8687 (pttm) REVERT: A 69 TRP cc_start: 0.7645 (m100) cc_final: 0.7228 (m100) REVERT: A 95 MET cc_start: 0.9271 (ptm) cc_final: 0.7347 (ppp) REVERT: A 155 LYS cc_start: 0.9098 (mmtt) cc_final: 0.8726 (mmmm) REVERT: A 161 MET cc_start: 0.9096 (tpp) cc_final: 0.8279 (tmm) REVERT: A 217 TYR cc_start: 0.8684 (m-80) cc_final: 0.8345 (m-10) REVERT: A 284 ILE cc_start: 0.9338 (mt) cc_final: 0.8900 (mm) REVERT: A 285 LEU cc_start: 0.9343 (mp) cc_final: 0.9090 (mp) REVERT: A 381 GLU cc_start: 0.9057 (tp30) cc_final: 0.8834 (tp30) REVERT: B 530 MET cc_start: 0.8314 (mpp) cc_final: 0.6990 (mmp) REVERT: B 540 GLN cc_start: 0.8978 (mp10) cc_final: 0.8603 (mp10) REVERT: B 622 ILE cc_start: 0.9774 (mm) cc_final: 0.9529 (mm) REVERT: B 641 ILE cc_start: 0.8884 (mp) cc_final: 0.8543 (tp) REVERT: B 654 GLU cc_start: 0.9204 (tp30) cc_final: 0.8902 (tp30) REVERT: E 80 ASN cc_start: 0.8743 (t0) cc_final: 0.8340 (p0) REVERT: E 95 MET cc_start: 0.8786 (ptm) cc_final: 0.8536 (ptm) REVERT: E 161 MET cc_start: 0.9377 (tpp) cc_final: 0.9176 (tpt) REVERT: E 195 ASN cc_start: 0.9396 (p0) cc_final: 0.9175 (p0) REVERT: E 217 TYR cc_start: 0.9341 (m-80) cc_final: 0.8724 (m-10) REVERT: E 285 LEU cc_start: 0.9026 (mt) cc_final: 0.8225 (pp) REVERT: E 426 MET cc_start: 0.7720 (ttt) cc_final: 0.7385 (ttt) REVERT: E 492 GLU cc_start: 0.7964 (mp0) cc_final: 0.7681 (mp0) REVERT: F 603 ILE cc_start: 0.8764 (mm) cc_final: 0.8223 (mm) REVERT: F 655 LYS cc_start: 0.9049 (pptt) cc_final: 0.8692 (pptt) outliers start: 1 outliers final: 0 residues processed: 255 average time/residue: 0.1219 time to fit residues: 47.1735 Evaluate side-chains 197 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 156 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 165 optimal weight: 20.0000 chunk 83 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 113 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 625 ASN D 653 GLN A 258 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 658 GLN ** 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 = 0.3074 r_free = 0.3074 target = 0.063267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.053810 restraints weight = 81697.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.055286 restraints weight = 48380.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.056332 restraints weight = 33208.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.057079 restraints weight = 25200.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.057663 restraints weight = 20423.428| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.6210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.108 15852 Z= 0.348 Angle : 0.941 13.579 21713 Z= 0.455 Chirality : 0.052 0.530 2710 Planarity : 0.005 0.079 2630 Dihedral : 5.672 22.823 1988 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.07 % Allowed : 1.07 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -0.97 (0.20), residues: 1635 helix: 0.17 (0.26), residues: 401 sheet: -0.35 (0.24), residues: 450 loop : -1.20 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 500 TYR 0.033 0.003 TYR A 217 PHE 0.022 0.002 PHE A 361 TRP 0.113 0.004 TRP F 610 HIS 0.010 0.002 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00754 / 0.35 (15737) covalent geometry : angle 0.89840 / 0.45 (21401) SS BOND : bond 0.00536 / 0.36 ( 33) SS BOND : angle 1.41791 / 0.95 ( 66) hydrogen bonds : bond 0.05210 / 3.39 ( 560) hydrogen bonds : angle 5.92576 / 4.07 ( 1533) link_ALPHA1-2 : bond 0.00402 / 0.21 ( 1) link_ALPHA1-2 : angle 2.53093 / 1.47 ( 3) link_ALPHA1-3 : bond 0.00490 / 0.25 ( 4) link_ALPHA1-3 : angle 1.92037 / 1.00 ( 12) link_ALPHA1-6 : bond 0.00658 / 0.35 ( 3) link_ALPHA1-6 : angle 2.22727 / 1.17 ( 9) link_BETA1-4 : bond 0.00455 / 0.26 ( 15) link_BETA1-4 : angle 1.93988 / 1.27 ( 45) link_NAG-ASN : bond 0.00691 / 0.47 ( 59) link_NAG-ASN : angle 2.94859 / 1.89 ( 177) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 233 time to evaluate : 0.502 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: C 49 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7330 (mm-30) REVERT: C 69 TRP cc_start: 0.9034 (m-90) cc_final: 0.8522 (m-90) REVERT: C 95 MET cc_start: 0.9224 (ptm) cc_final: 0.8633 (tmm) REVERT: C 99 ASN cc_start: 0.8669 (m-40) cc_final: 0.8380 (m-40) REVERT: C 432 GLN cc_start: 0.9107 (mp10) cc_final: 0.8773 (mp10) REVERT: C 434 MET cc_start: 0.8980 (ptp) cc_final: 0.8674 (ptp) REVERT: D 522 PHE cc_start: 0.8994 (t80) cc_final: 0.8467 (t80) REVERT: D 584 GLU cc_start: 0.9277 (mt-10) cc_final: 0.8789 (tm-30) REVERT: D 601 LYS cc_start: 0.8903 (ttmt) cc_final: 0.8695 (ttmm) REVERT: D 654 GLU cc_start: 0.9309 (tp30) cc_final: 0.9066 (tp30) REVERT: D 655 LYS cc_start: 0.9088 (pttm) cc_final: 0.8872 (pttm) REVERT: A 95 MET cc_start: 0.9262 (ptm) cc_final: 0.8626 (ppp) REVERT: A 155 LYS cc_start: 0.9040 (mmtt) cc_final: 0.8786 (mmmm) REVERT: A 161 MET cc_start: 0.9092 (tpp) cc_final: 0.8256 (tmm) REVERT: A 177 TYR cc_start: 0.8935 (m-80) cc_final: 0.8668 (m-80) REVERT: A 284 ILE cc_start: 0.9339 (mt) cc_final: 0.8903 (mm) REVERT: B 530 MET cc_start: 0.8478 (mpp) cc_final: 0.7368 (mmp) REVERT: B 540 GLN cc_start: 0.8997 (mp10) cc_final: 0.8596 (mp10) REVERT: B 571 TRP cc_start: 0.8363 (t60) cc_final: 0.8054 (t60) REVERT: B 577 GLN cc_start: 0.8872 (tm-30) cc_final: 0.8519 (tm-30) REVERT: B 585 ARG cc_start: 0.8812 (mtm-85) cc_final: 0.8515 (mtm-85) REVERT: B 654 GLU cc_start: 0.9251 (tp30) cc_final: 0.8987 (tp30) REVERT: E 80 ASN cc_start: 0.8813 (t0) cc_final: 0.8322 (p0) REVERT: E 161 MET cc_start: 0.9474 (tpp) cc_final: 0.9272 (tpt) REVERT: E 195 ASN cc_start: 0.9429 (p0) cc_final: 0.9213 (p0) REVERT: E 285 LEU cc_start: 0.9018 (mt) cc_final: 0.8235 (pp) REVERT: E 376 PHE cc_start: 0.8597 (t80) cc_final: 0.8388 (t80) REVERT: E 420 ILE cc_start: 0.9412 (mm) cc_final: 0.9204 (mm) REVERT: E 492 GLU cc_start: 0.8005 (mp0) cc_final: 0.7713 (mp0) REVERT: E 502 LYS cc_start: 0.8921 (tmmt) cc_final: 0.8604 (tptm) REVERT: F 642 ILE cc_start: 0.9451 (mp) cc_final: 0.9090 (mp) REVERT: F 646 LEU cc_start: 0.9115 (tt) cc_final: 0.8376 (mm) outliers start: 1 outliers final: 0 residues processed: 234 average time/residue: 0.1221 time to fit residues: 42.7518 Evaluate side-chains 172 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 156 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 195 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN ** E 374 HIS ** 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 = 0.3121 r_free = 0.3121 target = 0.065185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.055643 restraints weight = 80205.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.057167 restraints weight = 47546.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.058153 restraints weight = 32633.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.058999 restraints weight = 25232.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.059561 restraints weight = 20211.700| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.6310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 15852 Z= 0.197 Angle : 0.782 14.206 21713 Z= 0.379 Chirality : 0.048 0.501 2710 Planarity : 0.004 0.043 2630 Dihedral : 5.380 22.578 1988 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.07 % Allowed : 0.40 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -0.89 (0.20), residues: 1635 helix: 0.19 (0.25), residues: 404 sheet: -0.24 (0.25), residues: 443 loop : -1.17 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 542 TYR 0.027 0.002 TYR A 39 PHE 0.013 0.002 PHE E 210 TRP 0.078 0.003 TRP F 610 HIS 0.008 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (15737) covalent geometry : angle 0.74063 / 0.37 (21401) SS BOND : bond 0.00365 / 0.22 ( 33) SS BOND : angle 1.47041 / 0.86 ( 66) hydrogen bonds : bond 0.04629 / 3.02 ( 560) hydrogen bonds : angle 5.61925 / 3.84 ( 1533) link_ALPHA1-2 : bond 0.00615 / 0.32 ( 1) link_ALPHA1-2 : angle 2.02839 / 1.15 ( 3) link_ALPHA1-3 : bond 0.00365 / 0.18 ( 4) link_ALPHA1-3 : angle 1.59875 / 0.82 ( 12) link_ALPHA1-6 : bond 0.00762 / 0.39 ( 3) link_ALPHA1-6 : angle 1.74432 / 0.92 ( 9) link_BETA1-4 : bond 0.00373 / 0.26 ( 15) link_BETA1-4 : angle 1.57903 / 1.01 ( 45) link_NAG-ASN : bond 0.00418 / 0.30 ( 59) link_NAG-ASN : angle 2.62547 / 1.68 ( 177) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 245 time to evaluate : 0.558 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: C 69 TRP cc_start: 0.8951 (m-90) cc_final: 0.8539 (m-90) REVERT: C 95 MET cc_start: 0.9121 (ptm) cc_final: 0.8398 (tmm) REVERT: C 150 MET cc_start: 0.9047 (mpp) cc_final: 0.8541 (mpp) REVERT: C 432 GLN cc_start: 0.9045 (mp10) cc_final: 0.8731 (mp10) REVERT: C 434 MET cc_start: 0.8949 (ptp) cc_final: 0.8643 (ptp) REVERT: C 446 VAL cc_start: 0.8934 (t) cc_final: 0.8696 (t) REVERT: D 522 PHE cc_start: 0.8891 (t80) cc_final: 0.8184 (t80) REVERT: D 543 ASN cc_start: 0.8629 (m110) cc_final: 0.8399 (m110) REVERT: D 584 GLU cc_start: 0.9253 (mt-10) cc_final: 0.8785 (tm-30) REVERT: D 585 ARG cc_start: 0.9272 (tpp80) cc_final: 0.9012 (tpp80) REVERT: D 596 TRP cc_start: 0.9093 (m-10) cc_final: 0.8301 (m-90) REVERT: D 648 GLU cc_start: 0.9260 (tm-30) cc_final: 0.8584 (tm-30) REVERT: D 652 GLN cc_start: 0.9231 (mm110) cc_final: 0.8798 (mm110) REVERT: D 654 GLU cc_start: 0.9283 (tp30) cc_final: 0.9000 (tp30) REVERT: D 655 LYS cc_start: 0.9035 (pttm) cc_final: 0.8717 (pttm) REVERT: A 95 MET cc_start: 0.9256 (ptm) cc_final: 0.7357 (ppp) REVERT: A 150 MET cc_start: 0.7854 (ptp) cc_final: 0.7612 (ptp) REVERT: A 155 LYS cc_start: 0.9023 (mmtt) cc_final: 0.8711 (mmmm) REVERT: A 161 MET cc_start: 0.9134 (tpp) cc_final: 0.8305 (tmm) REVERT: A 284 ILE cc_start: 0.9310 (mt) cc_final: 0.8962 (mp) REVERT: A 285 LEU cc_start: 0.9341 (mp) cc_final: 0.9080 (mp) REVERT: A 381 GLU cc_start: 0.9190 (tp30) cc_final: 0.8578 (tp30) REVERT: B 530 MET cc_start: 0.8339 (mpp) cc_final: 0.7554 (mmp) REVERT: B 538 THR cc_start: 0.9416 (p) cc_final: 0.9146 (p) REVERT: B 540 GLN cc_start: 0.9004 (mp10) cc_final: 0.8581 (mp10) REVERT: B 577 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8452 (tm-30) REVERT: B 585 ARG cc_start: 0.8745 (mtm-85) cc_final: 0.8438 (mtm-85) REVERT: B 626 MET cc_start: 0.7854 (ppp) cc_final: 0.7029 (ppp) REVERT: B 641 ILE cc_start: 0.8815 (mp) cc_final: 0.8521 (tp) REVERT: E 80 ASN cc_start: 0.8809 (t0) cc_final: 0.8318 (p0) REVERT: E 95 MET cc_start: 0.8487 (ppp) cc_final: 0.8250 (ppp) REVERT: E 195 ASN cc_start: 0.9435 (p0) cc_final: 0.9233 (p0) REVERT: E 285 LEU cc_start: 0.8976 (mt) cc_final: 0.8133 (pp) REVERT: E 420 ILE cc_start: 0.9415 (mm) cc_final: 0.9170 (mm) REVERT: E 492 GLU cc_start: 0.8003 (mp0) cc_final: 0.7684 (mp0) REVERT: F 603 ILE cc_start: 0.8765 (mm) cc_final: 0.7969 (mm) outliers start: 1 outliers final: 0 residues processed: 246 average time/residue: 0.1193 time to fit residues: 43.8131 Evaluate side-chains 188 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 72 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 195 ASN ** D 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.065512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.056012 restraints weight = 79675.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.057538 restraints weight = 47170.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.058641 restraints weight = 32315.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.059392 restraints weight = 24351.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.059951 restraints weight = 19711.369| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.6446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15852 Z= 0.179 Angle : 0.755 14.160 21713 Z= 0.369 Chirality : 0.047 0.492 2710 Planarity : 0.004 0.043 2630 Dihedral : 5.192 22.942 1988 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.07 % Allowed : 0.20 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.21), residues: 1635 helix: 0.18 (0.26), residues: 405 sheet: -0.33 (0.25), residues: 452 loop : -1.18 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 542 TYR 0.030 0.002 TYR A 217 PHE 0.022 0.002 PHE C 176 TRP 0.071 0.003 TRP F 610 HIS 0.007 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (15737) covalent geometry : angle 0.71515 / 0.36 (21401) SS BOND : bond 0.00333 / 0.21 ( 33) SS BOND : angle 1.45262 / 0.85 ( 66) hydrogen bonds : bond 0.04523 / 2.97 ( 560) hydrogen bonds : angle 5.59495 / 3.82 ( 1533) link_ALPHA1-2 : bond 0.00624 / 0.33 ( 1) link_ALPHA1-2 : angle 1.93610 / 1.09 ( 3) link_ALPHA1-3 : bond 0.00415 / 0.21 ( 4) link_ALPHA1-3 : angle 1.51872 / 0.78 ( 12) link_ALPHA1-6 : bond 0.00773 / 0.40 ( 3) link_ALPHA1-6 : angle 1.68154 / 0.89 ( 9) link_BETA1-4 : bond 0.00385 / 0.27 ( 15) link_BETA1-4 : angle 1.47604 / 0.94 ( 45) link_NAG-ASN : bond 0.00398 / 0.28 ( 59) link_NAG-ASN : angle 2.52101 / 1.61 ( 177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2348.96 seconds wall clock time: 41 minutes 47.63 seconds (2507.63 seconds total)