Starting phenix.real_space_refine on Wed Mar 4 19:12:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l8u_23237/03_2026/7l8u_23237.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l8u_23237/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7l8u_23237/03_2026/7l8u_23237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l8u_23237/03_2026/7l8u_23237.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l8u_23237/03_2026/7l8u_23237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l8u_23237/03_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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 21 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 45 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 dihedrals: 45 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 dihedrals: 6 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 dihedrals: 36 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.14, per 1000 atoms: 0.20 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: 1.66 Conformation dependent library (CDL) restraints added in 593.7 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: 0.59 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: 2.70 Time building geometry restraints manager: 2.00 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 - 21.79: 10168 21.79 - 43.57: 242 43.57 - 65.36: 73 65.36 - 87.14: 40 87.14 - 108.93: 13 Dihedral angle restraints: 10536 sinusoidal: 5049 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 10533 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: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.540 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 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 : 12.079 108.930 6863 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 covalent geometry : bond 0.02146 (15737) covalent geometry : angle 1.76859 (21401) SS BOND : bond 0.04266 ( 33) SS BOND : angle 3.20252 ( 66) hydrogen bonds : bond 0.17806 ( 560) hydrogen bonds : angle 8.21381 ( 1533) link_ALPHA1-2 : bond 0.08531 ( 1) link_ALPHA1-2 : angle 4.23687 ( 3) link_ALPHA1-3 : bond 0.04965 ( 4) link_ALPHA1-3 : angle 3.06554 ( 12) link_ALPHA1-6 : bond 0.03783 ( 3) link_ALPHA1-6 : angle 2.28305 ( 9) link_BETA1-4 : bond 0.05993 ( 15) link_BETA1-4 : angle 4.59942 ( 45) link_NAG-ASN : bond 0.07633 ( 59) link_NAG-ASN : angle 2.71802 ( 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 : 0.566 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: 0.1392 time to fit residues: 96.9010 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 : 0.524 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: C 103 GLN C 130 GLN D 630 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.070751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.060481 restraints weight = 76188.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.062245 restraints weight = 43366.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.063482 restraints weight = 29146.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.064423 restraints weight = 21732.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.065108 restraints weight = 17204.660| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15852 Z= 0.203 Angle : 0.871 15.732 21713 Z= 0.430 Chirality : 0.049 0.276 2710 Planarity : 0.004 0.042 2630 Dihedral : 8.975 85.540 3688 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.45 % Favored : 97.49 % Rotamer: Outliers : 0.20 % Allowed : 2.68 % Favored : 97.12 % 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: 0.33 (0.20), residues: 1635 helix: 0.58 (0.26), residues: 394 sheet: 0.66 (0.23), residues: 439 loop : -0.11 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 151 TYR 0.038 0.003 TYR A 39 PHE 0.028 0.003 PHE E 376 TRP 0.046 0.003 TRP F 610 HIS 0.008 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00442 (15737) covalent geometry : angle 0.80687 (21401) SS BOND : bond 0.00478 ( 33) SS BOND : angle 1.58752 ( 66) hydrogen bonds : bond 0.06553 ( 560) hydrogen bonds : angle 6.37875 ( 1533) link_ALPHA1-2 : bond 0.00432 ( 1) link_ALPHA1-2 : angle 2.24161 ( 3) link_ALPHA1-3 : bond 0.00795 ( 4) link_ALPHA1-3 : angle 1.93757 ( 12) link_ALPHA1-6 : bond 0.01290 ( 3) link_ALPHA1-6 : angle 1.26901 ( 9) link_BETA1-4 : bond 0.00618 ( 15) link_BETA1-4 : angle 2.63202 ( 45) link_NAG-ASN : bond 0.00710 ( 59) link_NAG-ASN : angle 3.36503 ( 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 338 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 335 time to evaluate : 0.567 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: C 69 TRP cc_start: 0.8748 (m-90) cc_final: 0.8478 (m-90) REVERT: C 107 ASP cc_start: 0.9559 (m-30) cc_final: 0.9249 (m-30) REVERT: C 432 GLN cc_start: 0.9095 (mp10) cc_final: 0.8721 (mp10) REVERT: C 435 TYR cc_start: 0.8798 (t80) cc_final: 0.8514 (t80) REVERT: D 584 GLU cc_start: 0.9367 (mt-10) cc_final: 0.8856 (tm-30) REVERT: D 596 TRP cc_start: 0.9034 (m-10) cc_final: 0.8479 (m-10) REVERT: D 628 TRP cc_start: 0.6803 (m100) cc_final: 0.5807 (m100) REVERT: D 652 GLN cc_start: 0.9064 (mm-40) cc_final: 0.8684 (mm-40) REVERT: A 155 LYS cc_start: 0.9181 (mmtt) cc_final: 0.8760 (mmtm) REVERT: A 284 ILE cc_start: 0.9330 (mt) cc_final: 0.9110 (mp) REVERT: A 381 GLU cc_start: 0.9300 (tp30) cc_final: 0.8928 (tp30) REVERT: A 487 LYS cc_start: 0.9241 (ttmm) cc_final: 0.8872 (ttmm) REVERT: B 530 MET cc_start: 0.8380 (mtm) cc_final: 0.8102 (mtm) REVERT: B 629 LEU cc_start: 0.9508 (mp) cc_final: 0.9172 (mm) REVERT: E 37 THR cc_start: 0.8903 (m) cc_final: 0.8606 (p) REVERT: E 45 TRP cc_start: 0.8891 (p90) cc_final: 0.8647 (p90) REVERT: E 80 ASN cc_start: 0.8496 (t0) cc_final: 0.8137 (p0) REVERT: E 91 GLU cc_start: 0.7629 (tp30) cc_final: 0.6436 (tp30) REVERT: E 150 MET cc_start: 0.9015 (mmp) cc_final: 0.8718 (mmm) REVERT: E 227 LYS cc_start: 0.8828 (ttpt) cc_final: 0.8452 (tmtt) REVERT: E 249 HIS cc_start: 0.8639 (p90) cc_final: 0.8328 (p90) REVERT: E 434 MET cc_start: 0.8068 (tmm) cc_final: 0.7719 (tmm) REVERT: E 474 ASP cc_start: 0.8486 (t0) cc_final: 0.7994 (t0) REVERT: F 586 TYR cc_start: 0.9067 (t80) cc_final: 0.8810 (t80) REVERT: F 593 LEU cc_start: 0.9714 (mp) cc_final: 0.9509 (tp) REVERT: F 631 TRP cc_start: 0.8901 (t60) cc_final: 0.8469 (t-100) REVERT: F 658 GLN cc_start: 0.9151 (tm130) cc_final: 0.8944 (tm-30) outliers start: 3 outliers final: 0 residues processed: 336 average time/residue: 0.1239 time to fit residues: 61.3339 Evaluate side-chains 220 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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: 8.9990 chunk 78 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 chunk 177 optimal weight: 30.0000 chunk 2 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 101 optimal weight: 0.0050 chunk 170 optimal weight: 10.0000 chunk 135 optimal weight: 6.9990 overall best weight: 4.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 F 591 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.066043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.056243 restraints weight = 80767.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.057866 restraints weight = 47260.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.058957 restraints weight = 32146.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.059826 restraints weight = 24429.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.060418 restraints weight = 19498.527| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 15852 Z= 0.272 Angle : 0.865 17.037 21713 Z= 0.423 Chirality : 0.049 0.382 2710 Planarity : 0.005 0.055 2630 Dihedral : 8.670 82.725 3688 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.07 % Allowed : 4.16 % Favored : 95.78 % 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: -0.03 (0.20), residues: 1635 helix: 0.59 (0.26), residues: 384 sheet: 0.32 (0.24), residues: 431 loop : -0.41 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 178 TYR 0.022 0.003 TYR C 318 PHE 0.033 0.003 PHE C 382 TRP 0.038 0.003 TRP F 610 HIS 0.009 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00589 (15737) covalent geometry : angle 0.81799 (21401) SS BOND : bond 0.00450 ( 33) SS BOND : angle 1.32670 ( 66) hydrogen bonds : bond 0.05629 ( 560) hydrogen bonds : angle 6.02003 ( 1533) link_ALPHA1-2 : bond 0.00354 ( 1) link_ALPHA1-2 : angle 2.25532 ( 3) link_ALPHA1-3 : bond 0.00748 ( 4) link_ALPHA1-3 : angle 1.64983 ( 12) link_ALPHA1-6 : bond 0.01128 ( 3) link_ALPHA1-6 : angle 2.13325 ( 9) link_BETA1-4 : bond 0.00484 ( 15) link_BETA1-4 : angle 1.98235 ( 45) link_NAG-ASN : bond 0.00565 ( 59) link_NAG-ASN : angle 2.96793 ( 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 272 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 271 time to evaluate : 0.550 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 69 TRP cc_start: 0.9011 (m-90) cc_final: 0.8697 (m-90) REVERT: C 107 ASP cc_start: 0.9377 (m-30) cc_final: 0.9141 (m-30) REVERT: C 217 TYR cc_start: 0.8941 (m-10) cc_final: 0.8725 (m-80) REVERT: C 432 GLN cc_start: 0.8992 (mp10) cc_final: 0.8583 (mp10) REVERT: D 584 GLU cc_start: 0.9354 (mt-10) cc_final: 0.8882 (tm-30) REVERT: D 585 ARG cc_start: 0.9194 (tpp80) cc_final: 0.8919 (tpp80) REVERT: D 596 TRP cc_start: 0.8836 (m-10) cc_final: 0.8344 (m-10) REVERT: A 104 MET cc_start: 0.9150 (mmp) cc_final: 0.8921 (mmp) REVERT: A 116 LEU cc_start: 0.9447 (mt) cc_final: 0.9239 (tt) REVERT: A 155 LYS cc_start: 0.9238 (mmtt) cc_final: 0.8976 (mmmt) REVERT: A 161 MET cc_start: 0.9211 (tpp) cc_final: 0.8352 (tmm) REVERT: A 177 TYR cc_start: 0.8874 (m-80) cc_final: 0.8586 (m-80) REVERT: A 284 ILE cc_start: 0.9348 (mt) cc_final: 0.8930 (mm) REVERT: A 285 LEU cc_start: 0.9433 (mp) cc_final: 0.9171 (mp) REVERT: A 381 GLU cc_start: 0.9285 (tp30) cc_final: 0.8894 (tp30) REVERT: A 487 LYS cc_start: 0.9280 (ttmm) cc_final: 0.9035 (ttmm) REVERT: B 530 MET cc_start: 0.8158 (mtm) cc_final: 0.7265 (mtm) REVERT: B 593 LEU cc_start: 0.9663 (mm) cc_final: 0.9451 (tp) REVERT: B 628 TRP cc_start: 0.8594 (m100) cc_final: 0.7486 (m100) REVERT: B 654 GLU cc_start: 0.9285 (tp30) cc_final: 0.9071 (tp30) REVERT: E 37 THR cc_start: 0.9251 (m) cc_final: 0.8895 (p) REVERT: E 80 ASN cc_start: 0.8640 (t0) cc_final: 0.8243 (p0) REVERT: E 104 MET cc_start: 0.9056 (tpp) cc_final: 0.8208 (tpp) REVERT: E 150 MET cc_start: 0.8976 (mmp) cc_final: 0.8761 (mmm) REVERT: E 211 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7843 (tm-30) REVERT: E 217 TYR cc_start: 0.8501 (m-80) cc_final: 0.7289 (m-80) REVERT: E 434 MET cc_start: 0.8342 (tmm) cc_final: 0.7316 (tmm) REVERT: E 475 MET cc_start: 0.9314 (mmm) cc_final: 0.9009 (mmm) REVERT: F 646 LEU cc_start: 0.9559 (mt) cc_final: 0.8901 (mt) outliers start: 1 outliers final: 0 residues processed: 272 average time/residue: 0.1169 time to fit residues: 47.7945 Evaluate side-chains 189 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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: 20.0000 chunk 79 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 175 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 543 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN E 302 ASN E 352 HIS ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 650 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.066559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.057055 restraints weight = 79946.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.058591 restraints weight = 46234.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.059755 restraints weight = 31532.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.060577 restraints weight = 23356.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.061195 restraints weight = 18574.189| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 15852 Z= 0.189 Angle : 0.740 15.820 21713 Z= 0.361 Chirality : 0.047 0.468 2710 Planarity : 0.004 0.042 2630 Dihedral : 8.054 79.070 3688 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.07 % Allowed : 3.49 % Favored : 96.45 % 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 (0.20), residues: 1635 helix: 0.63 (0.26), residues: 386 sheet: 0.26 (0.26), residues: 420 loop : -0.50 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 476 TYR 0.026 0.002 TYR A 39 PHE 0.025 0.002 PHE E 376 TRP 0.081 0.002 TRP F 610 HIS 0.007 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00413 (15737) covalent geometry : angle 0.68647 (21401) SS BOND : bond 0.00334 ( 33) SS BOND : angle 1.17730 ( 66) hydrogen bonds : bond 0.04965 ( 560) hydrogen bonds : angle 5.67138 ( 1533) link_ALPHA1-2 : bond 0.00539 ( 1) link_ALPHA1-2 : angle 1.77275 ( 3) link_ALPHA1-3 : bond 0.00766 ( 4) link_ALPHA1-3 : angle 1.58333 ( 12) link_ALPHA1-6 : bond 0.01219 ( 3) link_ALPHA1-6 : angle 1.81451 ( 9) link_BETA1-4 : bond 0.00494 ( 15) link_BETA1-4 : angle 1.71629 ( 45) link_NAG-ASN : bond 0.00642 ( 59) link_NAG-ASN : angle 2.91946 ( 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 271 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 270 time to evaluate : 0.491 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: 0.8465 (m-80) cc_final: 0.8246 (m-80) REVERT: C 69 TRP cc_start: 0.8996 (m-90) cc_final: 0.8672 (m-90) REVERT: C 95 MET cc_start: 0.9211 (ptm) cc_final: 0.7462 (ppp) REVERT: C 107 ASP cc_start: 0.9456 (m-30) cc_final: 0.9101 (m-30) REVERT: C 432 GLN cc_start: 0.9014 (mp10) cc_final: 0.8717 (mp10) REVERT: D 530 MET cc_start: 0.8290 (ppp) cc_final: 0.7953 (ppp) REVERT: D 577 GLN cc_start: 0.9129 (pp30) cc_final: 0.8848 (pp30) REVERT: D 584 GLU cc_start: 0.9318 (mt-10) cc_final: 0.8792 (tm-30) REVERT: D 593 LEU cc_start: 0.9525 (tp) cc_final: 0.9322 (tp) REVERT: D 596 TRP cc_start: 0.8831 (m-10) cc_final: 0.8222 (m-10) REVERT: D 648 GLU cc_start: 0.9253 (tm-30) cc_final: 0.8811 (tm-30) REVERT: D 652 GLN cc_start: 0.9159 (mm-40) cc_final: 0.8888 (mm-40) REVERT: A 95 MET cc_start: 0.9373 (ptm) cc_final: 0.7577 (ppp) REVERT: A 155 LYS cc_start: 0.9181 (mmtt) cc_final: 0.8736 (mmmm) REVERT: A 177 TYR cc_start: 0.8888 (m-80) cc_final: 0.8588 (m-80) REVERT: A 284 ILE cc_start: 0.9315 (mt) cc_final: 0.8890 (mm) REVERT: A 285 LEU cc_start: 0.9412 (mp) cc_final: 0.9099 (mp) REVERT: A 338 TRP cc_start: 0.8521 (t-100) cc_final: 0.8215 (t-100) REVERT: A 381 GLU cc_start: 0.9163 (tp30) cc_final: 0.8797 (tp30) REVERT: B 530 MET cc_start: 0.8126 (mtm) cc_final: 0.6963 (mtm) REVERT: B 628 TRP cc_start: 0.8547 (m100) cc_final: 0.7301 (m100) REVERT: B 647 GLU cc_start: 0.8755 (pp20) cc_final: 0.8410 (pp20) REVERT: B 654 GLU cc_start: 0.9208 (tp30) cc_final: 0.8946 (tp30) REVERT: E 34 LEU cc_start: 0.8845 (mm) cc_final: 0.8528 (mt) REVERT: E 37 THR cc_start: 0.8820 (m) cc_final: 0.8295 (p) REVERT: E 80 ASN cc_start: 0.8591 (t0) cc_final: 0.8263 (p0) REVERT: E 104 MET cc_start: 0.9006 (tpp) cc_final: 0.8230 (tpp) REVERT: E 150 MET cc_start: 0.8967 (mmp) cc_final: 0.8758 (mmm) REVERT: E 155 LYS cc_start: 0.8863 (mmtt) cc_final: 0.8293 (tptt) REVERT: E 211 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7793 (tm-30) REVERT: E 217 TYR cc_start: 0.8462 (m-80) cc_final: 0.7471 (m-80) REVERT: F 581 LEU cc_start: 0.9320 (tt) cc_final: 0.8970 (tt) REVERT: F 595 ILE cc_start: 0.9469 (pt) cc_final: 0.8991 (tt) REVERT: F 630 GLN cc_start: 0.9096 (mt0) cc_final: 0.8888 (mt0) REVERT: F 640 GLN cc_start: 0.8732 (pm20) cc_final: 0.8504 (pm20) REVERT: F 646 LEU cc_start: 0.9438 (mt) cc_final: 0.8825 (mt) REVERT: F 650 GLN cc_start: 0.9194 (tp40) cc_final: 0.8974 (tm-30) outliers start: 1 outliers final: 1 residues processed: 271 average time/residue: 0.1210 time to fit residues: 48.4509 Evaluate side-chains 194 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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: 8.9990 chunk 20 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 105 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 chunk 170 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 203 GLN C 258 GLN D 656 ASN A 170 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.064902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.055400 restraints weight = 80631.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.056888 restraints weight = 47840.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.057978 restraints weight = 33177.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.058769 restraints weight = 24849.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.059356 restraints weight = 20019.736| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 15852 Z= 0.279 Angle : 0.826 15.826 21713 Z= 0.402 Chirality : 0.049 0.522 2710 Planarity : 0.005 0.055 2630 Dihedral : 8.335 77.651 3688 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.07 % Allowed : 3.35 % Favored : 96.58 % 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: -0.44 (0.20), residues: 1635 helix: 0.48 (0.26), residues: 381 sheet: 0.04 (0.25), residues: 427 loop : -0.79 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 500 TYR 0.029 0.002 TYR A 484 PHE 0.022 0.002 PHE A 233 TRP 0.050 0.003 TRP F 610 HIS 0.011 0.002 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00600 (15737) covalent geometry : angle 0.77721 (21401) SS BOND : bond 0.00460 ( 33) SS BOND : angle 1.37471 ( 66) hydrogen bonds : bond 0.05096 ( 560) hydrogen bonds : angle 5.88238 ( 1533) link_ALPHA1-2 : bond 0.00550 ( 1) link_ALPHA1-2 : angle 2.06616 ( 3) link_ALPHA1-3 : bond 0.00768 ( 4) link_ALPHA1-3 : angle 1.80585 ( 12) link_ALPHA1-6 : bond 0.00912 ( 3) link_ALPHA1-6 : angle 2.11979 ( 9) link_BETA1-4 : bond 0.00462 ( 15) link_BETA1-4 : angle 1.84409 ( 45) link_NAG-ASN : bond 0.00582 ( 59) link_NAG-ASN : angle 2.92734 ( 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 254 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 253 time to evaluate : 0.488 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: C 69 TRP cc_start: 0.9094 (m-90) cc_final: 0.8827 (m-90) REVERT: C 102 GLU cc_start: 0.8876 (mp0) cc_final: 0.8662 (mp0) REVERT: C 432 GLN cc_start: 0.9105 (mp10) cc_final: 0.8740 (mp10) REVERT: D 522 PHE cc_start: 0.8837 (t80) cc_final: 0.8576 (t80) REVERT: D 584 GLU cc_start: 0.9304 (mt-10) cc_final: 0.8759 (tm-30) REVERT: D 585 ARG cc_start: 0.9292 (ttm-80) cc_final: 0.9080 (ttm-80) REVERT: D 596 TRP cc_start: 0.8874 (m-10) cc_final: 0.8235 (m-90) REVERT: D 653 GLN cc_start: 0.8824 (mt0) cc_final: 0.8599 (mt0) REVERT: A 100 MET cc_start: 0.9649 (mtm) cc_final: 0.9423 (mtm) REVERT: A 104 MET cc_start: 0.9167 (mmp) cc_final: 0.8861 (mmp) REVERT: A 155 LYS cc_start: 0.9173 (mmtt) cc_final: 0.8792 (mmmm) REVERT: A 161 MET cc_start: 0.9136 (tpp) cc_final: 0.8429 (tmm) REVERT: A 177 TYR cc_start: 0.8941 (m-80) cc_final: 0.8692 (m-80) REVERT: A 217 TYR cc_start: 0.9102 (m-80) cc_final: 0.8419 (m-80) REVERT: A 284 ILE cc_start: 0.9358 (mt) cc_final: 0.8938 (mm) REVERT: A 285 LEU cc_start: 0.9396 (mp) cc_final: 0.9140 (mp) REVERT: A 381 GLU cc_start: 0.9164 (tp30) cc_final: 0.8800 (tp30) REVERT: B 530 MET cc_start: 0.8057 (mtm) cc_final: 0.6593 (mtt) REVERT: B 602 LEU cc_start: 0.9366 (mt) cc_final: 0.9159 (mt) REVERT: B 626 MET cc_start: 0.8113 (tpp) cc_final: 0.7707 (tpp) REVERT: B 628 TRP cc_start: 0.8341 (m100) cc_final: 0.7069 (m100) REVERT: B 647 GLU cc_start: 0.8811 (pp20) cc_final: 0.8422 (pp20) REVERT: B 654 GLU cc_start: 0.9248 (tp30) cc_final: 0.8972 (tp30) REVERT: B 655 LYS cc_start: 0.8982 (mttt) cc_final: 0.8759 (tptp) REVERT: E 37 THR cc_start: 0.9030 (m) cc_final: 0.8715 (p) REVERT: E 80 ASN cc_start: 0.8709 (t0) cc_final: 0.8286 (p0) REVERT: E 150 MET cc_start: 0.9054 (mmp) cc_final: 0.8826 (mmm) REVERT: E 155 LYS cc_start: 0.8974 (mmtt) cc_final: 0.8344 (mmmt) REVERT: E 211 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7819 (tm-30) REVERT: E 492 GLU cc_start: 0.7942 (mp0) cc_final: 0.7722 (mp0) REVERT: F 577 GLN cc_start: 0.9139 (tm-30) cc_final: 0.8567 (tm-30) REVERT: F 581 LEU cc_start: 0.9291 (tt) cc_final: 0.8897 (mm) REVERT: F 590 GLN cc_start: 0.8962 (tm-30) cc_final: 0.8695 (tm-30) REVERT: F 621 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7820 (mt-10) REVERT: F 630 GLN cc_start: 0.9171 (mt0) cc_final: 0.8955 (mt0) REVERT: F 652 GLN cc_start: 0.9345 (mm-40) cc_final: 0.9079 (mm-40) REVERT: F 653 GLN cc_start: 0.9069 (mt0) cc_final: 0.8762 (mt0) outliers start: 1 outliers final: 0 residues processed: 253 average time/residue: 0.1243 time to fit residues: 46.0909 Evaluate side-chains 190 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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: 2.9990 chunk 58 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 173 optimal weight: 20.0000 chunk 75 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 178 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 HIS B 577 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** 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 = 0.3116 r_free = 0.3116 target = 0.064548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.054774 restraints weight = 79928.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.056341 restraints weight = 46567.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.057458 restraints weight = 31606.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.058222 restraints weight = 23733.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.058811 restraints weight = 19214.820| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 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 : 0.005 0.046 15852 Z= 0.229 Angle : 0.766 16.055 21713 Z= 0.373 Chirality : 0.048 0.531 2710 Planarity : 0.004 0.042 2630 Dihedral : 7.958 74.402 3688 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.07 % Allowed : 2.21 % Favored : 97.72 % 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: -0.65 (0.20), residues: 1635 helix: 0.43 (0.26), residues: 392 sheet: -0.13 (0.26), residues: 428 loop : -0.97 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 585 TYR 0.019 0.002 TYR C 39 PHE 0.018 0.002 PHE E 53 TRP 0.044 0.002 TRP F 610 HIS 0.007 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00498 (15737) covalent geometry : angle 0.71873 (21401) SS BOND : bond 0.00402 ( 33) SS BOND : angle 1.40684 ( 66) hydrogen bonds : bond 0.04829 ( 560) hydrogen bonds : angle 5.66136 ( 1533) link_ALPHA1-2 : bond 0.00849 ( 1) link_ALPHA1-2 : angle 1.82912 ( 3) link_ALPHA1-3 : bond 0.00770 ( 4) link_ALPHA1-3 : angle 1.67594 ( 12) link_ALPHA1-6 : bond 0.01206 ( 3) link_ALPHA1-6 : angle 1.96332 ( 9) link_BETA1-4 : bond 0.00412 ( 15) link_BETA1-4 : angle 1.72609 ( 45) link_NAG-ASN : bond 0.00482 ( 59) link_NAG-ASN : angle 2.75168 ( 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 251 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 250 time to evaluate : 0.539 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: C 69 TRP cc_start: 0.9098 (m-90) cc_final: 0.8755 (m-90) REVERT: C 95 MET cc_start: 0.9217 (ptp) cc_final: 0.7866 (mmm) REVERT: C 102 GLU cc_start: 0.8913 (mp0) cc_final: 0.8654 (mp0) REVERT: C 103 GLN cc_start: 0.8629 (mt0) cc_final: 0.8324 (tt0) REVERT: C 107 ASP cc_start: 0.9416 (m-30) cc_final: 0.9009 (m-30) REVERT: C 432 GLN cc_start: 0.9035 (mp10) cc_final: 0.8731 (mp10) REVERT: D 522 PHE cc_start: 0.8879 (t80) cc_final: 0.8541 (t80) REVERT: D 584 GLU cc_start: 0.9296 (mt-10) cc_final: 0.8776 (tm-30) REVERT: D 596 TRP cc_start: 0.8872 (m-10) cc_final: 0.8259 (m-90) REVERT: D 653 GLN cc_start: 0.8891 (mt0) cc_final: 0.8684 (pt0) REVERT: D 654 GLU cc_start: 0.9339 (tt0) cc_final: 0.9031 (tm-30) REVERT: A 95 MET cc_start: 0.9316 (ptm) cc_final: 0.7499 (ppp) REVERT: A 100 MET cc_start: 0.9635 (mtm) cc_final: 0.9405 (mtm) REVERT: A 104 MET cc_start: 0.9170 (mmp) cc_final: 0.8791 (mmp) REVERT: A 161 MET cc_start: 0.9148 (tpp) cc_final: 0.8276 (tmm) REVERT: A 217 TYR cc_start: 0.9001 (m-80) cc_final: 0.8221 (m-80) REVERT: A 284 ILE cc_start: 0.9333 (mt) cc_final: 0.8889 (mm) REVERT: A 285 LEU cc_start: 0.9385 (mp) cc_final: 0.9094 (mp) REVERT: A 338 TRP cc_start: 0.8625 (t-100) cc_final: 0.8418 (t-100) REVERT: A 381 GLU cc_start: 0.9170 (tp30) cc_final: 0.8505 (tp30) REVERT: B 530 MET cc_start: 0.8165 (mtm) cc_final: 0.6687 (mtt) REVERT: B 540 GLN cc_start: 0.8979 (mp10) cc_final: 0.8467 (mp10) REVERT: B 577 GLN cc_start: 0.8784 (tm130) cc_final: 0.8492 (tm-30) REVERT: B 628 TRP cc_start: 0.8315 (m100) cc_final: 0.7199 (m100) REVERT: B 647 GLU cc_start: 0.8826 (pp20) cc_final: 0.8462 (pp20) REVERT: B 654 GLU cc_start: 0.9245 (tp30) cc_final: 0.8960 (tp30) REVERT: B 655 LYS cc_start: 0.9020 (mttt) cc_final: 0.8784 (tptp) REVERT: E 37 THR cc_start: 0.8924 (m) cc_final: 0.8613 (p) REVERT: E 80 ASN cc_start: 0.8774 (t0) cc_final: 0.8347 (p0) REVERT: E 150 MET cc_start: 0.9055 (mmp) cc_final: 0.8762 (mmm) REVERT: E 195 ASN cc_start: 0.9485 (p0) cc_final: 0.9281 (p0) REVERT: E 376 PHE cc_start: 0.8512 (t80) cc_final: 0.8275 (t80) REVERT: E 434 MET cc_start: 0.8393 (tmm) cc_final: 0.8092 (tmm) REVERT: E 492 GLU cc_start: 0.7955 (mp0) cc_final: 0.7679 (mp0) REVERT: E 502 LYS cc_start: 0.9054 (tmmt) cc_final: 0.8691 (tptm) REVERT: F 535 MET cc_start: 0.8294 (mmm) cc_final: 0.7712 (mmt) REVERT: F 536 THR cc_start: 0.8799 (p) cc_final: 0.8307 (t) REVERT: F 581 LEU cc_start: 0.9325 (tt) cc_final: 0.8976 (mm) REVERT: F 584 GLU cc_start: 0.8873 (mp0) cc_final: 0.8663 (mp0) REVERT: F 596 TRP cc_start: 0.9106 (m-10) cc_final: 0.8486 (m-90) REVERT: F 621 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7753 (mt-10) REVERT: F 642 ILE cc_start: 0.9345 (mp) cc_final: 0.9136 (mp) REVERT: F 646 LEU cc_start: 0.9513 (mt) cc_final: 0.9265 (mt) outliers start: 1 outliers final: 0 residues processed: 251 average time/residue: 0.1271 time to fit residues: 46.4170 Evaluate side-chains 195 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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: 0.2980 chunk 47 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 166 optimal weight: 20.0000 chunk 79 optimal weight: 9.9990 chunk 83 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 543 ASN D 564 HIS A 258 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN B 577 GLN E 302 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.066078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.056298 restraints weight = 78813.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.057894 restraints weight = 45915.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.059044 restraints weight = 31158.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.059845 restraints weight = 23281.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.060434 restraints weight = 18723.850| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.5725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15852 Z= 0.136 Angle : 0.703 15.809 21713 Z= 0.344 Chirality : 0.048 0.510 2710 Planarity : 0.004 0.041 2630 Dihedral : 7.406 71.900 3688 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % 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: -0.56 (0.21), residues: 1635 helix: 0.45 (0.26), residues: 404 sheet: -0.15 (0.25), residues: 443 loop : -0.87 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 585 TYR 0.021 0.002 TYR D 586 PHE 0.020 0.002 PHE C 382 TRP 0.035 0.002 TRP D 631 HIS 0.011 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00299 (15737) covalent geometry : angle 0.65423 (21401) SS BOND : bond 0.00283 ( 33) SS BOND : angle 1.39909 ( 66) hydrogen bonds : bond 0.04424 ( 560) hydrogen bonds : angle 5.45580 ( 1533) link_ALPHA1-2 : bond 0.00967 ( 1) link_ALPHA1-2 : angle 1.40709 ( 3) link_ALPHA1-3 : bond 0.00827 ( 4) link_ALPHA1-3 : angle 1.50593 ( 12) link_ALPHA1-6 : bond 0.01222 ( 3) link_ALPHA1-6 : angle 1.56590 ( 9) link_BETA1-4 : bond 0.00454 ( 15) link_BETA1-4 : angle 1.57571 ( 45) link_NAG-ASN : bond 0.00392 ( 59) link_NAG-ASN : angle 2.69585 ( 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 272 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 271 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7269 (mm-30) REVERT: C 69 TRP cc_start: 0.8943 (m-90) cc_final: 0.8683 (m-90) REVERT: C 95 MET cc_start: 0.9137 (ptm) cc_final: 0.8098 (mmm) REVERT: C 99 ASN cc_start: 0.8618 (m-40) cc_final: 0.8191 (m-40) REVERT: C 102 GLU cc_start: 0.8945 (mp0) cc_final: 0.8674 (mp0) REVERT: C 103 GLN cc_start: 0.8505 (mt0) cc_final: 0.8274 (tt0) REVERT: C 107 ASP cc_start: 0.9399 (m-30) cc_final: 0.9000 (m-30) REVERT: C 217 TYR cc_start: 0.8779 (m-80) cc_final: 0.8481 (m-80) REVERT: C 432 GLN cc_start: 0.9040 (mp10) cc_final: 0.8740 (mp10) REVERT: D 522 PHE cc_start: 0.8864 (t80) cc_final: 0.8309 (t80) REVERT: D 584 GLU cc_start: 0.9251 (mt-10) cc_final: 0.8737 (tm-30) REVERT: D 596 TRP cc_start: 0.8766 (m-10) cc_final: 0.8390 (m-10) REVERT: D 653 GLN cc_start: 0.8887 (mt0) cc_final: 0.8675 (pt0) REVERT: D 654 GLU cc_start: 0.9373 (tt0) cc_final: 0.9113 (tm-30) REVERT: A 95 MET cc_start: 0.9296 (ptm) cc_final: 0.7430 (ppp) REVERT: A 100 MET cc_start: 0.9591 (mtm) cc_final: 0.9278 (mtm) REVERT: A 104 MET cc_start: 0.9122 (mmp) cc_final: 0.8714 (mmp) REVERT: A 114 GLN cc_start: 0.9238 (tp40) cc_final: 0.8724 (tm-30) REVERT: A 161 MET cc_start: 0.9127 (tpp) cc_final: 0.8310 (tmm) REVERT: A 211 GLU cc_start: 0.8929 (pp20) cc_final: 0.8649 (pm20) REVERT: A 217 TYR cc_start: 0.8885 (m-80) cc_final: 0.7944 (m-80) REVERT: A 284 ILE cc_start: 0.9324 (mt) cc_final: 0.8883 (mm) REVERT: A 285 LEU cc_start: 0.9377 (mp) cc_final: 0.9077 (mp) REVERT: A 381 GLU cc_start: 0.8990 (tp30) cc_final: 0.8426 (tp30) REVERT: B 530 MET cc_start: 0.8290 (mtm) cc_final: 0.6907 (mtt) REVERT: B 538 THR cc_start: 0.9384 (p) cc_final: 0.8924 (p) REVERT: B 540 GLN cc_start: 0.9064 (mp10) cc_final: 0.8581 (mp10) REVERT: B 577 GLN cc_start: 0.8746 (tm130) cc_final: 0.8439 (tm-30) REVERT: B 628 TRP cc_start: 0.8346 (m100) cc_final: 0.7060 (m100) REVERT: B 647 GLU cc_start: 0.8783 (pp20) cc_final: 0.8387 (pp20) REVERT: B 654 GLU cc_start: 0.9217 (tp30) cc_final: 0.8929 (tp30) REVERT: B 655 LYS cc_start: 0.8958 (mttt) cc_final: 0.8742 (tptp) REVERT: E 34 LEU cc_start: 0.9026 (mm) cc_final: 0.8817 (mm) REVERT: E 37 THR cc_start: 0.8734 (m) cc_final: 0.8510 (p) REVERT: E 80 ASN cc_start: 0.8783 (t0) cc_final: 0.8356 (p0) REVERT: E 161 MET cc_start: 0.9353 (tpp) cc_final: 0.9152 (tpt) REVERT: E 434 MET cc_start: 0.8366 (tmm) cc_final: 0.7993 (tmm) REVERT: E 483 LEU cc_start: 0.9218 (mt) cc_final: 0.8761 (mt) REVERT: E 492 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8176 (mp0) REVERT: E 502 LYS cc_start: 0.8959 (tmmt) cc_final: 0.8675 (tptm) REVERT: F 536 THR cc_start: 0.8791 (p) cc_final: 0.8412 (t) REVERT: F 581 LEU cc_start: 0.9328 (tt) cc_final: 0.8800 (mm) REVERT: F 621 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7734 (mt-10) REVERT: F 655 LYS cc_start: 0.9031 (pptt) cc_final: 0.8778 (pptt) outliers start: 1 outliers final: 0 residues processed: 272 average time/residue: 0.1268 time to fit residues: 50.7902 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 : 0.384 ------------------------------------------------------------------------------- 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: 0.9980 chunk 105 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 52 optimal weight: 0.3980 chunk 107 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 258 GLN D 543 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN ** 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 = 0.3165 r_free = 0.3165 target = 0.066738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.056864 restraints weight = 79601.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.058488 restraints weight = 45992.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.059644 restraints weight = 31166.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.060511 restraints weight = 23189.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.061076 restraints weight = 18487.576| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.5891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15852 Z= 0.130 Angle : 0.687 15.456 21713 Z= 0.337 Chirality : 0.047 0.504 2710 Planarity : 0.004 0.041 2630 Dihedral : 6.987 69.718 3688 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % 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: -0.55 (0.21), residues: 1635 helix: 0.49 (0.26), residues: 402 sheet: -0.14 (0.25), residues: 444 loop : -0.88 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 585 TYR 0.016 0.002 TYR A 217 PHE 0.028 0.002 PHE E 376 TRP 0.095 0.003 TRP F 610 HIS 0.011 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00286 (15737) covalent geometry : angle 0.64304 (21401) SS BOND : bond 0.00288 ( 33) SS BOND : angle 1.33062 ( 66) hydrogen bonds : bond 0.04210 ( 560) hydrogen bonds : angle 5.38950 ( 1533) link_ALPHA1-2 : bond 0.00876 ( 1) link_ALPHA1-2 : angle 1.45077 ( 3) link_ALPHA1-3 : bond 0.00708 ( 4) link_ALPHA1-3 : angle 1.45747 ( 12) link_ALPHA1-6 : bond 0.01253 ( 3) link_ALPHA1-6 : angle 1.58085 ( 9) link_BETA1-4 : bond 0.00451 ( 15) link_BETA1-4 : angle 1.55376 ( 45) link_NAG-ASN : bond 0.00405 ( 59) link_NAG-ASN : angle 2.51223 ( 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 273 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.490 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: C 69 TRP cc_start: 0.8971 (m-90) cc_final: 0.8597 (m-90) REVERT: C 95 MET cc_start: 0.9129 (ptm) cc_final: 0.8052 (mmm) REVERT: C 100 MET cc_start: 0.8755 (mmm) cc_final: 0.8422 (tpt) REVERT: C 102 GLU cc_start: 0.8943 (mp0) cc_final: 0.8694 (mp0) REVERT: C 103 GLN cc_start: 0.8616 (mt0) cc_final: 0.8359 (tt0) REVERT: C 107 ASP cc_start: 0.9390 (m-30) cc_final: 0.8953 (m-30) REVERT: C 217 TYR cc_start: 0.8732 (m-80) cc_final: 0.8506 (m-80) REVERT: C 432 GLN cc_start: 0.9005 (mp10) cc_final: 0.8735 (mp10) REVERT: D 522 PHE cc_start: 0.8861 (t80) cc_final: 0.8307 (t80) REVERT: D 543 ASN cc_start: 0.8401 (m110) cc_final: 0.8158 (m-40) REVERT: D 584 GLU cc_start: 0.9186 (mt-10) cc_final: 0.8729 (tm-30) REVERT: D 596 TRP cc_start: 0.8795 (m-10) cc_final: 0.8282 (m-10) REVERT: D 648 GLU cc_start: 0.9205 (tm-30) cc_final: 0.8659 (tp30) REVERT: D 652 GLN cc_start: 0.9207 (mm-40) cc_final: 0.8676 (mm110) REVERT: D 653 GLN cc_start: 0.8843 (mt0) cc_final: 0.8595 (pt0) REVERT: D 659 ASP cc_start: 0.8493 (m-30) cc_final: 0.8186 (m-30) REVERT: A 42 VAL cc_start: 0.9499 (t) cc_final: 0.9192 (p) REVERT: A 95 MET cc_start: 0.9217 (ptm) cc_final: 0.7359 (ppp) REVERT: A 100 MET cc_start: 0.9579 (mtm) cc_final: 0.9378 (mtm) REVERT: A 104 MET cc_start: 0.9064 (mmp) cc_final: 0.8762 (mmp) REVERT: A 114 GLN cc_start: 0.9231 (tp40) cc_final: 0.8726 (tm-30) REVERT: A 150 MET cc_start: 0.8459 (mtm) cc_final: 0.7909 (ptp) REVERT: A 161 MET cc_start: 0.9051 (tpp) cc_final: 0.8153 (tmm) REVERT: A 211 GLU cc_start: 0.8902 (pp20) cc_final: 0.8667 (pm20) REVERT: A 217 TYR cc_start: 0.8905 (m-80) cc_final: 0.8187 (m-80) REVERT: A 284 ILE cc_start: 0.9336 (mt) cc_final: 0.8910 (mm) REVERT: A 285 LEU cc_start: 0.9397 (mp) cc_final: 0.9139 (mp) REVERT: A 338 TRP cc_start: 0.8573 (t-100) cc_final: 0.8365 (t-100) REVERT: A 381 GLU cc_start: 0.9023 (tp30) cc_final: 0.8787 (tp30) REVERT: B 540 GLN cc_start: 0.9087 (mp10) cc_final: 0.8547 (mp10) REVERT: B 577 GLN cc_start: 0.8709 (tm130) cc_final: 0.8424 (tm-30) REVERT: B 626 MET cc_start: 0.8312 (tpt) cc_final: 0.7957 (tpp) REVERT: B 647 GLU cc_start: 0.8832 (pp20) cc_final: 0.8517 (pp20) REVERT: B 654 GLU cc_start: 0.9211 (tp30) cc_final: 0.8916 (tp30) REVERT: E 37 THR cc_start: 0.8403 (m) cc_final: 0.8101 (p) REVERT: E 80 ASN cc_start: 0.8806 (t0) cc_final: 0.8344 (p0) REVERT: E 95 MET cc_start: 0.8387 (ppp) cc_final: 0.8165 (ppp) REVERT: E 100 MET cc_start: 0.9124 (ptm) cc_final: 0.8872 (ppp) REVERT: E 112 TRP cc_start: 0.8620 (t-100) cc_final: 0.8411 (t60) REVERT: E 161 MET cc_start: 0.9369 (tpp) cc_final: 0.9165 (tpt) REVERT: E 434 MET cc_start: 0.8353 (tmm) cc_final: 0.7937 (tmm) REVERT: E 492 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8185 (mp0) REVERT: E 502 LYS cc_start: 0.8950 (tmmt) cc_final: 0.8654 (tptm) REVERT: F 536 THR cc_start: 0.8809 (p) cc_final: 0.8426 (t) REVERT: F 621 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7699 (mt-10) REVERT: F 647 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8075 (tm-30) REVERT: F 651 ASN cc_start: 0.9266 (t0) cc_final: 0.8730 (m110) REVERT: F 655 LYS cc_start: 0.8919 (pptt) cc_final: 0.8620 (pptt) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.1182 time to fit residues: 48.0701 Evaluate side-chains 212 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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: 10.0000 chunk 11 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 165 optimal weight: 20.0000 chunk 83 optimal weight: 0.0000 chunk 100 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 113 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 258 GLN ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 GLN ** 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 = 0.3177 r_free = 0.3177 target = 0.067251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.057436 restraints weight = 79022.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.059041 restraints weight = 46409.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.060174 restraints weight = 31597.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.061000 restraints weight = 23726.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.061579 restraints weight = 19086.810| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.6042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15852 Z= 0.123 Angle : 0.673 14.958 21713 Z= 0.328 Chirality : 0.046 0.490 2710 Planarity : 0.004 0.089 2630 Dihedral : 6.687 67.406 3688 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % 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: -0.45 (0.21), residues: 1635 helix: 0.48 (0.26), residues: 403 sheet: -0.07 (0.24), residues: 463 loop : -0.79 (0.23), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 178 TYR 0.013 0.001 TYR A 484 PHE 0.011 0.001 PHE D 522 TRP 0.072 0.002 TRP C 479 HIS 0.009 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00269 (15737) covalent geometry : angle 0.62767 (21401) SS BOND : bond 0.00252 ( 33) SS BOND : angle 1.19511 ( 66) hydrogen bonds : bond 0.04124 ( 560) hydrogen bonds : angle 5.30051 ( 1533) link_ALPHA1-2 : bond 0.00663 ( 1) link_ALPHA1-2 : angle 1.30379 ( 3) link_ALPHA1-3 : bond 0.00884 ( 4) link_ALPHA1-3 : angle 1.47856 ( 12) link_ALPHA1-6 : bond 0.01269 ( 3) link_ALPHA1-6 : angle 1.53667 ( 9) link_BETA1-4 : bond 0.00444 ( 15) link_BETA1-4 : angle 1.49940 ( 45) link_NAG-ASN : bond 0.00375 ( 59) link_NAG-ASN : angle 2.55187 ( 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 262 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 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: C 49 GLU cc_start: 0.7786 (mm-30) cc_final: 0.6905 (pt0) REVERT: C 50 THR cc_start: 0.8778 (m) cc_final: 0.8468 (m) REVERT: C 95 MET cc_start: 0.9087 (ptm) cc_final: 0.8024 (mmm) REVERT: C 100 MET cc_start: 0.8629 (mmm) cc_final: 0.8280 (tpt) REVERT: C 102 GLU cc_start: 0.8941 (mp0) cc_final: 0.8740 (mp0) REVERT: C 103 GLN cc_start: 0.8570 (mt0) cc_final: 0.8342 (tt0) REVERT: C 107 ASP cc_start: 0.9348 (m-30) cc_final: 0.8933 (m-30) REVERT: C 432 GLN cc_start: 0.8997 (mp10) cc_final: 0.8753 (mp10) REVERT: D 522 PHE cc_start: 0.8918 (t80) cc_final: 0.8269 (t80) REVERT: D 543 ASN cc_start: 0.8365 (m110) cc_final: 0.8067 (m-40) REVERT: D 584 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8698 (tm-30) REVERT: D 596 TRP cc_start: 0.8739 (m-10) cc_final: 0.8099 (m-90) REVERT: D 652 GLN cc_start: 0.9235 (mm-40) cc_final: 0.8973 (mm110) REVERT: D 653 GLN cc_start: 0.8809 (mt0) cc_final: 0.8514 (pt0) REVERT: D 659 ASP cc_start: 0.8483 (m-30) cc_final: 0.8196 (m-30) REVERT: A 95 MET cc_start: 0.9234 (ptm) cc_final: 0.7363 (ppp) REVERT: A 114 GLN cc_start: 0.9167 (tp40) cc_final: 0.8698 (tm-30) REVERT: A 150 MET cc_start: 0.8397 (mtm) cc_final: 0.7965 (ptp) REVERT: A 161 MET cc_start: 0.9078 (tpp) cc_final: 0.8183 (tmm) REVERT: A 211 GLU cc_start: 0.8922 (pp20) cc_final: 0.8639 (pm20) REVERT: A 284 ILE cc_start: 0.9331 (mt) cc_final: 0.8904 (mm) REVERT: A 285 LEU cc_start: 0.9374 (mp) cc_final: 0.9106 (mp) REVERT: A 381 GLU cc_start: 0.9004 (tp30) cc_final: 0.8483 (tp30) REVERT: B 530 MET cc_start: 0.8310 (mpp) cc_final: 0.6766 (mmp) REVERT: B 540 GLN cc_start: 0.9149 (mp10) cc_final: 0.8570 (mp10) REVERT: B 577 GLN cc_start: 0.8715 (tm-30) cc_final: 0.8463 (tm-30) REVERT: B 647 GLU cc_start: 0.8996 (pp20) cc_final: 0.8539 (pp20) REVERT: B 654 GLU cc_start: 0.9164 (tp30) cc_final: 0.8862 (tp30) REVERT: E 37 THR cc_start: 0.8498 (m) cc_final: 0.8083 (p) REVERT: E 80 ASN cc_start: 0.8811 (t0) cc_final: 0.8370 (p0) REVERT: E 95 MET cc_start: 0.8389 (ppp) cc_final: 0.8101 (ppp) REVERT: E 100 MET cc_start: 0.9141 (ptm) cc_final: 0.8731 (ptp) REVERT: E 150 MET cc_start: 0.8930 (mmp) cc_final: 0.8672 (mmm) REVERT: E 376 PHE cc_start: 0.8352 (t80) cc_final: 0.8150 (t80) REVERT: E 420 ILE cc_start: 0.9451 (mm) cc_final: 0.9215 (mm) REVERT: E 434 MET cc_start: 0.8363 (tmm) cc_final: 0.7931 (tmm) REVERT: E 492 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8179 (mp0) REVERT: E 502 LYS cc_start: 0.8995 (tmmt) cc_final: 0.8708 (tptm) REVERT: F 536 THR cc_start: 0.8764 (p) cc_final: 0.8327 (t) REVERT: F 621 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7707 (mt-10) REVERT: F 647 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8010 (tm-30) REVERT: F 651 ASN cc_start: 0.9243 (t0) cc_final: 0.8669 (m110) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.1156 time to fit residues: 45.5587 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 : 0.530 ------------------------------------------------------------------------------- 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: 1.9990 chunk 31 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 138 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.065815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.056227 restraints weight = 80027.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.057807 restraints weight = 46972.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.058908 restraints weight = 31965.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.059738 restraints weight = 24007.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.060332 restraints weight = 19174.227| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.6191 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= 0.183 Angle : 0.725 14.599 21713 Z= 0.356 Chirality : 0.047 0.504 2710 Planarity : 0.004 0.040 2630 Dihedral : 6.881 65.580 3688 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % 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: -0.62 (0.21), residues: 1635 helix: 0.34 (0.26), residues: 403 sheet: -0.13 (0.24), residues: 454 loop : -0.92 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 178 TYR 0.030 0.002 TYR C 484 PHE 0.016 0.002 PHE C 176 TRP 0.070 0.003 TRP F 610 HIS 0.009 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00400 (15737) covalent geometry : angle 0.68399 (21401) SS BOND : bond 0.00327 ( 33) SS BOND : angle 1.16059 ( 66) hydrogen bonds : bond 0.04347 ( 560) hydrogen bonds : angle 5.51758 ( 1533) link_ALPHA1-2 : bond 0.00448 ( 1) link_ALPHA1-2 : angle 1.50526 ( 3) link_ALPHA1-3 : bond 0.00591 ( 4) link_ALPHA1-3 : angle 1.58654 ( 12) link_ALPHA1-6 : bond 0.01189 ( 3) link_ALPHA1-6 : angle 1.68110 ( 9) link_BETA1-4 : bond 0.00400 ( 15) link_BETA1-4 : angle 1.59256 ( 45) link_NAG-ASN : bond 0.00433 ( 59) link_NAG-ASN : angle 2.52518 ( 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 248 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.489 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: 0.7778 (mm-30) cc_final: 0.6933 (pt0) REVERT: C 50 THR cc_start: 0.8857 (m) cc_final: 0.8540 (m) REVERT: C 100 MET cc_start: 0.8658 (mmm) cc_final: 0.8391 (tpt) REVERT: C 102 GLU cc_start: 0.8967 (mp0) cc_final: 0.8752 (mp0) REVERT: C 103 GLN cc_start: 0.8533 (mt0) cc_final: 0.8282 (tt0) REVERT: C 107 ASP cc_start: 0.9340 (m-30) cc_final: 0.9008 (m-30) REVERT: C 432 GLN cc_start: 0.9040 (mp10) cc_final: 0.8798 (mp10) REVERT: D 522 PHE cc_start: 0.8889 (t80) cc_final: 0.8336 (t80) REVERT: D 542 ARG cc_start: 0.8642 (ptp-170) cc_final: 0.8190 (ptt-90) REVERT: D 584 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8707 (tm-30) REVERT: D 596 TRP cc_start: 0.8797 (m-10) cc_final: 0.8107 (m-90) REVERT: D 648 GLU cc_start: 0.9290 (tm-30) cc_final: 0.8838 (tm-30) REVERT: D 652 GLN cc_start: 0.9243 (mm-40) cc_final: 0.8960 (mm-40) REVERT: D 653 GLN cc_start: 0.9017 (mt0) cc_final: 0.8717 (pt0) REVERT: D 657 GLU cc_start: 0.9328 (mp0) cc_final: 0.9090 (mp0) REVERT: D 659 ASP cc_start: 0.8497 (m-30) cc_final: 0.8185 (m-30) REVERT: A 95 MET cc_start: 0.9223 (ptm) cc_final: 0.7924 (ppp) REVERT: A 114 GLN cc_start: 0.9185 (tp40) cc_final: 0.8690 (tm-30) REVERT: A 150 MET cc_start: 0.8572 (mtm) cc_final: 0.8234 (ptp) REVERT: A 161 MET cc_start: 0.9074 (tpp) cc_final: 0.8258 (tmm) REVERT: A 211 GLU cc_start: 0.8909 (pp20) cc_final: 0.8615 (pm20) REVERT: A 284 ILE cc_start: 0.9329 (mt) cc_final: 0.8920 (mm) REVERT: A 285 LEU cc_start: 0.9364 (mp) cc_final: 0.9142 (mp) REVERT: B 530 MET cc_start: 0.8086 (mpp) cc_final: 0.6594 (mmp) REVERT: B 540 GLN cc_start: 0.9151 (mp10) cc_final: 0.8599 (mp10) REVERT: B 577 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8445 (tm-30) REVERT: B 647 GLU cc_start: 0.8979 (pp20) cc_final: 0.8467 (pp20) REVERT: B 654 GLU cc_start: 0.9191 (tp30) cc_final: 0.8892 (tp30) REVERT: E 80 ASN cc_start: 0.8796 (t0) cc_final: 0.8321 (p0) REVERT: E 95 MET cc_start: 0.8514 (ppp) cc_final: 0.8175 (ppp) REVERT: E 100 MET cc_start: 0.9237 (ptm) cc_final: 0.8702 (ppp) REVERT: E 150 MET cc_start: 0.9016 (mmp) cc_final: 0.8784 (mmm) REVERT: E 492 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8214 (mp0) REVERT: E 502 LYS cc_start: 0.9020 (tmmt) cc_final: 0.8708 (tptm) REVERT: F 536 THR cc_start: 0.8857 (p) cc_final: 0.8425 (t) REVERT: F 621 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7729 (mt-10) REVERT: F 642 ILE cc_start: 0.9239 (mp) cc_final: 0.9036 (mp) REVERT: F 655 LYS cc_start: 0.8965 (pptt) cc_final: 0.8691 (pptt) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.1192 time to fit residues: 44.4201 Evaluate side-chains 190 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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: 0.6980 chunk 41 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 157 optimal weight: 0.9990 chunk 170 optimal weight: 9.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN D 543 ASN D 653 GLN A 216 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 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 = 0.3151 r_free = 0.3151 target = 0.066233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.056462 restraints weight = 79699.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.058041 restraints weight = 47105.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.059160 restraints weight = 32198.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.059955 restraints weight = 24320.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.060437 restraints weight = 19616.442| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.6309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 15852 Z= 0.159 Angle : 0.696 14.336 21713 Z= 0.343 Chirality : 0.046 0.498 2710 Planarity : 0.004 0.045 2630 Dihedral : 6.798 62.939 3688 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % 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: -0.60 (0.21), residues: 1635 helix: 0.32 (0.26), residues: 403 sheet: -0.13 (0.24), residues: 453 loop : -0.87 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 178 TYR 0.017 0.002 TYR A 217 PHE 0.025 0.002 PHE E 376 TRP 0.065 0.003 TRP C 479 HIS 0.009 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00352 (15737) covalent geometry : angle 0.65679 (21401) SS BOND : bond 0.00309 ( 33) SS BOND : angle 1.15051 ( 66) hydrogen bonds : bond 0.04217 ( 560) hydrogen bonds : angle 5.44062 ( 1533) link_ALPHA1-2 : bond 0.00745 ( 1) link_ALPHA1-2 : angle 1.54694 ( 3) link_ALPHA1-3 : bond 0.00675 ( 4) link_ALPHA1-3 : angle 1.52163 ( 12) link_ALPHA1-6 : bond 0.01323 ( 3) link_ALPHA1-6 : angle 1.59022 ( 9) link_BETA1-4 : bond 0.00389 ( 15) link_BETA1-4 : angle 1.52274 ( 45) link_NAG-ASN : bond 0.00378 ( 59) link_NAG-ASN : angle 2.43038 ( 177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2150.83 seconds wall clock time: 38 minutes 12.87 seconds (2292.87 seconds total)