Starting phenix.real_space_refine on Tue May 5 02:04:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ovu_70919/05_2026/9ovu_70919.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ovu_70919/05_2026/9ovu_70919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ovu_70919/05_2026/9ovu_70919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ovu_70919/05_2026/9ovu_70919.map" model { file = "/net/cci-nas-00/data/ceres_data/9ovu_70919/05_2026/9ovu_70919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ovu_70919/05_2026/9ovu_70919.cif" } resolution = 3.2 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= 0.004 sd= 0.010 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: 5 Type Number sf(0) Gaussians S 126 5.16 5 Na 1 4.78 5 C 16040 2.51 5 N 4160 2.21 5 O 4684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25011 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 6175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 6175 Classifications: {'peptide': 775} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 748} Chain breaks: 2 Chain: "B" Number of atoms: 6153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6153 Classifications: {'peptide': 780} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 756} Chain breaks: 2 Chain: "C" Number of atoms: 6175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 6175 Classifications: {'peptide': 775} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 748} Chain breaks: 2 Chain: "D" Number of atoms: 6153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6153 Classifications: {'peptide': 780} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 756} Chain breaks: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "H" 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'FWF': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'FWF': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.28, per 1000 atoms: 0.21 Number of scatterers: 25011 At special positions: 0 Unit cell: (165.17, 126.16, 191.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 126 16.00 Na 1 11.00 O 4684 8.00 N 4160 7.00 C 16040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 311 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.04 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG E 1 " - " ASN A 51 " " NAG F 1 " - " ASN A 237 " " NAG G 1 " - " ASN A 351 " " NAG H 1 " - " ASN B 355 " " NAG I 1 " - " ASN C 51 " " NAG J 1 " - " ASN C 237 " " NAG K 1 " - " ASN C 351 " " NAG L 1 " - " ASN D 355 " Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 953.4 milliseconds 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5736 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 34 sheets defined 40.8% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 removed outlier: 3.501A pdb=" N PHE A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 31 " --> pdb=" O HIS A 27 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 34 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER A 35 " --> pdb=" O ARG A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 67 removed outlier: 3.801A pdb=" N GLN A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 93 removed outlier: 3.924A pdb=" N LEU A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER A 87 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE A 88 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 126 removed outlier: 3.717A pdb=" N ILE A 122 " --> pdb=" O GLN A 118 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 141 through 156 removed outlier: 3.577A pdb=" N VAL A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 146 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG A 148 " --> pdb=" O SER A 144 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.916A pdb=" N MET A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 171 through 176' Processing helix chain 'A' and resid 176 through 182 Processing helix chain 'A' and resid 193 through 205 removed outlier: 3.971A pdb=" N ASN A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 200 " --> pdb=" O ARG A 196 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLN A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 231 removed outlier: 3.760A pdb=" N LYS A 230 " --> pdb=" O ASP A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 261 removed outlier: 3.618A pdb=" N ILE A 254 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 299 removed outlier: 4.043A pdb=" N THR A 281 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS A 286 " --> pdb=" O TYR A 282 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 331 removed outlier: 3.604A pdb=" N ILE A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA A 328 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN A 331 " --> pdb=" O ARG A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 419 through 424 Processing helix chain 'A' and resid 424 through 432 removed outlier: 3.567A pdb=" N ALA A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS A 430 " --> pdb=" O ALA A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'A' and resid 478 through 483 removed outlier: 3.629A pdb=" N GLU A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 530 removed outlier: 4.126A pdb=" N VAL A 526 " --> pdb=" O TRP A 522 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N PHE A 527 " --> pdb=" O MET A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 540 removed outlier: 3.651A pdb=" N PHE A 537 " --> pdb=" O SER A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 579 removed outlier: 3.556A pdb=" N PHE A 575 " --> pdb=" O ASN A 571 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 578 " --> pdb=" O TRP A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 616 removed outlier: 3.672A pdb=" N PHE A 603 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU A 606 " --> pdb=" O TRP A 602 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE A 607 " --> pdb=" O PHE A 603 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 608 " --> pdb=" O PHE A 604 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN A 615 " --> pdb=" O SER A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 638 removed outlier: 3.780A pdb=" N LEU A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS A 637 " --> pdb=" O GLU A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 657 Processing helix chain 'A' and resid 662 through 672 removed outlier: 3.645A pdb=" N THR A 668 " --> pdb=" O GLU A 664 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 672 " --> pdb=" O THR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 689 Processing helix chain 'A' and resid 702 through 709 removed outlier: 4.248A pdb=" N TYR A 707 " --> pdb=" O THR A 703 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 708 " --> pdb=" O MET A 704 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU A 709 " --> pdb=" O ASN A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 752 removed outlier: 3.614A pdb=" N LEU A 747 " --> pdb=" O ASN A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 758 Processing helix chain 'A' and resid 758 through 764 removed outlier: 3.793A pdb=" N TRP A 762 " --> pdb=" O LEU A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 806 removed outlier: 3.793A pdb=" N LEU A 795 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU A 801 " --> pdb=" O GLY A 797 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N MET A 803 " --> pdb=" O LEU A 799 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU A 804 " --> pdb=" O GLY A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 812 removed outlier: 4.141A pdb=" N CYS A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 37 Processing helix chain 'B' and resid 54 through 67 removed outlier: 3.514A pdb=" N SER B 64 " --> pdb=" O ASN B 60 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.511A pdb=" N THR B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 123 removed outlier: 3.840A pdb=" N LEU B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 152 removed outlier: 4.026A pdb=" N VAL B 149 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 182 removed outlier: 4.089A pdb=" N LEU B 180 " --> pdb=" O THR B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 199 No H-bonds generated for 'chain 'B' and resid 197 through 199' Processing helix chain 'B' and resid 200 through 210 removed outlier: 3.697A pdb=" N ILE B 204 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP B 206 " --> pdb=" O ASN B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.587A pdb=" N PHE B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 303 removed outlier: 3.655A pdb=" N ASP B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG B 300 " --> pdb=" O PHE B 296 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS B 301 " --> pdb=" O ARG B 297 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 334 removed outlier: 3.945A pdb=" N ILE B 329 " --> pdb=" O GLN B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 425 through 436 removed outlier: 3.576A pdb=" N ALA B 430 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 469 removed outlier: 3.887A pdb=" N TYR B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 522 through 542 removed outlier: 3.991A pdb=" N TRP B 526 " --> pdb=" O ALA B 522 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N MET B 527 " --> pdb=" O TYR B 523 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N CYS B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 530 " --> pdb=" O TRP B 526 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE B 531 " --> pdb=" O MET B 527 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL B 539 " --> pdb=" O GLY B 535 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU B 540 " --> pdb=" O VAL B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 583 removed outlier: 3.665A pdb=" N SER B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TRP B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 579 " --> pdb=" O ASN B 575 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N SER B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LEU B 581 " --> pdb=" O LEU B 577 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 582 " --> pdb=" O TRP B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 599 Processing helix chain 'B' and resid 604 through 620 removed outlier: 3.924A pdb=" N LEU B 610 " --> pdb=" O TRP B 606 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 612 " --> pdb=" O PHE B 608 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 620 " --> pdb=" O TYR B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 664 through 677 removed outlier: 3.522A pdb=" N LYS B 669 " --> pdb=" O ALA B 665 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR B 673 " --> pdb=" O LYS B 669 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N MET B 674 " --> pdb=" O MET B 670 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 677 " --> pdb=" O TYR B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 696 removed outlier: 3.600A pdb=" N ARG B 692 " --> pdb=" O GLU B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 714 removed outlier: 3.938A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 removed outlier: 3.597A pdb=" N ASN B 747 " --> pdb=" O GLY B 743 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU B 755 " --> pdb=" O LEU B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 767 removed outlier: 3.547A pdb=" N LYS B 763 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN B 764 " --> pdb=" O ASP B 760 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS B 765 " --> pdb=" O LYS B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 811 removed outlier: 4.168A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU B 799 " --> pdb=" O VAL B 795 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY B 801 " --> pdb=" O TYR B 797 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY B 804 " --> pdb=" O VAL B 800 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU B 805 " --> pdb=" O GLY B 801 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA B 806 " --> pdb=" O GLY B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 818 Processing helix chain 'C' and resid 25 through 36 removed outlier: 3.501A pdb=" N PHE C 30 " --> pdb=" O GLU C 26 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG C 31 " --> pdb=" O HIS C 27 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE C 32 " --> pdb=" O ALA C 28 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU C 34 " --> pdb=" O PHE C 30 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER C 35 " --> pdb=" O ARG C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 67 removed outlier: 3.802A pdb=" N GLN C 65 " --> pdb=" O ARG C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 93 removed outlier: 3.926A pdb=" N LEU C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER C 87 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE C 88 " --> pdb=" O MET C 84 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 126 removed outlier: 3.717A pdb=" N ILE C 122 " --> pdb=" O GLN C 118 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER C 123 " --> pdb=" O GLU C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 140 No H-bonds generated for 'chain 'C' and resid 138 through 140' Processing helix chain 'C' and resid 141 through 156 removed outlier: 3.577A pdb=" N VAL C 145 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU C 146 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN C 147 " --> pdb=" O LEU C 143 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG C 148 " --> pdb=" O SER C 144 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL C 149 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 176 removed outlier: 3.915A pdb=" N MET C 175 " --> pdb=" O GLU C 171 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU C 176 " --> pdb=" O GLY C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 171 through 176' Processing helix chain 'C' and resid 176 through 182 Processing helix chain 'C' and resid 193 through 205 removed outlier: 3.971A pdb=" N ASN C 198 " --> pdb=" O SER C 194 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY C 202 " --> pdb=" O ASN C 198 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLN C 203 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL C 205 " --> pdb=" O LEU C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 231 removed outlier: 3.760A pdb=" N LYS C 230 " --> pdb=" O ASP C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 261 removed outlier: 3.619A pdb=" N ILE C 254 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 299 removed outlier: 4.042A pdb=" N THR C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS C 286 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE C 292 " --> pdb=" O MET C 288 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 331 removed outlier: 3.604A pdb=" N ILE C 325 " --> pdb=" O GLN C 321 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA C 328 " --> pdb=" O ASP C 324 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN C 331 " --> pdb=" O ARG C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 415 No H-bonds generated for 'chain 'C' and resid 413 through 415' Processing helix chain 'C' and resid 419 through 424 Processing helix chain 'C' and resid 424 through 432 removed outlier: 3.567A pdb=" N ALA C 429 " --> pdb=" O ALA C 425 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS C 430 " --> pdb=" O ALA C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 465 Processing helix chain 'C' and resid 478 through 483 removed outlier: 3.628A pdb=" N GLU C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 530 removed outlier: 4.126A pdb=" N VAL C 526 " --> pdb=" O TRP C 522 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N PHE C 527 " --> pdb=" O MET C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 540 removed outlier: 3.651A pdb=" N PHE C 537 " --> pdb=" O SER C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 579 removed outlier: 3.556A pdb=" N PHE C 575 " --> pdb=" O ASN C 571 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER C 576 " --> pdb=" O SER C 572 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU C 577 " --> pdb=" O LEU C 573 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY C 578 " --> pdb=" O TRP C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 616 removed outlier: 3.673A pdb=" N PHE C 603 " --> pdb=" O GLY C 599 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU C 606 " --> pdb=" O TRP C 602 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE C 607 " --> pdb=" O PHE C 603 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE C 608 " --> pdb=" O PHE C 604 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C 614 " --> pdb=" O SER C 610 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN C 615 " --> pdb=" O SER C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 638 removed outlier: 3.779A pdb=" N LEU C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS C 637 " --> pdb=" O GLU C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 657 Processing helix chain 'C' and resid 662 through 672 removed outlier: 3.644A pdb=" N THR C 668 " --> pdb=" O GLU C 664 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER C 672 " --> pdb=" O THR C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 689 Processing helix chain 'C' and resid 702 through 709 removed outlier: 4.249A pdb=" N TYR C 707 " --> pdb=" O THR C 703 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE C 708 " --> pdb=" O MET C 704 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU C 709 " --> pdb=" O ASN C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 752 removed outlier: 3.614A pdb=" N LEU C 747 " --> pdb=" O ASN C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 758 Processing helix chain 'C' and resid 758 through 764 removed outlier: 3.793A pdb=" N TRP C 762 " --> pdb=" O LEU C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 806 removed outlier: 3.793A pdb=" N LEU C 795 " --> pdb=" O VAL C 791 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU C 801 " --> pdb=" O GLY C 797 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N MET C 803 " --> pdb=" O LEU C 799 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU C 804 " --> pdb=" O GLY C 800 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 812 removed outlier: 4.142A pdb=" N CYS C 811 " --> pdb=" O LEU C 807 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 37 Processing helix chain 'D' and resid 54 through 67 removed outlier: 3.514A pdb=" N SER D 64 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN D 65 " --> pdb=" O ALA D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 93 removed outlier: 3.512A pdb=" N THR D 91 " --> pdb=" O SER D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 123 removed outlier: 3.840A pdb=" N LEU D 122 " --> pdb=" O LYS D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 152 removed outlier: 4.026A pdb=" N VAL D 149 " --> pdb=" O THR D 145 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 182 removed outlier: 4.088A pdb=" N LEU D 180 " --> pdb=" O THR D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 199 No H-bonds generated for 'chain 'D' and resid 197 through 199' Processing helix chain 'D' and resid 200 through 210 removed outlier: 3.697A pdb=" N ILE D 204 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP D 206 " --> pdb=" O ASN D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 264 removed outlier: 3.586A pdb=" N PHE D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 303 removed outlier: 3.654A pdb=" N ASP D 287 " --> pdb=" O ALA D 283 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL D 289 " --> pdb=" O THR D 285 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG D 300 " --> pdb=" O PHE D 296 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS D 301 " --> pdb=" O ARG D 297 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 334 removed outlier: 3.944A pdb=" N ILE D 329 " --> pdb=" O GLN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 415 Processing helix chain 'D' and resid 425 through 436 removed outlier: 3.574A pdb=" N ALA D 430 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS D 434 " --> pdb=" O ALA D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 469 removed outlier: 3.887A pdb=" N TYR D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 522 through 542 removed outlier: 3.991A pdb=" N TRP D 526 " --> pdb=" O ALA D 522 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N MET D 527 " --> pdb=" O TYR D 523 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N CYS D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL D 530 " --> pdb=" O TRP D 526 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE D 531 " --> pdb=" O MET D 527 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 539 " --> pdb=" O GLY D 535 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU D 540 " --> pdb=" O VAL D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 583 removed outlier: 3.664A pdb=" N SER D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N TRP D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE D 579 " --> pdb=" O ASN D 575 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N SER D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LEU D 581 " --> pdb=" O LEU D 577 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY D 582 " --> pdb=" O TRP D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 599 Processing helix chain 'D' and resid 604 through 620 removed outlier: 3.923A pdb=" N LEU D 610 " --> pdb=" O TRP D 606 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE D 612 " --> pdb=" O PHE D 608 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D 620 " --> pdb=" O TYR D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 677 removed outlier: 3.522A pdb=" N LYS D 669 " --> pdb=" O ALA D 665 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR D 673 " --> pdb=" O LYS D 669 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N MET D 674 " --> pdb=" O MET D 670 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA D 677 " --> pdb=" O TYR D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 removed outlier: 3.600A pdb=" N ARG D 692 " --> pdb=" O GLU D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 714 removed outlier: 3.940A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 756 removed outlier: 3.597A pdb=" N ASN D 747 " --> pdb=" O GLY D 743 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU D 755 " --> pdb=" O LEU D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 767 removed outlier: 3.546A pdb=" N LYS D 763 " --> pdb=" O LEU D 759 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN D 764 " --> pdb=" O ASP D 760 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS D 765 " --> pdb=" O LYS D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 811 removed outlier: 4.168A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU D 799 " --> pdb=" O VAL D 795 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY D 801 " --> pdb=" O TYR D 797 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY D 804 " --> pdb=" O VAL D 800 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU D 805 " --> pdb=" O GLY D 801 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA D 806 " --> pdb=" O GLY D 802 " (cutoff:3.500A) Processing helix chain 'D' and resid 812 through 818 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 removed outlier: 3.818A pdb=" N ILE A 13 " --> pdb=" O LYS A 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 18 removed outlier: 6.819A pdb=" N ILE A 73 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N PHE A 96 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 164 removed outlier: 6.626A pdb=" N TYR A 135 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL A 134 " --> pdb=" O VAL A 189 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 334 through 336 removed outlier: 3.880A pdb=" N PHE A 334 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 359 Processing sheet with id=AA6, first strand: chain 'A' and resid 437 through 440 Processing sheet with id=AA7, first strand: chain 'A' and resid 403 through 404 removed outlier: 3.608A pdb=" N GLU A 418 " --> pdb=" O MET A 403 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 449 through 450 removed outlier: 3.991A pdb=" N ALA A 455 " --> pdb=" O ASP A 450 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 493 through 494 Processing sheet with id=AB1, first strand: chain 'A' and resid 642 through 644 removed outlier: 6.935A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N TYR A 696 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LYS A 501 " --> pdb=" O TYR A 696 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 221 through 222 removed outlier: 4.166A pdb=" N PHE B 245 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY B 372 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLU B 362 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LYS B 370 " --> pdb=" O GLU B 362 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LYS B 364 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 346 through 347 removed outlier: 4.162A pdb=" N LYS B 346 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 395 through 399 removed outlier: 5.895A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB6, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AB7, first strand: chain 'B' and resid 496 through 498 removed outlier: 4.189A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.720A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 12 through 13 removed outlier: 3.818A pdb=" N ILE C 13 " --> pdb=" O LYS C 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 17 through 18 removed outlier: 6.819A pdb=" N ILE C 73 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N PHE C 96 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 163 through 164 removed outlier: 6.626A pdb=" N TYR C 135 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL C 134 " --> pdb=" O VAL C 189 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 334 through 336 removed outlier: 3.879A pdb=" N PHE C 334 " --> pdb=" O VAL C 341 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 357 through 359 Processing sheet with id=AC5, first strand: chain 'C' and resid 437 through 440 Processing sheet with id=AC6, first strand: chain 'C' and resid 403 through 404 removed outlier: 3.608A pdb=" N GLU C 418 " --> pdb=" O MET C 403 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 449 through 450 removed outlier: 3.990A pdb=" N ALA C 455 " --> pdb=" O ASP C 450 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 493 through 494 Processing sheet with id=AC9, first strand: chain 'C' and resid 642 through 644 removed outlier: 6.935A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N TYR C 696 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LYS C 501 " --> pdb=" O TYR C 696 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 221 through 222 removed outlier: 4.166A pdb=" N PHE D 245 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY D 372 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLU D 362 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LYS D 370 " --> pdb=" O GLU D 362 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LYS D 364 " --> pdb=" O PRO D 368 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 346 through 347 removed outlier: 4.161A pdb=" N LYS D 346 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 395 through 399 removed outlier: 5.895A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AD5, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AD6, first strand: chain 'D' and resid 496 through 498 removed outlier: 4.190A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.721A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 624 hydrogen bonds defined for protein. 1800 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: 4.41 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7847 1.34 - 1.46: 6163 1.46 - 1.58: 11315 1.58 - 1.70: 5 1.70 - 1.82: 204 Bond restraints: 25534 Sorted by residual: bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.522 -0.116 2.00e-02 2.50e+03 3.35e+01 bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.515 -0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.512 -0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" C1 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 1.406 1.510 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.510 -0.104 2.00e-02 2.50e+03 2.71e+01 ... (remaining 25529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 33734 3.35 - 6.70: 675 6.70 - 10.05: 83 10.05 - 13.40: 12 13.40 - 16.75: 4 Bond angle restraints: 34508 Sorted by residual: angle pdb=" N ILE C 212 " pdb=" CA ILE C 212 " pdb=" C ILE C 212 " ideal model delta sigma weight residual 113.71 106.62 7.09 9.50e-01 1.11e+00 5.57e+01 angle pdb=" N THR B 457 " pdb=" CA THR B 457 " pdb=" C THR B 457 " ideal model delta sigma weight residual 114.75 105.38 9.37 1.26e+00 6.30e-01 5.53e+01 angle pdb=" N THR D 457 " pdb=" CA THR D 457 " pdb=" C THR D 457 " ideal model delta sigma weight residual 114.75 105.42 9.33 1.26e+00 6.30e-01 5.48e+01 angle pdb=" N ILE A 212 " pdb=" CA ILE A 212 " pdb=" C ILE A 212 " ideal model delta sigma weight residual 113.71 106.69 7.02 9.50e-01 1.11e+00 5.46e+01 angle pdb=" C ILE B 591 " pdb=" N SER B 592 " pdb=" CA SER B 592 " ideal model delta sigma weight residual 121.80 138.55 -16.75 2.44e+00 1.68e-01 4.71e+01 ... (remaining 34503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.81: 14812 24.81 - 49.62: 518 49.62 - 74.44: 70 74.44 - 99.25: 26 99.25 - 124.06: 22 Dihedral angle restraints: 15448 sinusoidal: 6478 harmonic: 8970 Sorted by residual: dihedral pdb=" CA GLU D 678 " pdb=" C GLU D 678 " pdb=" N PRO D 679 " pdb=" CA PRO D 679 " ideal model delta harmonic sigma weight residual -180.00 -119.07 -60.93 0 5.00e+00 4.00e-02 1.49e+02 dihedral pdb=" CA GLU B 678 " pdb=" C GLU B 678 " pdb=" N PRO B 679 " pdb=" CA PRO B 679 " ideal model delta harmonic sigma weight residual -180.00 -119.12 -60.88 0 5.00e+00 4.00e-02 1.48e+02 dihedral pdb=" CA PRO B 632 " pdb=" C PRO B 632 " pdb=" N ILE B 633 " pdb=" CA ILE B 633 " ideal model delta harmonic sigma weight residual -180.00 -131.90 -48.10 0 5.00e+00 4.00e-02 9.26e+01 ... (remaining 15445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 3466 0.093 - 0.185: 344 0.185 - 0.278: 29 0.278 - 0.371: 8 0.371 - 0.463: 3 Chirality restraints: 3850 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN D 355 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN C 237 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.15e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 237 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.68e+00 ... (remaining 3847 not shown) Planarity restraints: 4358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 FWF C 902 " -0.030 2.00e-02 2.50e+03 4.88e-02 4.76e+01 pdb=" C10 FWF C 902 " 0.082 2.00e-02 2.50e+03 pdb=" C14 FWF C 902 " 0.087 2.00e-02 2.50e+03 pdb=" C2 FWF C 902 " -0.032 2.00e-02 2.50e+03 pdb=" C3 FWF C 902 " -0.027 2.00e-02 2.50e+03 pdb=" C4 FWF C 902 " -0.022 2.00e-02 2.50e+03 pdb=" C5 FWF C 902 " -0.027 2.00e-02 2.50e+03 pdb=" C6 FWF C 902 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 FWF D 902 " -0.015 2.00e-02 2.50e+03 4.27e-02 3.65e+01 pdb=" C11 FWF D 902 " -0.022 2.00e-02 2.50e+03 pdb=" C12 FWF D 902 " -0.029 2.00e-02 2.50e+03 pdb=" C13 FWF D 902 " 0.078 2.00e-02 2.50e+03 pdb=" C4 FWF D 902 " 0.068 2.00e-02 2.50e+03 pdb=" C7 FWF D 902 " -0.029 2.00e-02 2.50e+03 pdb=" C8 FWF D 902 " -0.030 2.00e-02 2.50e+03 pdb=" C9 FWF D 902 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 FWF D 902 " -0.022 2.00e-02 2.50e+03 4.18e-02 3.49e+01 pdb=" C10 FWF D 902 " 0.073 2.00e-02 2.50e+03 pdb=" C14 FWF D 902 " 0.071 2.00e-02 2.50e+03 pdb=" C2 FWF D 902 " -0.025 2.00e-02 2.50e+03 pdb=" C3 FWF D 902 " -0.026 2.00e-02 2.50e+03 pdb=" C4 FWF D 902 " -0.023 2.00e-02 2.50e+03 pdb=" C5 FWF D 902 " -0.025 2.00e-02 2.50e+03 pdb=" C6 FWF D 902 " -0.024 2.00e-02 2.50e+03 ... (remaining 4355 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 7229 2.81 - 3.33: 21397 3.33 - 3.86: 38813 3.86 - 4.38: 44893 4.38 - 4.90: 76516 Nonbonded interactions: 188848 Sorted by model distance: nonbonded pdb=" OG SER B 27 " pdb=" O PRO B 271 " model vdw 2.289 3.040 nonbonded pdb=" OG SER D 27 " pdb=" O PRO D 271 " model vdw 2.289 3.040 nonbonded pdb=" O MET D 33 " pdb=" OG SER D 37 " model vdw 2.313 3.040 nonbonded pdb=" O MET B 33 " pdb=" OG SER B 37 " model vdw 2.313 3.040 nonbonded pdb=" O GLU D 391 " pdb=" OG1 THR D 394 " model vdw 2.336 3.040 ... (remaining 188843 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' selection = (chain 'C' and resid 9 through 901) } ncs_group { reference = (chain 'B' and resid 10 through 901) selection = (chain 'D' and resid 10 through 901) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'J' } 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 individual isotropic 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: 5.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.850 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 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 : 0.006 0.116 25560 Z= 0.296 Angle : 1.224 16.750 34578 Z= 0.731 Chirality : 0.059 0.463 3850 Planarity : 0.008 0.098 4350 Dihedral : 13.709 124.061 9688 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.39 % Allowed : 13.29 % Favored : 86.33 % Rotamer: Outliers : 0.60 % Allowed : 6.38 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.67 % 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: -6.10 (0.10), residues: 3086 helix: -4.75 (0.05), residues: 1220 sheet: -3.12 (0.27), residues: 298 loop : -3.66 (0.13), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 178 TYR 0.025 0.002 TYR B 702 PHE 0.027 0.002 PHE D 237 TRP 0.024 0.003 TRP C 370 HIS 0.009 0.002 HIS C 431 Details of bonding type rmsd covalent geometry : bond 0.00602 (25534) covalent geometry : angle 1.21306 (34508) SS BOND : bond 0.00276 ( 8) SS BOND : angle 1.55100 ( 16) hydrogen bonds : bond 0.35419 ( 624) hydrogen bonds : angle 10.73172 ( 1800) link_BETA1-4 : bond 0.01593 ( 10) link_BETA1-4 : angle 4.54926 ( 30) link_NAG-ASN : bond 0.00664 ( 8) link_NAG-ASN : angle 3.87419 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 499 time to evaluate : 0.781 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: A 60 TYR cc_start: 0.7580 (t80) cc_final: 0.7048 (t80) REVERT: A 209 LYS cc_start: 0.5515 (mtmp) cc_final: 0.4634 (tptp) REVERT: A 223 PHE cc_start: 0.7629 (t80) cc_final: 0.7386 (t80) REVERT: A 585 CYS cc_start: 0.6813 (m) cc_final: 0.6498 (m) REVERT: B 211 ILE cc_start: 0.6031 (OUTLIER) cc_final: 0.5706 (pt) REVERT: B 605 TRP cc_start: 0.8360 (t-100) cc_final: 0.8153 (t-100) REVERT: B 814 PHE cc_start: 0.6527 (t80) cc_final: 0.6071 (t80) REVERT: C 192 CYS cc_start: 0.7709 (p) cc_final: 0.7508 (p) REVERT: C 232 LYS cc_start: 0.8082 (mtpt) cc_final: 0.6632 (tttt) REVERT: C 352 TYR cc_start: 0.6700 (m-10) cc_final: 0.6492 (m-10) REVERT: C 367 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7857 (pt) REVERT: D 41 PHE cc_start: 0.5818 (m-80) cc_final: 0.4853 (m-10) REVERT: D 46 HIS cc_start: 0.5827 (t-90) cc_final: 0.5546 (t-90) REVERT: D 52 VAL cc_start: 0.7836 (p) cc_final: 0.7630 (p) REVERT: D 209 ILE cc_start: 0.8673 (mt) cc_final: 0.8435 (mm) REVERT: D 262 TRP cc_start: 0.7919 (t-100) cc_final: 0.7598 (t-100) REVERT: D 374 TRP cc_start: 0.7165 (t60) cc_final: 0.6590 (t60) REVERT: D 463 MET cc_start: 0.8618 (mtm) cc_final: 0.8385 (mtp) outliers start: 16 outliers final: 5 residues processed: 512 average time/residue: 0.1971 time to fit residues: 148.0775 Evaluate side-chains 314 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 307 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 399 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.0050 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 83 ASN A 93 HIS A 203 GLN A 220 ASN A 331 GLN ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 ASN B 13 GLN B 60 ASN B 83 ASN B 107 HIS B 170 ASN B 318 ASN B 337 GLN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 HIS B 418 ASN B 619 ASN B 747 ASN B 764 ASN C 23 GLN C 25 GLN C 107 ASN ** C 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN C 355 HIS C 410 GLN C 571 ASN C 615 ASN D 60 ASN ** D 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 ASN D 318 ASN D 337 GLN D 344 ASN D 359 ASN D 411 ASN D 412 HIS D 418 ASN D 619 ASN D 747 ASN D 764 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.116975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.092597 restraints weight = 73928.493| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 3.24 r_work: 0.3332 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25560 Z= 0.146 Angle : 0.764 12.221 34578 Z= 0.390 Chirality : 0.046 0.233 3850 Planarity : 0.006 0.096 4350 Dihedral : 12.345 118.308 3844 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.02 % Favored : 87.75 % Rotamer: Outliers : 2.33 % Allowed : 10.77 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.27 % 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: -4.85 (0.12), residues: 3086 helix: -3.23 (0.10), residues: 1264 sheet: -2.85 (0.26), residues: 328 loop : -3.27 (0.14), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 309 TYR 0.020 0.002 TYR C 137 PHE 0.027 0.002 PHE A 513 TRP 0.020 0.002 TRP C 370 HIS 0.010 0.002 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.00312 (25534) covalent geometry : angle 0.75311 (34508) SS BOND : bond 0.01235 ( 8) SS BOND : angle 1.40475 ( 16) hydrogen bonds : bond 0.05419 ( 624) hydrogen bonds : angle 5.77288 ( 1800) link_BETA1-4 : bond 0.00957 ( 10) link_BETA1-4 : angle 3.10773 ( 30) link_NAG-ASN : bond 0.00489 ( 8) link_NAG-ASN : angle 3.51037 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 337 time to evaluate : 0.836 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: A 57 GLU cc_start: 0.8229 (tp30) cc_final: 0.7864 (tt0) REVERT: A 60 TYR cc_start: 0.8528 (t80) cc_final: 0.8307 (t80) REVERT: A 134 VAL cc_start: 0.7398 (t) cc_final: 0.7037 (p) REVERT: A 144 SER cc_start: 0.7613 (t) cc_final: 0.7099 (p) REVERT: A 223 PHE cc_start: 0.8110 (t80) cc_final: 0.7785 (t80) REVERT: A 334 PHE cc_start: 0.6464 (p90) cc_final: 0.6228 (p90) REVERT: A 535 VAL cc_start: 0.7951 (p) cc_final: 0.7747 (t) REVERT: A 585 CYS cc_start: 0.6631 (m) cc_final: 0.6267 (m) REVERT: A 592 LEU cc_start: 0.6347 (OUTLIER) cc_final: 0.5819 (tt) REVERT: B 80 LYS cc_start: 0.8226 (mtmm) cc_final: 0.7603 (mmtt) REVERT: B 182 GLN cc_start: 0.8018 (mm-40) cc_final: 0.7531 (mm-40) REVERT: B 186 LEU cc_start: 0.8755 (pp) cc_final: 0.8403 (mp) REVERT: B 318 ASN cc_start: 0.8624 (OUTLIER) cc_final: 0.8299 (m110) REVERT: B 376 GLU cc_start: 0.7682 (tp30) cc_final: 0.7214 (tm-30) REVERT: B 814 PHE cc_start: 0.5924 (t80) cc_final: 0.5579 (t80) REVERT: C 175 MET cc_start: 0.8049 (mmm) cc_final: 0.7410 (mpp) REVERT: C 201 LEU cc_start: 0.6842 (OUTLIER) cc_final: 0.6266 (tp) REVERT: C 224 MET cc_start: 0.7913 (mmt) cc_final: 0.7689 (mmm) REVERT: C 366 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7896 (tttt) REVERT: C 596 ILE cc_start: 0.7569 (mt) cc_final: 0.7261 (tp) REVERT: D 190 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7422 (mmp80) REVERT: D 250 TYR cc_start: 0.8048 (m-80) cc_final: 0.7802 (m-80) REVERT: D 261 ARG cc_start: 0.8429 (ttt180) cc_final: 0.7929 (mtp85) REVERT: D 262 TRP cc_start: 0.7862 (t-100) cc_final: 0.7525 (t-100) REVERT: D 292 MET cc_start: 0.8481 (mtp) cc_final: 0.8045 (mtm) REVERT: D 335 GLN cc_start: 0.8158 (tm130) cc_final: 0.7764 (tm-30) REVERT: D 344 ASN cc_start: 0.7836 (m-40) cc_final: 0.7340 (m-40) REVERT: D 345 ILE cc_start: 0.7441 (OUTLIER) cc_final: 0.7209 (mm) REVERT: D 374 TRP cc_start: 0.7477 (t60) cc_final: 0.6413 (t60) REVERT: D 638 ASP cc_start: 0.6196 (m-30) cc_final: 0.5929 (m-30) outliers start: 62 outliers final: 25 residues processed: 383 average time/residue: 0.1678 time to fit residues: 99.5204 Evaluate side-chains 312 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 281 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 366 LYS Chi-restraints excluded: chain C residue 409 ASN Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 769 CYS Chi-restraints excluded: chain C residue 788 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 741 SER Chi-restraints excluded: chain D residue 789 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 295 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 chunk 302 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 287 optimal weight: 7.9990 chunk 282 optimal weight: 0.4980 chunk 76 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 152 optimal weight: 0.3980 chunk 30 optimal weight: 10.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN A 355 HIS A 361 HIS A 410 GLN ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN C 355 HIS ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 GLN ** 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 = 0.4041 r_free = 0.4041 target = 0.113866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.089051 restraints weight = 72807.098| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 3.13 r_work: 0.3255 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25560 Z= 0.186 Angle : 0.761 11.682 34578 Z= 0.381 Chirality : 0.046 0.205 3850 Planarity : 0.006 0.092 4350 Dihedral : 11.394 120.051 3835 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.70 % Favored : 87.14 % Rotamer: Outliers : 3.26 % Allowed : 11.29 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.17 % 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: -4.05 (0.13), residues: 3086 helix: -2.18 (0.12), residues: 1252 sheet: -3.27 (0.26), residues: 320 loop : -3.00 (0.15), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 273 TYR 0.021 0.002 TYR D 533 PHE 0.037 0.002 PHE B 623 TRP 0.030 0.002 TRP C 574 HIS 0.009 0.001 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.00431 (25534) covalent geometry : angle 0.74264 (34508) SS BOND : bond 0.00392 ( 8) SS BOND : angle 1.65015 ( 16) hydrogen bonds : bond 0.04814 ( 624) hydrogen bonds : angle 5.12082 ( 1800) link_BETA1-4 : bond 0.00809 ( 10) link_BETA1-4 : angle 3.86054 ( 30) link_NAG-ASN : bond 0.00476 ( 8) link_NAG-ASN : angle 4.63440 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 321 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8146 (tp30) cc_final: 0.7902 (tt0) REVERT: A 58 MET cc_start: 0.8700 (mmm) cc_final: 0.8474 (tpt) REVERT: A 60 TYR cc_start: 0.8689 (t80) cc_final: 0.8309 (t80) REVERT: A 137 TYR cc_start: 0.7404 (p90) cc_final: 0.7157 (p90) REVERT: A 144 SER cc_start: 0.7729 (t) cc_final: 0.7245 (p) REVERT: A 148 ARG cc_start: 0.8186 (tpt90) cc_final: 0.7588 (tpt90) REVERT: A 223 PHE cc_start: 0.8198 (t80) cc_final: 0.7994 (t80) REVERT: A 585 CYS cc_start: 0.6696 (m) cc_final: 0.6205 (p) REVERT: A 804 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6304 (mp) REVERT: B 41 PHE cc_start: 0.5991 (m-10) cc_final: 0.5049 (m-10) REVERT: B 44 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8622 (p) REVERT: B 132 LYS cc_start: 0.8097 (tttp) cc_final: 0.7864 (ttpt) REVERT: B 182 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7579 (mm-40) REVERT: B 186 LEU cc_start: 0.8739 (pp) cc_final: 0.8425 (mt) REVERT: B 344 ASN cc_start: 0.8353 (t0) cc_final: 0.8078 (t0) REVERT: B 364 LYS cc_start: 0.7396 (ptmt) cc_final: 0.7161 (pttp) REVERT: B 704 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8935 (pp) REVERT: B 814 PHE cc_start: 0.6089 (t80) cc_final: 0.5862 (t80) REVERT: C 79 ARG cc_start: 0.6796 (tpp-160) cc_final: 0.6536 (ttp80) REVERT: C 84 MET cc_start: 0.6835 (mmm) cc_final: 0.6504 (mmt) REVERT: C 141 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.6939 (ptt90) REVERT: C 175 MET cc_start: 0.8232 (mmm) cc_final: 0.7625 (mpp) REVERT: C 201 LEU cc_start: 0.6654 (OUTLIER) cc_final: 0.6027 (tp) REVERT: C 223 PHE cc_start: 0.7599 (t80) cc_final: 0.7390 (t80) REVERT: C 246 TYR cc_start: 0.7491 (m-80) cc_final: 0.6741 (m-80) REVERT: C 370 TRP cc_start: 0.7869 (t60) cc_final: 0.7186 (t60) REVERT: C 595 ARG cc_start: 0.6879 (mtt-85) cc_final: 0.6656 (mtp85) REVERT: D 44 THR cc_start: 0.8356 (OUTLIER) cc_final: 0.8121 (p) REVERT: D 188 LYS cc_start: 0.8868 (mptt) cc_final: 0.8665 (mmtt) REVERT: D 190 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7529 (mmp80) REVERT: D 292 MET cc_start: 0.8579 (mtp) cc_final: 0.8172 (mtt) REVERT: D 293 THR cc_start: 0.8585 (m) cc_final: 0.8344 (p) REVERT: D 297 ARG cc_start: 0.8465 (ttp-110) cc_final: 0.7795 (ttm110) REVERT: D 335 GLN cc_start: 0.8170 (tm130) cc_final: 0.7804 (tm-30) REVERT: D 344 ASN cc_start: 0.8003 (m-40) cc_final: 0.7623 (m-40) REVERT: D 374 TRP cc_start: 0.7647 (t60) cc_final: 0.6384 (t60) outliers start: 87 outliers final: 41 residues processed: 387 average time/residue: 0.1716 time to fit residues: 103.5994 Evaluate side-chains 348 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 300 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 366 LYS Chi-restraints excluded: chain C residue 409 ASN Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 585 CYS Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 769 CYS Chi-restraints excluded: chain C residue 788 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 803 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 35 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 264 optimal weight: 5.9990 chunk 237 optimal weight: 4.9990 chunk 205 optimal weight: 0.0040 chunk 144 optimal weight: 0.7980 chunk 231 optimal weight: 7.9990 chunk 194 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 212 optimal weight: 3.9990 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 ASN C 355 HIS ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 ASN ** D 107 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 = 0.4051 r_free = 0.4051 target = 0.114530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.090069 restraints weight = 72952.547| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 3.11 r_work: 0.3290 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25560 Z= 0.135 Angle : 0.701 12.824 34578 Z= 0.350 Chirality : 0.044 0.195 3850 Planarity : 0.005 0.088 4350 Dihedral : 10.735 118.085 3835 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.89 % Favored : 87.95 % Rotamer: Outliers : 2.85 % Allowed : 13.17 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.52 (0.14), residues: 3086 helix: -1.58 (0.13), residues: 1268 sheet: -2.71 (0.26), residues: 340 loop : -2.93 (0.15), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 42 TYR 0.016 0.001 TYR D 533 PHE 0.029 0.001 PHE C 101 TRP 0.036 0.002 TRP A 574 HIS 0.004 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00304 (25534) covalent geometry : angle 0.68295 (34508) SS BOND : bond 0.00237 ( 8) SS BOND : angle 1.20057 ( 16) hydrogen bonds : bond 0.03586 ( 624) hydrogen bonds : angle 4.68878 ( 1800) link_BETA1-4 : bond 0.00715 ( 10) link_BETA1-4 : angle 3.76738 ( 30) link_NAG-ASN : bond 0.00395 ( 8) link_NAG-ASN : angle 4.35540 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 300 time to evaluate : 0.939 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: A 39 GLU cc_start: 0.5344 (OUTLIER) cc_final: 0.4640 (pt0) REVERT: A 57 GLU cc_start: 0.8085 (tp30) cc_final: 0.7816 (tt0) REVERT: A 58 MET cc_start: 0.8675 (mmm) cc_final: 0.8426 (tpt) REVERT: A 134 VAL cc_start: 0.7898 (t) cc_final: 0.7448 (m) REVERT: A 144 SER cc_start: 0.7774 (t) cc_final: 0.7313 (p) REVERT: A 148 ARG cc_start: 0.8212 (tpt90) cc_final: 0.7541 (tpt90) REVERT: A 359 MET cc_start: 0.7017 (mtp) cc_final: 0.6515 (ttt) REVERT: A 585 CYS cc_start: 0.6763 (m) cc_final: 0.6209 (p) REVERT: A 609 ILE cc_start: 0.7005 (mm) cc_final: 0.6653 (mp) REVERT: A 666 MET cc_start: 0.8409 (mtp) cc_final: 0.8196 (mtt) REVERT: A 804 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6269 (mp) REVERT: B 44 THR cc_start: 0.8929 (OUTLIER) cc_final: 0.8641 (p) REVERT: B 80 LYS cc_start: 0.8268 (mtmm) cc_final: 0.7609 (mmtt) REVERT: B 132 LYS cc_start: 0.8117 (tttp) cc_final: 0.7879 (ttpt) REVERT: B 182 GLN cc_start: 0.8009 (mm-40) cc_final: 0.7600 (mm-40) REVERT: B 186 LEU cc_start: 0.8717 (pp) cc_final: 0.8382 (mt) REVERT: B 344 ASN cc_start: 0.8355 (t0) cc_final: 0.8030 (t0) REVERT: B 704 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8943 (pp) REVERT: B 814 PHE cc_start: 0.6030 (t80) cc_final: 0.5774 (t80) REVERT: B 819 ARG cc_start: 0.4641 (mmt90) cc_final: 0.4435 (mmt90) REVERT: C 148 ARG cc_start: 0.8352 (tpt90) cc_final: 0.8073 (mtp180) REVERT: C 150 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7777 (tt) REVERT: C 175 MET cc_start: 0.8335 (mmm) cc_final: 0.8090 (mmm) REVERT: C 364 ILE cc_start: 0.6826 (OUTLIER) cc_final: 0.6577 (tt) REVERT: C 370 TRP cc_start: 0.7850 (t60) cc_final: 0.7267 (t60) REVERT: D 44 THR cc_start: 0.8357 (OUTLIER) cc_final: 0.8087 (p) REVERT: D 189 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7484 (tt0) REVERT: D 261 ARG cc_start: 0.8364 (ttt180) cc_final: 0.8156 (ttt180) REVERT: D 280 TYR cc_start: 0.7514 (p90) cc_final: 0.7080 (p90) REVERT: D 292 MET cc_start: 0.8573 (mtp) cc_final: 0.8257 (mtt) REVERT: D 344 ASN cc_start: 0.7983 (m-40) cc_final: 0.7648 (m-40) REVERT: D 345 ILE cc_start: 0.7590 (mm) cc_final: 0.7379 (mm) REVERT: D 488 VAL cc_start: 0.8332 (OUTLIER) cc_final: 0.8108 (m) outliers start: 76 outliers final: 50 residues processed: 354 average time/residue: 0.1700 time to fit residues: 93.4444 Evaluate side-chains 334 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 276 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 409 ASN Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 585 CYS Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 769 CYS Chi-restraints excluded: chain C residue 788 VAL Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 585 MET Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 811 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 153 optimal weight: 0.9990 chunk 245 optimal weight: 10.0000 chunk 127 optimal weight: 0.6980 chunk 227 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 289 optimal weight: 3.9990 chunk 258 optimal weight: 6.9990 chunk 199 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 GLN B 65 GLN B 214 HIS ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 ASN C 355 HIS C 383 ASN ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 583 GLN C 787 ASN D 13 GLN ** D 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.112454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.087669 restraints weight = 71954.219| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 3.17 r_work: 0.3205 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 25560 Z= 0.222 Angle : 0.750 11.447 34578 Z= 0.374 Chirality : 0.047 0.205 3850 Planarity : 0.005 0.109 4350 Dihedral : 10.621 123.533 3835 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.25 % Favored : 86.58 % Rotamer: Outliers : 3.60 % Allowed : 13.02 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.17 % 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: -3.36 (0.14), residues: 3086 helix: -1.25 (0.14), residues: 1244 sheet: -3.17 (0.25), residues: 330 loop : -2.88 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 599 TYR 0.017 0.002 TYR D 533 PHE 0.043 0.002 PHE C 223 TRP 0.053 0.002 TRP C 574 HIS 0.009 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00527 (25534) covalent geometry : angle 0.73235 (34508) SS BOND : bond 0.00340 ( 8) SS BOND : angle 1.35970 ( 16) hydrogen bonds : bond 0.04086 ( 624) hydrogen bonds : angle 4.71404 ( 1800) link_BETA1-4 : bond 0.00618 ( 10) link_BETA1-4 : angle 3.99774 ( 30) link_NAG-ASN : bond 0.00555 ( 8) link_NAG-ASN : angle 4.19741 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 326 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 GLU cc_start: 0.5395 (OUTLIER) cc_final: 0.4734 (pt0) REVERT: A 57 GLU cc_start: 0.8080 (tp30) cc_final: 0.7796 (tt0) REVERT: A 58 MET cc_start: 0.8617 (mmm) cc_final: 0.8375 (tpt) REVERT: A 134 VAL cc_start: 0.8036 (t) cc_final: 0.7629 (m) REVERT: A 144 SER cc_start: 0.7862 (t) cc_final: 0.7433 (p) REVERT: A 148 ARG cc_start: 0.8308 (tpt90) cc_final: 0.7663 (tpt90) REVERT: A 359 MET cc_start: 0.7206 (mtp) cc_final: 0.6789 (ttt) REVERT: A 523 MET cc_start: 0.6946 (OUTLIER) cc_final: 0.5982 (tpt) REVERT: A 585 CYS cc_start: 0.6875 (m) cc_final: 0.6255 (p) REVERT: A 609 ILE cc_start: 0.7068 (mm) cc_final: 0.6702 (mp) REVERT: A 804 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6288 (mp) REVERT: B 80 LYS cc_start: 0.8294 (mtmm) cc_final: 0.7623 (mmtt) REVERT: B 132 LYS cc_start: 0.8227 (tttp) cc_final: 0.8002 (ttpt) REVERT: B 182 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7634 (mm-40) REVERT: B 186 LEU cc_start: 0.8742 (pp) cc_final: 0.8437 (mt) REVERT: B 414 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7241 (ptp) REVERT: B 704 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8983 (pp) REVERT: B 814 PHE cc_start: 0.6019 (t80) cc_final: 0.5777 (t80) REVERT: C 79 ARG cc_start: 0.7098 (tpp-160) cc_final: 0.6764 (ttp80) REVERT: C 116 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8052 (mp0) REVERT: C 148 ARG cc_start: 0.8410 (tpt90) cc_final: 0.8050 (mtp180) REVERT: C 175 MET cc_start: 0.8391 (mmm) cc_final: 0.8125 (mmm) REVERT: C 232 LYS cc_start: 0.7075 (tptt) cc_final: 0.6699 (tptt) REVERT: C 370 TRP cc_start: 0.7934 (t60) cc_final: 0.7464 (t60) REVERT: C 581 MET cc_start: 0.6318 (mmm) cc_final: 0.5651 (mmm) REVERT: C 730 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.7092 (tp) REVERT: D 44 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8243 (p) REVERT: D 189 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7540 (tt0) REVERT: D 280 TYR cc_start: 0.7727 (p90) cc_final: 0.7315 (p90) REVERT: D 292 MET cc_start: 0.8595 (mtp) cc_final: 0.8340 (mtt) REVERT: D 297 ARG cc_start: 0.8469 (ttm110) cc_final: 0.8161 (ttm110) REVERT: D 345 ILE cc_start: 0.7810 (mm) cc_final: 0.7588 (mm) REVERT: D 394 THR cc_start: 0.6298 (m) cc_final: 0.5986 (p) REVERT: D 488 VAL cc_start: 0.8343 (OUTLIER) cc_final: 0.8069 (m) REVERT: D 722 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7574 (tttp) outliers start: 96 outliers final: 62 residues processed: 393 average time/residue: 0.1658 time to fit residues: 101.8353 Evaluate side-chains 368 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 297 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 409 ASN Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 585 CYS Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 769 CYS Chi-restraints excluded: chain C residue 788 VAL Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 585 MET Chi-restraints excluded: chain D residue 722 LYS Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 811 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 164 optimal weight: 9.9990 chunk 147 optimal weight: 1.9990 chunk 198 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 233 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 240 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 281 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 GLN ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 ASN B 366 ASN C 83 ASN C 355 HIS ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.113752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.090713 restraints weight = 72328.659| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.93 r_work: 0.3290 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25560 Z= 0.142 Angle : 0.701 11.137 34578 Z= 0.348 Chirality : 0.045 0.261 3850 Planarity : 0.005 0.101 4350 Dihedral : 10.231 119.774 3835 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.57 % Favored : 88.27 % Rotamer: Outliers : 3.60 % Allowed : 14.52 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.17 % 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: -2.99 (0.14), residues: 3086 helix: -0.86 (0.14), residues: 1252 sheet: -2.83 (0.25), residues: 348 loop : -2.80 (0.15), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 190 TYR 0.020 0.001 TYR B 533 PHE 0.035 0.002 PHE C 223 TRP 0.029 0.002 TRP A 370 HIS 0.013 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00330 (25534) covalent geometry : angle 0.68305 (34508) SS BOND : bond 0.00227 ( 8) SS BOND : angle 1.22607 ( 16) hydrogen bonds : bond 0.03319 ( 624) hydrogen bonds : angle 4.46758 ( 1800) link_BETA1-4 : bond 0.00746 ( 10) link_BETA1-4 : angle 3.97165 ( 30) link_NAG-ASN : bond 0.00684 ( 8) link_NAG-ASN : angle 4.03099 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 296 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 GLU cc_start: 0.5299 (OUTLIER) cc_final: 0.4625 (pt0) REVERT: A 57 GLU cc_start: 0.7904 (tp30) cc_final: 0.7686 (tt0) REVERT: A 58 MET cc_start: 0.8475 (mmm) cc_final: 0.8242 (tpt) REVERT: A 134 VAL cc_start: 0.7993 (t) cc_final: 0.7625 (m) REVERT: A 144 SER cc_start: 0.7838 (t) cc_final: 0.7428 (p) REVERT: A 255 MET cc_start: 0.8412 (tmm) cc_final: 0.8030 (tmm) REVERT: A 359 MET cc_start: 0.7111 (mtp) cc_final: 0.6663 (ttt) REVERT: A 411 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.6785 (p90) REVERT: A 523 MET cc_start: 0.6728 (OUTLIER) cc_final: 0.5852 (tpt) REVERT: A 581 MET cc_start: 0.5778 (mmm) cc_final: 0.5510 (mmm) REVERT: A 585 CYS cc_start: 0.6890 (m) cc_final: 0.6250 (p) REVERT: A 609 ILE cc_start: 0.6901 (mm) cc_final: 0.6517 (mp) REVERT: A 625 MET cc_start: 0.5228 (mpp) cc_final: 0.5009 (mpp) REVERT: A 666 MET cc_start: 0.8389 (mtp) cc_final: 0.8120 (mtt) REVERT: B 130 TRP cc_start: 0.7543 (m-10) cc_final: 0.6973 (m-10) REVERT: B 132 LYS cc_start: 0.8209 (tttp) cc_final: 0.7989 (ttpt) REVERT: B 182 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7668 (mm-40) REVERT: B 186 LEU cc_start: 0.8707 (pp) cc_final: 0.8360 (mt) REVERT: B 335 GLN cc_start: 0.7812 (tm130) cc_final: 0.7127 (tm-30) REVERT: B 344 ASN cc_start: 0.8309 (OUTLIER) cc_final: 0.8045 (t0) REVERT: B 704 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8907 (pp) REVERT: C 58 MET cc_start: 0.7925 (mmm) cc_final: 0.7663 (tpp) REVERT: C 79 ARG cc_start: 0.7084 (tpp-160) cc_final: 0.6794 (ttp80) REVERT: C 116 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7978 (mp0) REVERT: C 128 TYR cc_start: 0.8935 (m-80) cc_final: 0.8571 (m-10) REVERT: C 175 MET cc_start: 0.8374 (mmm) cc_final: 0.8110 (mmm) REVERT: C 352 TYR cc_start: 0.6803 (m-10) cc_final: 0.6573 (m-10) REVERT: C 370 TRP cc_start: 0.7894 (t60) cc_final: 0.7421 (t60) REVERT: C 411 PHE cc_start: 0.7560 (OUTLIER) cc_final: 0.7244 (p90) REVERT: C 730 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.7102 (tp) REVERT: D 44 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8219 (p) REVERT: D 47 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8693 (mt) REVERT: D 130 TRP cc_start: 0.7209 (m-10) cc_final: 0.6695 (m-10) REVERT: D 137 TYR cc_start: 0.8139 (p90) cc_final: 0.7869 (p90) REVERT: D 280 TYR cc_start: 0.7683 (p90) cc_final: 0.7312 (p90) REVERT: D 292 MET cc_start: 0.8471 (mtp) cc_final: 0.8242 (mtt) REVERT: D 297 ARG cc_start: 0.8447 (ttm110) cc_final: 0.8122 (ttm110) REVERT: D 345 ILE cc_start: 0.7613 (mm) cc_final: 0.7389 (mm) REVERT: D 361 MET cc_start: 0.6391 (ptp) cc_final: 0.6110 (mtt) REVERT: D 488 VAL cc_start: 0.8244 (OUTLIER) cc_final: 0.8013 (m) REVERT: D 585 MET cc_start: 0.6630 (OUTLIER) cc_final: 0.6280 (ttm) REVERT: D 610 LEU cc_start: 0.8171 (tp) cc_final: 0.7926 (tp) outliers start: 96 outliers final: 61 residues processed: 365 average time/residue: 0.1645 time to fit residues: 94.1713 Evaluate side-chains 352 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 280 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 411 PHE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 323 TRP Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 366 LYS Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 409 ASN Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 585 CYS Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 769 CYS Chi-restraints excluded: chain C residue 788 VAL Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 585 MET Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 803 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 42 optimal weight: 2.9990 chunk 211 optimal weight: 9.9990 chunk 306 optimal weight: 2.9990 chunk 49 optimal weight: 0.0870 chunk 186 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 279 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 178 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 237 optimal weight: 0.9980 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 HIS ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 GLN D 412 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.113185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.089887 restraints weight = 72234.228| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.95 r_work: 0.3270 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25560 Z= 0.169 Angle : 0.711 12.497 34578 Z= 0.353 Chirality : 0.045 0.250 3850 Planarity : 0.005 0.097 4350 Dihedral : 10.115 120.672 3835 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.90 % Favored : 86.97 % Rotamer: Outliers : 3.34 % Allowed : 15.45 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.15), residues: 3086 helix: -0.66 (0.14), residues: 1284 sheet: -3.21 (0.24), residues: 348 loop : -2.82 (0.15), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 190 TYR 0.018 0.001 TYR D 533 PHE 0.036 0.002 PHE B 517 TRP 0.031 0.001 TRP A 370 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00396 (25534) covalent geometry : angle 0.69445 (34508) SS BOND : bond 0.00246 ( 8) SS BOND : angle 1.21678 ( 16) hydrogen bonds : bond 0.03431 ( 624) hydrogen bonds : angle 4.42781 ( 1800) link_BETA1-4 : bond 0.00801 ( 10) link_BETA1-4 : angle 3.84787 ( 30) link_NAG-ASN : bond 0.00562 ( 8) link_NAG-ASN : angle 3.95574 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 298 time to evaluate : 0.927 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: A 39 GLU cc_start: 0.5379 (OUTLIER) cc_final: 0.4658 (pt0) REVERT: A 58 MET cc_start: 0.8464 (mmm) cc_final: 0.8228 (tpt) REVERT: A 134 VAL cc_start: 0.8101 (t) cc_final: 0.7730 (m) REVERT: A 137 TYR cc_start: 0.7299 (p90) cc_final: 0.7054 (p90) REVERT: A 255 MET cc_start: 0.8515 (tmm) cc_final: 0.8063 (tmm) REVERT: A 297 ARG cc_start: 0.7182 (mmp80) cc_final: 0.6821 (mtt-85) REVERT: A 359 MET cc_start: 0.7143 (mtp) cc_final: 0.6693 (ttt) REVERT: A 411 PHE cc_start: 0.7608 (OUTLIER) cc_final: 0.6822 (p90) REVERT: A 581 MET cc_start: 0.5883 (mmm) cc_final: 0.5552 (mmm) REVERT: A 585 CYS cc_start: 0.6977 (m) cc_final: 0.6290 (p) REVERT: A 609 ILE cc_start: 0.6905 (mm) cc_final: 0.6491 (mp) REVERT: A 625 MET cc_start: 0.5267 (mpp) cc_final: 0.5054 (mpp) REVERT: A 666 MET cc_start: 0.8401 (mtp) cc_final: 0.8168 (mtt) REVERT: B 132 LYS cc_start: 0.8241 (tttp) cc_final: 0.8016 (ttpt) REVERT: B 186 LEU cc_start: 0.8702 (pp) cc_final: 0.8363 (mt) REVERT: B 704 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8906 (pp) REVERT: C 79 ARG cc_start: 0.7128 (tpp-160) cc_final: 0.6850 (ttp80) REVERT: C 116 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7962 (mp0) REVERT: C 128 TYR cc_start: 0.8958 (m-80) cc_final: 0.8534 (m-10) REVERT: C 141 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7597 (ptt90) REVERT: C 175 MET cc_start: 0.8382 (mmm) cc_final: 0.8123 (mmm) REVERT: C 352 TYR cc_start: 0.6894 (m-10) cc_final: 0.6538 (m-10) REVERT: C 370 TRP cc_start: 0.7930 (t60) cc_final: 0.7557 (t60) REVERT: C 411 PHE cc_start: 0.7638 (OUTLIER) cc_final: 0.7339 (p90) REVERT: C 730 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.7051 (tp) REVERT: D 36 PHE cc_start: 0.7782 (m-80) cc_final: 0.7433 (m-10) REVERT: D 44 THR cc_start: 0.8483 (OUTLIER) cc_final: 0.8239 (p) REVERT: D 47 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8691 (mt) REVERT: D 130 TRP cc_start: 0.7157 (m-10) cc_final: 0.6810 (m-10) REVERT: D 280 TYR cc_start: 0.7759 (p90) cc_final: 0.7365 (p90) REVERT: D 292 MET cc_start: 0.8415 (mtp) cc_final: 0.8211 (mtt) REVERT: D 297 ARG cc_start: 0.8468 (ttm110) cc_final: 0.8141 (ttm110) REVERT: D 345 ILE cc_start: 0.7811 (mm) cc_final: 0.7597 (mm) REVERT: D 361 MET cc_start: 0.6390 (ptp) cc_final: 0.6084 (mtt) REVERT: D 394 THR cc_start: 0.5886 (m) cc_final: 0.5533 (p) REVERT: D 488 VAL cc_start: 0.8266 (OUTLIER) cc_final: 0.8018 (m) REVERT: D 610 LEU cc_start: 0.8264 (tp) cc_final: 0.8043 (tp) REVERT: D 741 SER cc_start: 0.8473 (OUTLIER) cc_final: 0.8224 (m) REVERT: D 796 PHE cc_start: 0.7891 (m-80) cc_final: 0.7682 (m-80) REVERT: D 819 ARG cc_start: 0.4059 (mmt90) cc_final: 0.3847 (mmt90) outliers start: 89 outliers final: 67 residues processed: 358 average time/residue: 0.1676 time to fit residues: 94.0642 Evaluate side-chains 363 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 286 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 411 PHE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 323 TRP Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 366 LYS Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 409 ASN Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 585 CYS Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 769 CYS Chi-restraints excluded: chain C residue 788 VAL Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 585 MET Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 741 SER Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 811 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 142 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 280 optimal weight: 0.7980 chunk 297 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 205 optimal weight: 0.0980 chunk 18 optimal weight: 8.9990 chunk 203 optimal weight: 0.8980 chunk 114 optimal weight: 0.0170 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 ASN ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 ASN C 355 HIS ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 583 GLN ** D 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.114214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.090301 restraints weight = 72480.519| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 3.00 r_work: 0.3290 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25560 Z= 0.118 Angle : 0.680 13.542 34578 Z= 0.337 Chirality : 0.044 0.223 3850 Planarity : 0.005 0.092 4350 Dihedral : 9.866 117.564 3835 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.63 % Favored : 88.20 % Rotamer: Outliers : 3.15 % Allowed : 15.87 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.15), residues: 3086 helix: -0.41 (0.15), residues: 1282 sheet: -2.95 (0.24), residues: 374 loop : -2.76 (0.16), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 253 TYR 0.019 0.001 TYR B 533 PHE 0.040 0.001 PHE B 517 TRP 0.032 0.001 TRP A 370 HIS 0.020 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00262 (25534) covalent geometry : angle 0.66326 (34508) SS BOND : bond 0.00189 ( 8) SS BOND : angle 1.08986 ( 16) hydrogen bonds : bond 0.02960 ( 624) hydrogen bonds : angle 4.26830 ( 1800) link_BETA1-4 : bond 0.00679 ( 10) link_BETA1-4 : angle 3.77010 ( 30) link_NAG-ASN : bond 0.00513 ( 8) link_NAG-ASN : angle 3.99450 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 279 time to evaluate : 0.994 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: A 39 GLU cc_start: 0.5353 (OUTLIER) cc_final: 0.4640 (pt0) REVERT: A 58 MET cc_start: 0.8434 (mmm) cc_final: 0.8199 (tpt) REVERT: A 134 VAL cc_start: 0.8079 (t) cc_final: 0.7725 (m) REVERT: A 137 TYR cc_start: 0.7299 (p90) cc_final: 0.7032 (p90) REVERT: A 255 MET cc_start: 0.8527 (tmm) cc_final: 0.8069 (tmm) REVERT: A 359 MET cc_start: 0.7134 (mtp) cc_final: 0.6783 (ttt) REVERT: A 411 PHE cc_start: 0.7514 (OUTLIER) cc_final: 0.6657 (p90) REVERT: A 585 CYS cc_start: 0.6977 (m) cc_final: 0.6271 (p) REVERT: A 601 TRP cc_start: 0.7315 (t-100) cc_final: 0.6895 (t-100) REVERT: A 609 ILE cc_start: 0.6795 (mm) cc_final: 0.6377 (mp) REVERT: A 666 MET cc_start: 0.8418 (mtp) cc_final: 0.8166 (mtt) REVERT: B 130 TRP cc_start: 0.7497 (m-10) cc_final: 0.6994 (m-10) REVERT: B 132 LYS cc_start: 0.8213 (tttp) cc_final: 0.7990 (ttpt) REVERT: B 186 LEU cc_start: 0.8711 (pp) cc_final: 0.8363 (mt) REVERT: B 335 GLN cc_start: 0.7842 (tm130) cc_final: 0.7400 (tm-30) REVERT: B 789 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8003 (tm) REVERT: C 58 MET cc_start: 0.8043 (mmm) cc_final: 0.7721 (tpp) REVERT: C 79 ARG cc_start: 0.7126 (tpp-160) cc_final: 0.6878 (ttp80) REVERT: C 116 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7909 (mp0) REVERT: C 128 TYR cc_start: 0.8922 (m-80) cc_final: 0.8519 (m-10) REVERT: C 141 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7609 (ptt-90) REVERT: C 175 MET cc_start: 0.8388 (mmm) cc_final: 0.8141 (mmm) REVERT: C 352 TYR cc_start: 0.6779 (m-10) cc_final: 0.6364 (m-10) REVERT: C 366 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8035 (tttt) REVERT: C 370 TRP cc_start: 0.7918 (t60) cc_final: 0.7558 (t60) REVERT: C 409 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.7948 (p0) REVERT: C 411 PHE cc_start: 0.7562 (OUTLIER) cc_final: 0.7309 (p90) REVERT: C 595 ARG cc_start: 0.5620 (mtp85) cc_final: 0.5259 (ptm160) REVERT: C 639 THR cc_start: 0.8275 (p) cc_final: 0.8015 (t) REVERT: D 44 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8199 (p) REVERT: D 47 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8669 (mt) REVERT: D 51 GLU cc_start: 0.7200 (tt0) cc_final: 0.6948 (tm-30) REVERT: D 280 TYR cc_start: 0.7700 (p90) cc_final: 0.7322 (p90) REVERT: D 345 ILE cc_start: 0.7722 (mm) cc_final: 0.7486 (mm) REVERT: D 361 MET cc_start: 0.6374 (ptp) cc_final: 0.6056 (mtt) REVERT: D 374 TRP cc_start: 0.7701 (t60) cc_final: 0.6289 (t60) REVERT: D 394 THR cc_start: 0.5807 (m) cc_final: 0.5417 (p) REVERT: D 488 VAL cc_start: 0.8222 (OUTLIER) cc_final: 0.7998 (m) REVERT: D 585 MET cc_start: 0.6426 (OUTLIER) cc_final: 0.6101 (ttm) REVERT: D 741 SER cc_start: 0.8470 (OUTLIER) cc_final: 0.8209 (m) REVERT: D 796 PHE cc_start: 0.7821 (m-80) cc_final: 0.7586 (m-80) REVERT: D 819 ARG cc_start: 0.4004 (mmt90) cc_final: 0.3765 (mmt90) outliers start: 84 outliers final: 54 residues processed: 341 average time/residue: 0.1700 time to fit residues: 91.0298 Evaluate side-chains 338 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 272 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 411 PHE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 323 TRP Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 215 HIS Chi-restraints excluded: chain C residue 366 LYS Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 409 ASN Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 585 CYS Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 769 CYS Chi-restraints excluded: chain C residue 788 VAL Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 585 MET Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 741 SER Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 811 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 281 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 172 optimal weight: 8.9990 chunk 120 optimal weight: 0.5980 chunk 154 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 200 optimal weight: 0.4980 chunk 169 optimal weight: 10.0000 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.113524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.090316 restraints weight = 72794.939| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.96 r_work: 0.3284 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25560 Z= 0.152 Angle : 0.700 12.441 34578 Z= 0.346 Chirality : 0.045 0.215 3850 Planarity : 0.005 0.092 4350 Dihedral : 9.805 118.569 3835 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.70 % Favored : 87.17 % Rotamer: Outliers : 3.11 % Allowed : 15.83 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.10 % 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: -2.63 (0.15), residues: 3086 helix: -0.31 (0.15), residues: 1278 sheet: -3.16 (0.24), residues: 348 loop : -2.74 (0.15), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 253 TYR 0.019 0.001 TYR B 533 PHE 0.036 0.002 PHE B 517 TRP 0.035 0.001 TRP A 370 HIS 0.017 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00358 (25534) covalent geometry : angle 0.68366 (34508) SS BOND : bond 0.00226 ( 8) SS BOND : angle 1.12736 ( 16) hydrogen bonds : bond 0.03192 ( 624) hydrogen bonds : angle 4.28677 ( 1800) link_BETA1-4 : bond 0.00642 ( 10) link_BETA1-4 : angle 3.77377 ( 30) link_NAG-ASN : bond 0.00514 ( 8) link_NAG-ASN : angle 3.96864 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 295 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 GLU cc_start: 0.5370 (OUTLIER) cc_final: 0.4612 (pt0) REVERT: A 134 VAL cc_start: 0.8099 (t) cc_final: 0.7742 (m) REVERT: A 254 ILE cc_start: 0.8774 (tp) cc_final: 0.8572 (tp) REVERT: A 255 MET cc_start: 0.8547 (tmm) cc_final: 0.8094 (tmm) REVERT: A 359 MET cc_start: 0.7153 (mtp) cc_final: 0.6816 (ttt) REVERT: A 411 PHE cc_start: 0.7563 (OUTLIER) cc_final: 0.6819 (p90) REVERT: A 585 CYS cc_start: 0.6994 (m) cc_final: 0.6278 (p) REVERT: A 609 ILE cc_start: 0.6789 (mm) cc_final: 0.6368 (mp) REVERT: A 666 MET cc_start: 0.8385 (mtp) cc_final: 0.8140 (mtt) REVERT: B 130 TRP cc_start: 0.7654 (m-10) cc_final: 0.7075 (m-10) REVERT: B 132 LYS cc_start: 0.8233 (tttp) cc_final: 0.8003 (ttpt) REVERT: B 186 LEU cc_start: 0.8707 (pp) cc_final: 0.8359 (mt) REVERT: B 335 GLN cc_start: 0.7881 (tm130) cc_final: 0.7187 (tm-30) REVERT: B 488 VAL cc_start: 0.8186 (OUTLIER) cc_final: 0.7921 (m) REVERT: B 789 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8046 (tm) REVERT: C 58 MET cc_start: 0.8087 (mmm) cc_final: 0.7761 (tpp) REVERT: C 79 ARG cc_start: 0.7163 (tpp-160) cc_final: 0.6920 (ttp80) REVERT: C 116 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7938 (mp0) REVERT: C 128 TYR cc_start: 0.8936 (m-80) cc_final: 0.8535 (m-10) REVERT: C 141 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7639 (ptt-90) REVERT: C 175 MET cc_start: 0.8447 (mmm) cc_final: 0.8184 (mmm) REVERT: C 352 TYR cc_start: 0.6859 (m-10) cc_final: 0.6536 (m-10) REVERT: C 366 LYS cc_start: 0.8416 (tttt) cc_final: 0.7990 (tttt) REVERT: C 370 TRP cc_start: 0.7927 (t60) cc_final: 0.7550 (t60) REVERT: C 409 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.7965 (p0) REVERT: C 411 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.7283 (p90) REVERT: C 595 ARG cc_start: 0.5593 (mtp85) cc_final: 0.5367 (ptm160) REVERT: C 639 THR cc_start: 0.8300 (p) cc_final: 0.8035 (t) REVERT: D 36 PHE cc_start: 0.7707 (m-80) cc_final: 0.7420 (m-10) REVERT: D 44 THR cc_start: 0.8480 (OUTLIER) cc_final: 0.8245 (p) REVERT: D 47 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8724 (mt) REVERT: D 280 TYR cc_start: 0.7719 (p90) cc_final: 0.7348 (p90) REVERT: D 297 ARG cc_start: 0.8569 (ttm110) cc_final: 0.8122 (ttm110) REVERT: D 345 ILE cc_start: 0.7831 (mm) cc_final: 0.7614 (mm) REVERT: D 361 MET cc_start: 0.6369 (ptp) cc_final: 0.6036 (mtt) REVERT: D 394 THR cc_start: 0.5912 (m) cc_final: 0.5547 (p) REVERT: D 488 VAL cc_start: 0.8248 (OUTLIER) cc_final: 0.8015 (m) REVERT: D 819 ARG cc_start: 0.3943 (mmt90) cc_final: 0.3694 (mmt90) outliers start: 83 outliers final: 65 residues processed: 355 average time/residue: 0.1644 time to fit residues: 92.0080 Evaluate side-chains 356 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 281 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 411 PHE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 323 TRP Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 215 HIS Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 409 ASN Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 585 CYS Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 769 CYS Chi-restraints excluded: chain C residue 788 VAL Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 585 MET Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 811 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 0.6980 chunk 48 optimal weight: 0.0980 chunk 96 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 226 optimal weight: 0.7980 chunk 282 optimal weight: 0.1980 chunk 47 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 227 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 ASN ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.114522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.090940 restraints weight = 72735.514| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.03 r_work: 0.3285 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25560 Z= 0.118 Angle : 0.690 11.928 34578 Z= 0.341 Chirality : 0.044 0.204 3850 Planarity : 0.005 0.090 4350 Dihedral : 9.625 115.920 3835 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.41 % Favored : 88.46 % Rotamer: Outliers : 2.74 % Allowed : 16.43 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.10 % 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: -2.45 (0.15), residues: 3086 helix: -0.14 (0.15), residues: 1270 sheet: -2.69 (0.25), residues: 362 loop : -2.76 (0.15), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG B 599 TYR 0.019 0.001 TYR D 533 PHE 0.033 0.001 PHE D 796 TRP 0.037 0.002 TRP A 370 HIS 0.027 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00265 (25534) covalent geometry : angle 0.67370 (34508) SS BOND : bond 0.00195 ( 8) SS BOND : angle 1.06327 ( 16) hydrogen bonds : bond 0.02879 ( 624) hydrogen bonds : angle 4.22721 ( 1800) link_BETA1-4 : bond 0.00672 ( 10) link_BETA1-4 : angle 3.72607 ( 30) link_NAG-ASN : bond 0.00497 ( 8) link_NAG-ASN : angle 3.94844 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 287 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 GLU cc_start: 0.5389 (OUTLIER) cc_final: 0.4572 (pt0) REVERT: A 134 VAL cc_start: 0.8082 (t) cc_final: 0.7730 (m) REVERT: A 137 TYR cc_start: 0.7265 (p90) cc_final: 0.7031 (p90) REVERT: A 255 MET cc_start: 0.8554 (tmm) cc_final: 0.8096 (tmm) REVERT: A 359 MET cc_start: 0.7169 (mtp) cc_final: 0.6837 (ttt) REVERT: A 411 PHE cc_start: 0.7475 (OUTLIER) cc_final: 0.6665 (p90) REVERT: A 585 CYS cc_start: 0.7004 (m) cc_final: 0.6284 (p) REVERT: A 601 TRP cc_start: 0.7217 (t-100) cc_final: 0.6802 (t-100) REVERT: A 609 ILE cc_start: 0.6764 (mm) cc_final: 0.6344 (mp) REVERT: B 132 LYS cc_start: 0.8221 (tttp) cc_final: 0.8000 (ttpt) REVERT: B 186 LEU cc_start: 0.8718 (pp) cc_final: 0.8376 (mt) REVERT: B 335 GLN cc_start: 0.7888 (tm130) cc_final: 0.7204 (tm-30) REVERT: B 488 VAL cc_start: 0.8220 (OUTLIER) cc_final: 0.7974 (m) REVERT: B 789 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8022 (tm) REVERT: C 79 ARG cc_start: 0.7206 (tpp-160) cc_final: 0.6943 (ttp80) REVERT: C 116 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7923 (mp0) REVERT: C 128 TYR cc_start: 0.8935 (m-80) cc_final: 0.8548 (m-10) REVERT: C 141 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7643 (ptt-90) REVERT: C 175 MET cc_start: 0.8483 (mmm) cc_final: 0.8221 (mmm) REVERT: C 352 TYR cc_start: 0.6762 (m-10) cc_final: 0.6388 (m-10) REVERT: C 370 TRP cc_start: 0.7917 (t60) cc_final: 0.7557 (t60) REVERT: C 409 ASN cc_start: 0.8340 (OUTLIER) cc_final: 0.7959 (p0) REVERT: C 411 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.7275 (p90) REVERT: C 639 THR cc_start: 0.8320 (p) cc_final: 0.8055 (t) REVERT: D 36 PHE cc_start: 0.7628 (m-80) cc_final: 0.7366 (m-10) REVERT: D 44 THR cc_start: 0.8480 (OUTLIER) cc_final: 0.8263 (p) REVERT: D 47 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8730 (mt) REVERT: D 56 PHE cc_start: 0.8598 (t80) cc_final: 0.8394 (t80) REVERT: D 280 TYR cc_start: 0.7666 (p90) cc_final: 0.7290 (p90) REVERT: D 297 ARG cc_start: 0.8566 (ttm110) cc_final: 0.8148 (ttm110) REVERT: D 361 MET cc_start: 0.6416 (ptp) cc_final: 0.6079 (mtt) REVERT: D 374 TRP cc_start: 0.7686 (t60) cc_final: 0.6564 (t60) REVERT: D 394 THR cc_start: 0.5771 (m) cc_final: 0.5384 (p) REVERT: D 488 VAL cc_start: 0.8230 (OUTLIER) cc_final: 0.8016 (m) REVERT: D 585 MET cc_start: 0.6309 (OUTLIER) cc_final: 0.6008 (ttm) REVERT: D 819 ARG cc_start: 0.3905 (mmt90) cc_final: 0.3659 (mmt90) outliers start: 73 outliers final: 57 residues processed: 339 average time/residue: 0.1677 time to fit residues: 89.0397 Evaluate side-chains 341 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 273 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 411 PHE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 323 TRP Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 716 LYS Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 215 HIS Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 409 ASN Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 585 CYS Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 769 CYS Chi-restraints excluded: chain C residue 788 VAL Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 585 MET Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 811 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 54 optimal weight: 9.9990 chunk 245 optimal weight: 0.8980 chunk 167 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 290 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 236 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.103648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.079908 restraints weight = 70206.435| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.79 r_work: 0.3272 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25560 Z= 0.149 Angle : 0.704 11.529 34578 Z= 0.350 Chirality : 0.045 0.191 3850 Planarity : 0.005 0.091 4350 Dihedral : 9.585 117.566 3835 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.09 % Favored : 87.78 % Rotamer: Outliers : 3.04 % Allowed : 16.28 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.07 % 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: -2.44 (0.15), residues: 3086 helix: -0.07 (0.15), residues: 1274 sheet: -3.08 (0.25), residues: 334 loop : -2.73 (0.15), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 178 TYR 0.019 0.001 TYR B 533 PHE 0.034 0.002 PHE D 623 TRP 0.072 0.002 TRP D 130 HIS 0.024 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00354 (25534) covalent geometry : angle 0.68826 (34508) SS BOND : bond 0.00228 ( 8) SS BOND : angle 1.10106 ( 16) hydrogen bonds : bond 0.03134 ( 624) hydrogen bonds : angle 4.24047 ( 1800) link_BETA1-4 : bond 0.00639 ( 10) link_BETA1-4 : angle 3.74308 ( 30) link_NAG-ASN : bond 0.00499 ( 8) link_NAG-ASN : angle 3.91204 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6977.68 seconds wall clock time: 119 minutes 48.50 seconds (7188.50 seconds total)