Starting phenix.real_space_refine on Mon Aug 25 23:05:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e4y_47520/08_2025/9e4y_47520.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e4y_47520/08_2025/9e4y_47520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e4y_47520/08_2025/9e4y_47520.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e4y_47520/08_2025/9e4y_47520.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e4y_47520/08_2025/9e4y_47520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e4y_47520/08_2025/9e4y_47520.map" } resolution = 4.3 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= 0.001 sd= 0.009 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 172 5.16 5 Cl 4 4.86 5 C 20061 2.51 5 N 5140 2.21 5 O 5804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31181 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 6269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6269 Classifications: {'peptide': 796} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 19, 'TRANS': 771} Chain breaks: 1 Chain: "B" Number of atoms: 6257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 6257 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 4, 'PTRANS': 19, 'TRANS': 771} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 6269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6269 Classifications: {'peptide': 796} Link IDs: {'PCIS': 4, 'PTRANS': 19, 'TRANS': 772} Chain breaks: 1 Chain: "D" Number of atoms: 6253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 6253 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 19, 'TRANS': 771} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1496 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1496 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1496 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1496 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 71 Unusual residues: {'377': 1, 'CYZ': 2} Inner-chain residues flagged as termini: ['pdbres="GLU A1402 "'] Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 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} Time building chain proxies: 6.80, per 1000 atoms: 0.22 Number of scatterers: 31181 At special positions: 0 Unit cell: (164.61, 118.11, 198.09, 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) Cl 4 17.00 S 172 16.00 O 5804 8.00 N 5140 7.00 C 20061 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS A 589 " - pdb=" SG CYS C 589 " distance=2.06 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.04 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS E1039 " - pdb=" SG CYS E1067 " distance=2.02 Simple disulfide: pdb=" SG CYS E1066 " - pdb=" SG CYS E1076 " distance=2.03 Simple disulfide: pdb=" SG CYS F1039 " - pdb=" SG CYS F1067 " distance=2.03 Simple disulfide: pdb=" SG CYS F1066 " - pdb=" SG CYS F1076 " distance=2.03 Simple disulfide: pdb=" SG CYS G1039 " - pdb=" SG CYS G1067 " distance=2.03 Simple disulfide: pdb=" SG CYS G1066 " - pdb=" SG CYS G1076 " distance=2.03 Simple disulfide: pdb=" SG CYS H1039 " - pdb=" SG CYS H1067 " distance=2.03 Simple disulfide: pdb=" SG CYS H1066 " - pdb=" SG CYS H1076 " 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=11, symmetry=0 Number of additional bonds: simple=11, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.21 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 476.8 nanoseconds 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7252 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 35 sheets defined 51.6% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 22 through 37 Processing helix chain 'A' and resid 54 through 67 Processing helix chain 'A' and resid 81 through 93 removed outlier: 4.293A pdb=" N SER A 87 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE A 88 " --> pdb=" O THR A 84 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 129 removed outlier: 4.407A pdb=" N ALA A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 152 Processing helix chain 'A' and resid 152 through 157 removed outlier: 3.868A pdb=" N LYS A 156 " --> pdb=" O SER A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 186 Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.829A pdb=" N ASN A 202 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASP A 203 " --> pdb=" O ASP A 199 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 204 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.656A pdb=" N LYS A 234 " --> pdb=" O ASP A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.812A pdb=" N PHE A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 302 Processing helix chain 'A' and resid 323 through 336 removed outlier: 3.730A pdb=" N VAL A 327 " --> pdb=" O TRP A 323 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 336 " --> pdb=" O ALA A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 415 removed outlier: 3.586A pdb=" N LEU A 415 " --> pdb=" O HIS A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.882A pdb=" N LYS A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 546 removed outlier: 4.124A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE A 531 " --> pdb=" O MET A 527 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A 532 " --> pdb=" O CYS A 528 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N PHE A 541 " --> pdb=" O SER A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 569 removed outlier: 4.189A pdb=" N ASN A 569 " --> pdb=" O GLU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 620 removed outlier: 3.711A pdb=" N LEU A 620 " --> pdb=" O TYR A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'A' and resid 633 through 637 removed outlier: 3.707A pdb=" N ALA A 636 " --> pdb=" O ILE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 664 through 677 Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 706 through 711 Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'A' and resid 788 through 793 Processing helix chain 'A' and resid 793 through 803 removed outlier: 3.995A pdb=" N ILE A 798 " --> pdb=" O GLY A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 806 No H-bonds generated for 'chain 'A' and resid 804 through 806' Processing helix chain 'A' and resid 807 through 818 Processing helix chain 'B' and resid 22 through 37 Processing helix chain 'B' and resid 54 through 68 removed outlier: 4.020A pdb=" N VAL B 58 " --> pdb=" O ASN B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 93 removed outlier: 4.546A pdb=" N ASN B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N THR B 84 " --> pdb=" O LYS B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 139 through 142 Processing helix chain 'B' and resid 143 through 156 removed outlier: 3.974A pdb=" N ALA B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA B 153 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 173 removed outlier: 3.661A pdb=" N LYS B 172 " --> pdb=" O ASN B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 185 Processing helix chain 'B' and resid 197 through 212 removed outlier: 4.354A pdb=" N ASP B 203 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 removed outlier: 3.840A pdb=" N PHE B 237 " --> pdb=" O LYS B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 265 Processing helix chain 'B' and resid 279 through 303 Processing helix chain 'B' and resid 325 through 335 Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 411 through 415 removed outlier: 3.589A pdb=" N LEU B 415 " --> pdb=" O HIS B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 436 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 484 through 487 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.646A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 544 removed outlier: 3.580A pdb=" N MET B 527 " --> pdb=" O TYR B 523 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N CYS B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE B 534 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL B 539 " --> pdb=" O GLY B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 removed outlier: 4.246A pdb=" N SER B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU B 581 " --> pdb=" O LEU B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 617 removed outlier: 3.774A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE B 608 " --> pdb=" O VAL B 604 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 609 " --> pdb=" O TRP B 605 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N SER B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 637 through 642 Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 664 through 675 removed outlier: 3.912A pdb=" N MET B 670 " --> pdb=" O VAL B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 715 Processing helix chain 'B' and resid 742 through 757 removed outlier: 3.774A pdb=" N GLU B 755 " --> pdb=" O LEU B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 767 removed outlier: 3.711A pdb=" N LYS B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 777 Processing helix chain 'B' and resid 788 through 792 Processing helix chain 'B' and resid 793 through 818 removed outlier: 3.541A pdb=" N TYR B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA B 810 " --> pdb=" O ALA B 806 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N CYS B 815 " --> pdb=" O LEU B 811 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR B 816 " --> pdb=" O ILE B 812 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 37 Processing helix chain 'C' and resid 54 through 67 Processing helix chain 'C' and resid 81 through 93 removed outlier: 4.125A pdb=" N SER C 87 " --> pdb=" O ASN C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 129 removed outlier: 4.760A pdb=" N ALA C 120 " --> pdb=" O ASP C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 142 Processing helix chain 'C' and resid 143 through 152 Processing helix chain 'C' and resid 152 through 157 removed outlier: 3.902A pdb=" N LYS C 156 " --> pdb=" O SER C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 187 Processing helix chain 'C' and resid 197 through 211 removed outlier: 3.900A pdb=" N ASN C 202 " --> pdb=" O ARG C 198 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ASP C 203 " --> pdb=" O ASP C 199 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C 204 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 removed outlier: 4.166A pdb=" N ILE C 235 " --> pdb=" O ASP C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 265 removed outlier: 4.088A pdb=" N PHE C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 302 removed outlier: 3.702A pdb=" N TYR C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP C 287 " --> pdb=" O ALA C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 335 removed outlier: 3.843A pdb=" N GLU C 328 " --> pdb=" O GLY C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'C' and resid 423 through 437 removed outlier: 3.651A pdb=" N LYS C 434 " --> pdb=" O ALA C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 469 removed outlier: 3.715A pdb=" N GLY C 465 " --> pdb=" O ASN C 461 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU C 466 " --> pdb=" O GLY C 462 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C 467 " --> pdb=" O MET C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 522 through 544 removed outlier: 4.256A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N PHE C 531 " --> pdb=" O MET C 527 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 532 " --> pdb=" O CYS C 528 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU C 540 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N PHE C 541 " --> pdb=" O SER C 537 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU C 542 " --> pdb=" O VAL C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 569 removed outlier: 4.415A pdb=" N ASN C 569 " --> pdb=" O GLU C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 586 Processing helix chain 'C' and resid 595 through 625 removed outlier: 4.460A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 604 " --> pdb=" O ILE C 600 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR C 616 " --> pdb=" O ILE C 612 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR C 617 " --> pdb=" O ILE C 613 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA C 618 " --> pdb=" O SER C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 641 Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 664 through 675 Processing helix chain 'C' and resid 685 through 696 Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'C' and resid 792 through 818 removed outlier: 3.696A pdb=" N MET C 807 " --> pdb=" O LEU C 803 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU C 808 " --> pdb=" O GLY C 804 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 37 Processing helix chain 'D' and resid 54 through 68 removed outlier: 3.956A pdb=" N VAL D 58 " --> pdb=" O ASN D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 93 removed outlier: 4.717A pdb=" N ASN D 83 " --> pdb=" O LYS D 79 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N THR D 84 " --> pdb=" O LYS D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 138 through 142 removed outlier: 3.661A pdb=" N ARG D 141 " --> pdb=" O ASP D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 156 removed outlier: 3.996A pdb=" N SER D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 173 removed outlier: 3.524A pdb=" N LYS D 172 " --> pdb=" O ASN D 169 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS D 173 " --> pdb=" O ASN D 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 169 through 173' Processing helix chain 'D' and resid 174 through 187 Processing helix chain 'D' and resid 197 through 212 removed outlier: 3.915A pdb=" N ASP D 203 " --> pdb=" O ASP D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 239 removed outlier: 3.662A pdb=" N LYS D 234 " --> pdb=" O ASP D 231 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLN D 236 " --> pdb=" O LEU D 233 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N PHE D 237 " --> pdb=" O LYS D 234 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY D 239 " --> pdb=" O GLN D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 265 removed outlier: 3.775A pdb=" N LYS D 257 " --> pdb=" O SER D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 302 Processing helix chain 'D' and resid 325 through 335 Processing helix chain 'D' and resid 386 through 390 removed outlier: 3.750A pdb=" N GLY D 389 " --> pdb=" O ASP D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 415 removed outlier: 3.834A pdb=" N MET D 414 " --> pdb=" O LYS D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 421 Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 513 through 519 removed outlier: 4.553A pdb=" N PHE D 517 " --> pdb=" O VAL D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 544 removed outlier: 3.507A pdb=" N TYR D 533 " --> pdb=" O ILE D 529 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE D 534 " --> pdb=" O VAL D 530 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER D 537 " --> pdb=" O TYR D 533 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL D 539 " --> pdb=" O GLY D 535 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU D 540 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE D 541 " --> pdb=" O SER D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 removed outlier: 5.048A pdb=" N SER D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU D 581 " --> pdb=" O LEU D 577 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY D 582 " --> pdb=" O TRP D 578 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA D 583 " --> pdb=" O PHE D 579 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE D 584 " --> pdb=" O SER D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 618 removed outlier: 3.639A pdb=" N GLY D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TRP D 605 " --> pdb=" O VAL D 601 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA D 618 " --> pdb=" O SER D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 626 removed outlier: 3.650A pdb=" N VAL D 626 " --> pdb=" O PHE D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 642 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 675 Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 742 through 756 removed outlier: 3.532A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS D 752 " --> pdb=" O LEU D 748 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU D 755 " --> pdb=" O LEU D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 767 Processing helix chain 'D' and resid 768 through 771 removed outlier: 3.533A pdb=" N GLY D 771 " --> pdb=" O TYR D 768 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 768 through 771' Processing helix chain 'D' and resid 774 through 779 Processing helix chain 'D' and resid 794 through 818 removed outlier: 3.795A pdb=" N ILE D 798 " --> pdb=" O GLY D 794 " (cutoff:3.500A) Processing helix chain 'E' and resid 1007 through 1029 Processing helix chain 'E' and resid 1091 through 1103 removed outlier: 3.848A pdb=" N SER E1103 " --> pdb=" O ALA E1099 " (cutoff:3.500A) Processing helix chain 'E' and resid 1104 through 1123 removed outlier: 4.396A pdb=" N ILE E1108 " --> pdb=" O SER E1104 " (cutoff:3.500A) Processing helix chain 'E' and resid 1130 through 1134 removed outlier: 3.660A pdb=" N ILE E1133 " --> pdb=" O ARG E1130 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE E1134 " --> pdb=" O HIS E1131 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1130 through 1134' Processing helix chain 'E' and resid 1135 through 1160 removed outlier: 3.541A pdb=" N ILE E1139 " --> pdb=" O LEU E1135 " (cutoff:3.500A) Processing helix chain 'E' and resid 1176 through 1209 removed outlier: 4.007A pdb=" N GLY E1182 " --> pdb=" O SER E1178 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA E1183 " --> pdb=" O PHE E1179 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE E1186 " --> pdb=" O GLY E1182 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASP E1202 " --> pdb=" O HIS E1198 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LYS E1205 " --> pdb=" O ILE E1201 " (cutoff:3.500A) Processing helix chain 'F' and resid 1004 through 1029 removed outlier: 4.155A pdb=" N MET F1009 " --> pdb=" O ARG F1005 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LEU F1010 " --> pdb=" O GLY F1006 " (cutoff:3.500A) Processing helix chain 'F' and resid 1084 through 1093 removed outlier: 4.350A pdb=" N ASP F1087 " --> pdb=" O GLU F1084 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU F1089 " --> pdb=" O ALA F1086 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ALA F1090 " --> pdb=" O ASP F1087 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ALA F1093 " --> pdb=" O ALA F1090 " (cutoff:3.500A) Processing helix chain 'F' and resid 1094 through 1103 removed outlier: 3.977A pdb=" N ARG F1098 " --> pdb=" O GLU F1094 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG F1101 " --> pdb=" O LEU F1097 " (cutoff:3.500A) Processing helix chain 'F' and resid 1104 through 1123 removed outlier: 4.303A pdb=" N ILE F1108 " --> pdb=" O SER F1104 " (cutoff:3.500A) Processing helix chain 'F' and resid 1131 through 1161 removed outlier: 4.020A pdb=" N LEU F1135 " --> pdb=" O HIS F1131 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN F1148 " --> pdb=" O ALA F1144 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE F1149 " --> pdb=" O GLY F1145 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE F1150 " --> pdb=" O LEU F1146 " (cutoff:3.500A) Processing helix chain 'F' and resid 1176 through 1190 removed outlier: 4.531A pdb=" N ILE F1187 " --> pdb=" O ALA F1183 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ILE F1188 " --> pdb=" O LEU F1184 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA F1189 " --> pdb=" O SER F1185 " (cutoff:3.500A) Processing helix chain 'F' and resid 1191 through 1204 removed outlier: 4.087A pdb=" N MET F1199 " --> pdb=" O LEU F1195 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP F1202 " --> pdb=" O HIS F1198 " (cutoff:3.500A) Processing helix chain 'F' and resid 1204 through 1209 Processing helix chain 'G' and resid 1004 through 1029 removed outlier: 4.027A pdb=" N MET G1009 " --> pdb=" O ARG G1005 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LEU G1010 " --> pdb=" O GLY G1006 " (cutoff:3.500A) Processing helix chain 'G' and resid 1091 through 1102 removed outlier: 3.719A pdb=" N PHE G1096 " --> pdb=" O THR G1092 " (cutoff:3.500A) Processing helix chain 'G' and resid 1104 through 1122 Processing helix chain 'G' and resid 1123 through 1125 No H-bonds generated for 'chain 'G' and resid 1123 through 1125' Processing helix chain 'G' and resid 1130 through 1133 Processing helix chain 'G' and resid 1134 through 1160 removed outlier: 3.841A pdb=" N GLY G1138 " --> pdb=" O ILE G1134 " (cutoff:3.500A) Processing helix chain 'G' and resid 1176 through 1209 removed outlier: 3.742A pdb=" N PHE G1186 " --> pdb=" O GLY G1182 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE G1187 " --> pdb=" O ALA G1183 " (cutoff:3.500A) Processing helix chain 'H' and resid 1007 through 1029 removed outlier: 4.099A pdb=" N LEU H1011 " --> pdb=" O VAL H1007 " (cutoff:3.500A) Processing helix chain 'H' and resid 1088 through 1091 Processing helix chain 'H' and resid 1092 through 1102 removed outlier: 3.674A pdb=" N ARG H1098 " --> pdb=" O GLU H1094 " (cutoff:3.500A) Processing helix chain 'H' and resid 1104 through 1121 removed outlier: 4.013A pdb=" N ILE H1108 " --> pdb=" O SER H1104 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N SER H1110 " --> pdb=" O PHE H1106 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL H1111 " --> pdb=" O PRO H1107 " (cutoff:3.500A) Processing helix chain 'H' and resid 1131 through 1145 removed outlier: 3.631A pdb=" N GLY H1145 " --> pdb=" O PHE H1141 " (cutoff:3.500A) Processing helix chain 'H' and resid 1145 through 1160 removed outlier: 4.484A pdb=" N ILE H1149 " --> pdb=" O GLY H1145 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ILE H1150 " --> pdb=" O LEU H1146 " (cutoff:3.500A) Processing helix chain 'H' and resid 1176 through 1208 removed outlier: 3.533A pdb=" N MET H1191 " --> pdb=" O ILE H1187 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL H1197 " --> pdb=" O GLY H1193 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN H1206 " --> pdb=" O ASP H1202 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 48 removed outlier: 6.075A pdb=" N GLY A 15 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE A 96 " --> pdb=" O ILE A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 164 removed outlier: 3.654A pdb=" N THR A 161 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR A 137 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 245 through 246 removed outlier: 5.749A pdb=" N GLU A 362 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N LYS A 370 " --> pdb=" O GLU A 362 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LYS A 364 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 338 through 340 removed outlier: 3.529A pdb=" N VAL A 338 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS A 346 " --> pdb=" O ILE A 354 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 396 through 399 Processing sheet with id=AA6, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA7, first strand: chain 'A' and resid 489 through 497 removed outlier: 4.775A pdb=" N ILE A 734 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TYR A 732 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 646 through 649 removed outlier: 6.771A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.127A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 42 through 48 removed outlier: 6.427A pdb=" N ILE B 12 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N HIS B 46 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE B 14 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ASP B 48 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLY B 16 " --> pdb=" O ASP B 48 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N PHE B 74 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLY B 15 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE B 73 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N PHE B 96 " --> pdb=" O ILE B 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 161 through 164 removed outlier: 6.227A pdb=" N TYR B 135 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL B 192 " --> pdb=" O HIS B 219 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE B 245 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY B 372 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N GLU B 362 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LYS B 370 " --> pdb=" O GLU B 362 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LYS B 364 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 337 through 340 removed outlier: 3.534A pdb=" N VAL B 338 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 440 through 444 Processing sheet with id=AB4, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB5, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AB6, first strand: chain 'B' and resid 646 through 649 removed outlier: 6.793A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.166A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 42 through 49 removed outlier: 6.304A pdb=" N ILE C 12 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N HIS C 46 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ILE C 14 " --> pdb=" O HIS C 46 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ASP C 48 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLY C 16 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 9.703A pdb=" N ALA C 72 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N GLN C 13 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N PHE C 74 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N GLY C 15 " --> pdb=" O PHE C 74 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 159 through 164 removed outlier: 3.526A pdb=" N THR C 161 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR C 137 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ARG C 191 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR C 220 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N PHE C 245 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE C 222 " --> pdb=" O PHE C 245 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLU C 362 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N LYS C 370 " --> pdb=" O GLU C 362 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS C 364 " --> pdb=" O PRO C 368 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 337 through 340 removed outlier: 3.916A pdb=" N LYS C 346 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 440 through 444 removed outlier: 3.623A pdb=" N ILE C 474 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AC3, first strand: chain 'C' and resid 489 through 494 removed outlier: 5.234A pdb=" N ILE C 734 " --> pdb=" O SER C 492 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.689A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.533A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 42 through 48 removed outlier: 6.537A pdb=" N ILE D 12 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N HIS D 46 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE D 14 " --> pdb=" O HIS D 46 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ASP D 48 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLY D 16 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA D 72 " --> pdb=" O GLN D 13 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE D 73 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N PHE D 96 " --> pdb=" O ILE D 111 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 161 through 164 removed outlier: 3.963A pdb=" N PHE D 245 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY D 372 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N GLU D 362 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LYS D 370 " --> pdb=" O GLU D 362 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LYS D 364 " --> pdb=" O PRO D 368 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 337 through 340 Processing sheet with id=AC8, first strand: chain 'D' and resid 440 through 444 Processing sheet with id=AC9, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AD1, first strand: chain 'D' and resid 497 through 498 Processing sheet with id=AD2, first strand: chain 'D' and resid 646 through 649 removed outlier: 6.750A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 1056 through 1058 Processing sheet with id=AD4, first strand: chain 'E' and resid 1064 through 1065 Processing sheet with id=AD5, first strand: chain 'F' and resid 1056 through 1060 removed outlier: 3.522A pdb=" N SER F1060 " --> pdb=" O LEU F1033 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 1064 through 1065 Processing sheet with id=AD7, first strand: chain 'G' and resid 1033 through 1034 removed outlier: 3.834A pdb=" N MET G1057 " --> pdb=" O LEU G1068 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 1035 through 1037 removed outlier: 3.838A pdb=" N SER H1035 " --> pdb=" O THR H1058 " (cutoff:3.500A) 1467 hydrogen bonds defined for protein. 4188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.72 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.03 - 1.20: 16 1.20 - 1.37: 10141 1.37 - 1.54: 21284 1.54 - 1.71: 134 1.71 - 1.89: 280 Bond restraints: 31855 Sorted by residual: bond pdb=" C4 CYZ A1404 " pdb=" C5 CYZ A1404 " ideal model delta sigma weight residual 1.512 1.030 0.482 2.00e-02 2.50e+03 5.80e+02 bond pdb=" C4 CYZ C1302 " pdb=" C5 CYZ C1302 " ideal model delta sigma weight residual 1.512 1.031 0.481 2.00e-02 2.50e+03 5.78e+02 bond pdb=" C4 CYZ B1302 " pdb=" C5 CYZ B1302 " ideal model delta sigma weight residual 1.512 1.032 0.480 2.00e-02 2.50e+03 5.76e+02 bond pdb=" C4 CYZ A1403 " pdb=" C5 CYZ A1403 " ideal model delta sigma weight residual 1.512 1.033 0.479 2.00e-02 2.50e+03 5.73e+02 bond pdb=" C5 CYZ B1302 " pdb=" C6 CYZ B1302 " ideal model delta sigma weight residual 1.553 1.076 0.477 2.00e-02 2.50e+03 5.69e+02 ... (remaining 31850 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.23: 42883 4.23 - 8.47: 142 8.47 - 12.70: 15 12.70 - 16.93: 11 16.93 - 21.16: 10 Bond angle restraints: 43061 Sorted by residual: angle pdb=" CA MET B 496 " pdb=" CB MET B 496 " pdb=" CG MET B 496 " ideal model delta sigma weight residual 114.10 98.69 15.41 2.00e+00 2.50e-01 5.94e+01 angle pdb=" C1 CYZ B1302 " pdb=" C2 CYZ B1302 " pdb=" C3 CYZ B1302 " ideal model delta sigma weight residual 106.92 128.08 -21.16 3.00e+00 1.11e-01 4.98e+01 angle pdb=" CA SER C 729 " pdb=" CB SER C 729 " pdb=" OG SER C 729 " ideal model delta sigma weight residual 111.10 124.81 -13.71 2.00e+00 2.50e-01 4.70e+01 angle pdb=" C1 CYZ C1302 " pdb=" C2 CYZ C1302 " pdb=" C3 CYZ C1302 " ideal model delta sigma weight residual 106.92 127.43 -20.51 3.00e+00 1.11e-01 4.67e+01 angle pdb=" C1 CYZ A1403 " pdb=" C2 CYZ A1403 " pdb=" C3 CYZ A1403 " ideal model delta sigma weight residual 106.92 127.32 -20.40 3.00e+00 1.11e-01 4.62e+01 ... (remaining 43056 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.56: 18012 22.56 - 45.12: 767 45.12 - 67.68: 82 67.68 - 90.24: 33 90.24 - 112.80: 10 Dihedral angle restraints: 18904 sinusoidal: 7546 harmonic: 11358 Sorted by residual: dihedral pdb=" CB CYS C 718 " pdb=" SG CYS C 718 " pdb=" SG CYS C 773 " pdb=" CB CYS C 773 " ideal model delta sinusoidal sigma weight residual 93.00 -177.96 -89.04 1 1.00e+01 1.00e-02 9.44e+01 dihedral pdb=" CB CYS F1039 " pdb=" SG CYS F1039 " pdb=" SG CYS F1067 " pdb=" CB CYS F1067 " ideal model delta sinusoidal sigma weight residual 93.00 42.84 50.16 1 1.00e+01 1.00e-02 3.45e+01 dihedral pdb=" CA THR B 720 " pdb=" C THR B 720 " pdb=" N MET B 721 " pdb=" CA MET B 721 " ideal model delta harmonic sigma weight residual -180.00 -151.54 -28.46 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 18901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.427: 4763 0.427 - 0.854: 7 0.854 - 1.281: 0 1.281 - 1.708: 0 1.708 - 2.135: 8 Chirality restraints: 4778 Sorted by residual: chirality pdb=" C5 CYZ A1404 " pdb=" C4 CYZ A1404 " pdb=" C6 CYZ A1404 " pdb=" C7 CYZ A1404 " both_signs ideal model delta sigma weight residual False 3.31 1.17 2.14 2.00e-01 2.50e+01 1.14e+02 chirality pdb=" C5 CYZ C1302 " pdb=" C4 CYZ C1302 " pdb=" C6 CYZ C1302 " pdb=" C7 CYZ C1302 " both_signs ideal model delta sigma weight residual False 3.31 1.17 2.13 2.00e-01 2.50e+01 1.14e+02 chirality pdb=" C5 CYZ B1302 " pdb=" C4 CYZ B1302 " pdb=" C6 CYZ B1302 " pdb=" C7 CYZ B1302 " both_signs ideal model delta sigma weight residual False 3.31 1.17 2.13 2.00e-01 2.50e+01 1.14e+02 ... (remaining 4775 not shown) Planarity restraints: 5408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 CYZ B1302 " 0.032 2.00e-02 2.50e+03 4.32e-02 4.66e+01 pdb=" C11 CYZ B1302 " 0.093 2.00e-02 2.50e+03 pdb=" C12 CYZ B1302 " 0.011 2.00e-02 2.50e+03 pdb=" C13 CYZ B1302 " -0.051 2.00e-02 2.50e+03 pdb=" C14 CYZ B1302 " 0.024 2.00e-02 2.50e+03 pdb=" C9 CYZ B1302 " -0.002 2.00e-02 2.50e+03 pdb=" N2 CYZ B1302 " -0.005 2.00e-02 2.50e+03 pdb=" S1 CYZ B1302 " -0.064 2.00e-02 2.50e+03 pdb=" S2 CYZ B1302 " -0.037 2.00e-02 2.50e+03 pdb="CL CYZ B1302 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 631 " 0.102 5.00e-02 4.00e+02 1.59e-01 4.02e+01 pdb=" N PRO C 632 " -0.274 5.00e-02 4.00e+02 pdb=" CA PRO C 632 " 0.095 5.00e-02 4.00e+02 pdb=" CD PRO C 632 " 0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C10 CYZ C1302 " -0.031 2.00e-02 2.50e+03 3.27e-02 2.67e+01 pdb=" C11 CYZ C1302 " -0.070 2.00e-02 2.50e+03 pdb=" C12 CYZ C1302 " -0.004 2.00e-02 2.50e+03 pdb=" C13 CYZ C1302 " 0.035 2.00e-02 2.50e+03 pdb=" C14 CYZ C1302 " -0.001 2.00e-02 2.50e+03 pdb=" C9 CYZ C1302 " -0.008 2.00e-02 2.50e+03 pdb=" N2 CYZ C1302 " 0.017 2.00e-02 2.50e+03 pdb=" S1 CYZ C1302 " 0.040 2.00e-02 2.50e+03 pdb=" S2 CYZ C1302 " 0.037 2.00e-02 2.50e+03 pdb="CL CYZ C1302 " -0.014 2.00e-02 2.50e+03 ... (remaining 5405 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 241 2.55 - 3.14: 27139 3.14 - 3.73: 49376 3.73 - 4.31: 69082 4.31 - 4.90: 109985 Nonbonded interactions: 255823 Sorted by model distance: nonbonded pdb=" OG SER B 729 " pdb="CL CYZ C1302 " model vdw 1.967 2.616 nonbonded pdb=" OH TYR B 533 " pdb=" O LEU B 577 " model vdw 1.985 3.040 nonbonded pdb=" OG SER D 729 " pdb="CL CYZ A1404 " model vdw 2.014 2.616 nonbonded pdb=" OG SER D 729 " pdb=" N3 CYZ A1404 " model vdw 2.045 3.120 nonbonded pdb=" OE1 GLU A 705 " pdb=" OH TYR A 732 " model vdw 2.091 3.040 ... (remaining 255818 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 504 or (resid 505 and (name N or name CA or nam \ e C or name O or name CB )) or resid 506 through 817 or (resid 818 through 819 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1402)) selection = (chain 'B' and (resid 10 through 504 or (resid 505 and (name N or name CA or nam \ e C or name O or name CB )) or resid 506 through 1301)) selection = (chain 'C' and (resid 10 through 504 or (resid 505 and (name N or name CA or nam \ e C or name O or name CB )) or resid 506 through 817 or (resid 818 through 819 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1301)) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.200 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: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 26.050 Find NCS groups from input model: 0.920 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 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 : 0.012 0.482 31881 Z= 0.629 Angle : 0.857 21.163 43091 Z= 0.452 Chirality : 0.098 2.135 4778 Planarity : 0.007 0.159 5408 Dihedral : 13.233 112.798 11607 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.14 % Favored : 92.69 % Rotamer: Outliers : 0.30 % Allowed : 0.99 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.12), residues: 3910 helix: -1.33 (0.10), residues: 1777 sheet: -1.22 (0.26), residues: 306 loop : -1.30 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.002 ARG D 420 TYR 0.026 0.004 TYR F1088 PHE 0.036 0.002 PHE C 608 TRP 0.044 0.003 TRP A 262 HIS 0.014 0.001 HIS E1059 Details of bonding type rmsd covalent geometry : bond 0.01246 (31855) covalent geometry : angle 0.85677 (43061) SS BOND : bond 0.00717 ( 15) SS BOND : angle 1.49241 ( 30) hydrogen bonds : bond 0.16391 ( 1467) hydrogen bonds : angle 7.22662 ( 4188) Misc. bond : bond 0.01260 ( 11) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 804 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.7931 (mp) cc_final: 0.7718 (mm) REVERT: A 147 GLN cc_start: 0.8475 (mt0) cc_final: 0.8032 (mp10) REVERT: A 249 ASP cc_start: 0.8034 (t0) cc_final: 0.7101 (t0) REVERT: A 261 ARG cc_start: 0.9064 (ttt180) cc_final: 0.8566 (tpm170) REVERT: A 270 TYR cc_start: 0.7468 (m-80) cc_final: 0.7171 (m-10) REVERT: A 359 ASN cc_start: 0.7758 (m-40) cc_final: 0.6957 (m-40) REVERT: A 361 MET cc_start: 0.4406 (mmm) cc_final: 0.4040 (mmm) REVERT: A 458 LYS cc_start: 0.8337 (mmmt) cc_final: 0.8040 (tppt) REVERT: A 486 GLU cc_start: 0.9332 (tt0) cc_final: 0.8976 (tm-30) REVERT: A 655 THR cc_start: 0.8185 (m) cc_final: 0.7581 (t) REVERT: A 688 GLU cc_start: 0.8311 (tt0) cc_final: 0.8022 (tt0) REVERT: A 708 MET cc_start: 0.7617 (ttm) cc_final: 0.7275 (tpt) REVERT: A 714 GLN cc_start: 0.7743 (mm-40) cc_final: 0.7105 (pp30) REVERT: A 734 ILE cc_start: 0.7283 (mm) cc_final: 0.6960 (mm) REVERT: A 787 LEU cc_start: 0.8286 (tp) cc_final: 0.8044 (tp) REVERT: A 791 ASN cc_start: 0.8762 (m-40) cc_final: 0.8368 (m-40) REVERT: B 96 PHE cc_start: 0.8205 (t80) cc_final: 0.7951 (t80) REVERT: B 157 LYS cc_start: 0.9277 (ptpt) cc_final: 0.8891 (ptmm) REVERT: B 168 ILE cc_start: 0.9049 (mt) cc_final: 0.8724 (mp) REVERT: B 193 ILE cc_start: 0.8979 (mt) cc_final: 0.8711 (mm) REVERT: B 330 GLU cc_start: 0.8514 (tt0) cc_final: 0.7928 (tp30) REVERT: B 359 ASN cc_start: 0.8766 (m-40) cc_final: 0.8286 (m-40) REVERT: B 527 MET cc_start: 0.5212 (ttm) cc_final: 0.4969 (tpp) REVERT: B 538 VAL cc_start: 0.8994 (p) cc_final: 0.8780 (m) REVERT: B 807 MET cc_start: 0.7355 (mtm) cc_final: 0.6640 (mmm) REVERT: C 14 ILE cc_start: 0.7797 (pt) cc_final: 0.7362 (mm) REVERT: C 27 SER cc_start: 0.8603 (m) cc_final: 0.8265 (p) REVERT: C 101 PHE cc_start: 0.8569 (p90) cc_final: 0.8353 (p90) REVERT: C 104 ASP cc_start: 0.7502 (m-30) cc_final: 0.7159 (t0) REVERT: C 122 LEU cc_start: 0.8275 (mt) cc_final: 0.7719 (tt) REVERT: C 147 GLN cc_start: 0.8654 (mt0) cc_final: 0.8303 (mp10) REVERT: C 170 ASN cc_start: 0.8871 (m-40) cc_final: 0.8005 (p0) REVERT: C 191 ARG cc_start: 0.6477 (mtt90) cc_final: 0.5569 (mtm-85) REVERT: C 249 ASP cc_start: 0.8084 (t0) cc_final: 0.7360 (t0) REVERT: C 258 PHE cc_start: 0.9306 (t80) cc_final: 0.8884 (m-80) REVERT: C 262 TRP cc_start: 0.7944 (t-100) cc_final: 0.7637 (t60) REVERT: C 270 TYR cc_start: 0.7727 (m-80) cc_final: 0.7254 (m-80) REVERT: C 359 ASN cc_start: 0.8076 (m-40) cc_final: 0.7617 (m-40) REVERT: C 406 VAL cc_start: 0.7576 (t) cc_final: 0.7135 (p) REVERT: C 411 ASN cc_start: 0.8396 (m110) cc_final: 0.8161 (t0) REVERT: C 473 ASP cc_start: 0.7560 (m-30) cc_final: 0.6521 (t0) REVERT: C 523 TYR cc_start: 0.8746 (t80) cc_final: 0.8354 (t80) REVERT: C 527 MET cc_start: 0.8863 (ttt) cc_final: 0.8580 (ttp) REVERT: C 670 MET cc_start: 0.9659 (mtp) cc_final: 0.9402 (mmm) REVERT: C 673 TYR cc_start: 0.8868 (t80) cc_final: 0.8612 (t80) REVERT: C 688 GLU cc_start: 0.8106 (tt0) cc_final: 0.7643 (tt0) REVERT: C 734 ILE cc_start: 0.6784 (mm) cc_final: 0.6571 (mm) REVERT: D 89 CYS cc_start: 0.9226 (m) cc_final: 0.9014 (m) REVERT: D 96 PHE cc_start: 0.8053 (t80) cc_final: 0.7425 (t80) REVERT: D 151 ASP cc_start: 0.8532 (m-30) cc_final: 0.7868 (t70) REVERT: D 157 LYS cc_start: 0.9236 (ptpt) cc_final: 0.8895 (ptmm) REVERT: D 168 ILE cc_start: 0.9149 (mt) cc_final: 0.8882 (tp) REVERT: D 227 PHE cc_start: 0.6957 (t80) cc_final: 0.6536 (t80) REVERT: D 330 GLU cc_start: 0.8369 (tt0) cc_final: 0.7632 (tp30) REVERT: D 359 ASN cc_start: 0.8815 (m-40) cc_final: 0.8457 (m-40) REVERT: D 361 MET cc_start: 0.7467 (mmm) cc_final: 0.7193 (mmm) REVERT: D 463 MET cc_start: 0.8413 (mtp) cc_final: 0.7401 (mpp) REVERT: D 519 ASP cc_start: 0.8796 (m-30) cc_final: 0.8275 (t70) REVERT: D 607 PHE cc_start: 0.7620 (t80) cc_final: 0.7353 (t80) REVERT: D 670 MET cc_start: 0.9428 (mtp) cc_final: 0.9183 (mmm) REVERT: E 1012 THR cc_start: 0.9277 (t) cc_final: 0.8988 (p) REVERT: E 1027 VAL cc_start: 0.4159 (t) cc_final: 0.3810 (p) REVERT: E 1089 GLU cc_start: 0.7574 (tp30) cc_final: 0.5925 (pt0) REVERT: E 1155 TYR cc_start: 0.7775 (t80) cc_final: 0.7278 (t80) REVERT: E 1180 TYR cc_start: 0.7550 (m-80) cc_final: 0.7310 (m-10) REVERT: F 1009 MET cc_start: 0.7175 (tpp) cc_final: 0.6518 (mmm) REVERT: F 1034 TYR cc_start: 0.7947 (m-80) cc_final: 0.7230 (m-10) REVERT: F 1081 HIS cc_start: 0.4229 (t70) cc_final: 0.3648 (t70) REVERT: G 1023 MET cc_start: 0.7064 (tpp) cc_final: 0.6828 (ttp) REVERT: G 1085 ASP cc_start: 0.6149 (m-30) cc_final: 0.5911 (p0) REVERT: G 1155 TYR cc_start: 0.8049 (t80) cc_final: 0.7584 (t80) REVERT: G 1190 GLU cc_start: 0.7389 (mm-30) cc_final: 0.7165 (mm-30) REVERT: G 1191 MET cc_start: 0.8847 (mmm) cc_final: 0.8621 (mmm) REVERT: G 1195 LEU cc_start: 0.9231 (mt) cc_final: 0.8796 (pp) REVERT: G 1202 ASP cc_start: 0.9343 (t0) cc_final: 0.8925 (m-30) REVERT: G 1206 GLN cc_start: 0.6753 (mt0) cc_final: 0.6419 (tm-30) outliers start: 10 outliers final: 0 residues processed: 806 average time/residue: 0.1934 time to fit residues: 242.6701 Evaluate side-chains 488 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 488 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.0770 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 112 GLN A 214 HIS ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN C 83 ASN ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 HIS C 224 ASN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 GLN D 60 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.148772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.124025 restraints weight = 101771.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.125278 restraints weight = 85864.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.126252 restraints weight = 68846.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.126372 restraints weight = 53187.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.128336 restraints weight = 48000.533| |-----------------------------------------------------------------------------| r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 31881 Z= 0.166 Angle : 0.700 19.476 43091 Z= 0.370 Chirality : 0.044 0.247 4778 Planarity : 0.005 0.118 5408 Dihedral : 7.687 102.720 4421 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.14 % Favored : 94.73 % Rotamer: Outliers : 0.33 % Allowed : 2.79 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.13), residues: 3910 helix: 0.03 (0.12), residues: 1823 sheet: -1.00 (0.26), residues: 317 loop : -1.13 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 353 TYR 0.022 0.002 TYR B 71 PHE 0.030 0.002 PHE H1141 TRP 0.045 0.003 TRP D 606 HIS 0.014 0.001 HIS E1059 Details of bonding type rmsd covalent geometry : bond 0.00353 (31855) covalent geometry : angle 0.69933 (43061) SS BOND : bond 0.00553 ( 15) SS BOND : angle 1.50689 ( 30) hydrogen bonds : bond 0.04678 ( 1467) hydrogen bonds : angle 5.54812 ( 4188) Misc. bond : bond 0.01432 ( 11) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 614 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.7528 (mt0) cc_final: 0.7080 (mp10) REVERT: A 249 ASP cc_start: 0.8117 (t0) cc_final: 0.7050 (t0) REVERT: A 270 TYR cc_start: 0.6945 (m-80) cc_final: 0.6639 (m-10) REVERT: A 442 LEU cc_start: 0.7522 (mt) cc_final: 0.7282 (mt) REVERT: A 458 LYS cc_start: 0.8328 (mmmt) cc_final: 0.7268 (tppt) REVERT: A 463 MET cc_start: 0.5183 (tpp) cc_final: 0.4788 (tpp) REVERT: A 479 LEU cc_start: 0.7258 (tp) cc_final: 0.6881 (tp) REVERT: A 787 LEU cc_start: 0.8256 (tp) cc_final: 0.7915 (tt) REVERT: A 791 ASN cc_start: 0.8530 (m-40) cc_final: 0.8270 (m-40) REVERT: B 25 GLU cc_start: 0.8583 (mp0) cc_final: 0.8194 (mp0) REVERT: B 330 GLU cc_start: 0.7897 (tt0) cc_final: 0.7363 (tp30) REVERT: B 527 MET cc_start: 0.5862 (ttm) cc_final: 0.5452 (tpp) REVERT: B 629 MET cc_start: 0.6299 (mmp) cc_final: 0.5425 (tpt) REVERT: B 807 MET cc_start: 0.7370 (mtm) cc_final: 0.6697 (mmt) REVERT: C 13 GLN cc_start: 0.6054 (mp10) cc_final: 0.5230 (tp-100) REVERT: C 14 ILE cc_start: 0.7494 (pt) cc_final: 0.7180 (mm) REVERT: C 27 SER cc_start: 0.8496 (m) cc_final: 0.8213 (p) REVERT: C 104 ASP cc_start: 0.7352 (m-30) cc_final: 0.6848 (t0) REVERT: C 113 MET cc_start: 0.4622 (tpp) cc_final: 0.4287 (tpp) REVERT: C 122 LEU cc_start: 0.8287 (mt) cc_final: 0.7571 (tt) REVERT: C 147 GLN cc_start: 0.7973 (mt0) cc_final: 0.7591 (mp10) REVERT: C 170 ASN cc_start: 0.8147 (m-40) cc_final: 0.7671 (p0) REVERT: C 249 ASP cc_start: 0.7864 (t0) cc_final: 0.7596 (t0) REVERT: C 262 TRP cc_start: 0.8250 (t-100) cc_final: 0.7916 (t60) REVERT: C 361 MET cc_start: 0.5557 (mmm) cc_final: 0.5050 (mmm) REVERT: C 369 ARG cc_start: 0.7591 (mtm110) cc_final: 0.7352 (mtm110) REVERT: C 370 LYS cc_start: 0.8269 (ttmt) cc_final: 0.7624 (ttmt) REVERT: C 473 ASP cc_start: 0.7829 (m-30) cc_final: 0.7088 (t0) REVERT: C 523 TYR cc_start: 0.7924 (t80) cc_final: 0.7710 (t80) REVERT: C 712 ILE cc_start: 0.9230 (mm) cc_final: 0.8941 (tp) REVERT: D 25 GLU cc_start: 0.8475 (mp0) cc_final: 0.8041 (mp0) REVERT: D 147 GLN cc_start: 0.6881 (pp30) cc_final: 0.6505 (pp30) REVERT: D 151 ASP cc_start: 0.7630 (m-30) cc_final: 0.7270 (t0) REVERT: D 330 GLU cc_start: 0.7790 (tt0) cc_final: 0.7281 (tp30) REVERT: D 414 MET cc_start: 0.9475 (pmm) cc_final: 0.9241 (pmm) REVERT: D 527 MET cc_start: 0.7742 (mmp) cc_final: 0.7313 (mmp) REVERT: D 620 LEU cc_start: 0.7607 (tp) cc_final: 0.7318 (tp) REVERT: D 629 MET cc_start: 0.5804 (mpp) cc_final: 0.4955 (mmt) REVERT: D 659 PHE cc_start: 0.6843 (m-80) cc_final: 0.6589 (m-80) REVERT: E 1089 GLU cc_start: 0.5295 (tp30) cc_final: 0.4254 (pt0) REVERT: E 1155 TYR cc_start: 0.7220 (t80) cc_final: 0.6716 (t80) REVERT: E 1199 MET cc_start: 0.8974 (mtt) cc_final: 0.8565 (mtm) REVERT: F 1034 TYR cc_start: 0.7135 (m-80) cc_final: 0.6173 (m-10) REVERT: G 1191 MET cc_start: 0.9205 (mmm) cc_final: 0.8823 (mmm) REVERT: G 1195 LEU cc_start: 0.9085 (mt) cc_final: 0.8640 (tt) REVERT: H 1009 MET cc_start: 0.6417 (tpp) cc_final: 0.5650 (mtp) REVERT: H 1012 THR cc_start: 0.8663 (p) cc_final: 0.8243 (p) outliers start: 11 outliers final: 2 residues processed: 621 average time/residue: 0.1771 time to fit residues: 175.4041 Evaluate side-chains 434 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 432 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 40 optimal weight: 3.9990 chunk 11 optimal weight: 0.4980 chunk 370 optimal weight: 0.9980 chunk 354 optimal weight: 20.0000 chunk 265 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 300 optimal weight: 8.9990 chunk 301 optimal weight: 0.9980 chunk 268 optimal weight: 7.9990 chunk 197 optimal weight: 6.9990 chunk 63 optimal weight: 0.0570 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 ASN ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN C 392 GLN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN D 791 ASN ** F1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1059 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.151114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.131784 restraints weight = 109731.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.132285 restraints weight = 144795.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.133120 restraints weight = 123456.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.133849 restraints weight = 84577.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.134270 restraints weight = 76262.582| |-----------------------------------------------------------------------------| r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 31881 Z= 0.149 Angle : 0.645 11.940 43091 Z= 0.340 Chirality : 0.043 0.261 4778 Planarity : 0.005 0.134 5408 Dihedral : 7.260 103.048 4421 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.37 % Favored : 94.50 % Rotamer: Outliers : 0.12 % Allowed : 3.26 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.13), residues: 3910 helix: 0.31 (0.12), residues: 1827 sheet: -0.95 (0.27), residues: 319 loop : -1.15 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 353 TYR 0.024 0.002 TYR A 616 PHE 0.024 0.002 PHE F1017 TRP 0.054 0.002 TRP D 606 HIS 0.011 0.001 HIS E1059 Details of bonding type rmsd covalent geometry : bond 0.00317 (31855) covalent geometry : angle 0.64300 (43061) SS BOND : bond 0.00396 ( 15) SS BOND : angle 1.99942 ( 30) hydrogen bonds : bond 0.04095 ( 1467) hydrogen bonds : angle 5.28810 ( 4188) Misc. bond : bond 0.01320 ( 11) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 570 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.7883 (mt0) cc_final: 0.7255 (mp10) REVERT: A 249 ASP cc_start: 0.8028 (t0) cc_final: 0.6991 (t0) REVERT: A 458 LYS cc_start: 0.8203 (mmmt) cc_final: 0.7284 (tppt) REVERT: A 714 GLN cc_start: 0.7228 (mt0) cc_final: 0.6641 (mt0) REVERT: A 722 LYS cc_start: 0.7764 (ptmt) cc_final: 0.7283 (ptmt) REVERT: A 787 LEU cc_start: 0.7947 (tp) cc_final: 0.7446 (tt) REVERT: B 25 GLU cc_start: 0.8495 (mp0) cc_final: 0.8168 (mp0) REVERT: B 79 LYS cc_start: 0.7810 (tttt) cc_final: 0.6944 (tppt) REVERT: B 330 GLU cc_start: 0.7852 (tt0) cc_final: 0.7389 (tp30) REVERT: B 527 MET cc_start: 0.5970 (ttm) cc_final: 0.5558 (tpp) REVERT: B 629 MET cc_start: 0.5900 (mmp) cc_final: 0.4866 (tpt) REVERT: B 807 MET cc_start: 0.7184 (mtm) cc_final: 0.6504 (mmp) REVERT: C 13 GLN cc_start: 0.5852 (mp10) cc_final: 0.5160 (tp-100) REVERT: C 14 ILE cc_start: 0.7367 (pt) cc_final: 0.7074 (mm) REVERT: C 27 SER cc_start: 0.8413 (m) cc_final: 0.8171 (p) REVERT: C 104 ASP cc_start: 0.7334 (m-30) cc_final: 0.6815 (t0) REVERT: C 147 GLN cc_start: 0.8193 (mt0) cc_final: 0.7696 (mp10) REVERT: C 170 ASN cc_start: 0.8057 (m-40) cc_final: 0.7677 (p0) REVERT: C 249 ASP cc_start: 0.7681 (t0) cc_final: 0.7390 (t0) REVERT: C 262 TRP cc_start: 0.8077 (t-100) cc_final: 0.7869 (t60) REVERT: C 361 MET cc_start: 0.5182 (mmm) cc_final: 0.4937 (mmm) REVERT: C 473 ASP cc_start: 0.7731 (m-30) cc_final: 0.7255 (t0) REVERT: C 521 LEU cc_start: 0.8872 (mm) cc_final: 0.8583 (mm) REVERT: C 527 MET cc_start: 0.7622 (ptt) cc_final: 0.6658 (ptt) REVERT: C 606 TRP cc_start: 0.6548 (m-10) cc_final: 0.6219 (m100) REVERT: D 25 GLU cc_start: 0.8478 (mp0) cc_final: 0.8107 (mp0) REVERT: D 26 TYR cc_start: 0.7301 (t80) cc_final: 0.7077 (t80) REVERT: D 147 GLN cc_start: 0.7004 (pp30) cc_final: 0.6714 (pp30) REVERT: D 151 ASP cc_start: 0.7916 (m-30) cc_final: 0.7430 (t0) REVERT: D 193 ILE cc_start: 0.8928 (mt) cc_final: 0.8275 (tt) REVERT: D 299 LEU cc_start: 0.9253 (tt) cc_final: 0.8620 (tt) REVERT: D 330 GLU cc_start: 0.8004 (tt0) cc_final: 0.7403 (tp30) REVERT: D 359 ASN cc_start: 0.7324 (m-40) cc_final: 0.7090 (m-40) REVERT: D 407 MET cc_start: 0.7284 (mpp) cc_final: 0.6980 (mpp) REVERT: D 414 MET cc_start: 0.9345 (pmm) cc_final: 0.9117 (pmm) REVERT: D 527 MET cc_start: 0.7818 (mmp) cc_final: 0.7428 (mmp) REVERT: D 721 MET cc_start: 0.7592 (ptt) cc_final: 0.7286 (ptt) REVERT: E 1012 THR cc_start: 0.8621 (p) cc_final: 0.8356 (p) REVERT: E 1089 GLU cc_start: 0.4346 (tp30) cc_final: 0.3832 (pt0) REVERT: E 1155 TYR cc_start: 0.6667 (t80) cc_final: 0.6215 (t80) REVERT: G 1073 LYS cc_start: 0.6771 (mmpt) cc_final: 0.6030 (mmmt) REVERT: G 1155 TYR cc_start: 0.7148 (t80) cc_final: 0.6758 (t80) REVERT: G 1191 MET cc_start: 0.9078 (mmm) cc_final: 0.8754 (mmm) REVERT: H 1009 MET cc_start: 0.5954 (tpp) cc_final: 0.5465 (mtt) REVERT: H 1012 THR cc_start: 0.8308 (p) cc_final: 0.8019 (p) outliers start: 4 outliers final: 0 residues processed: 573 average time/residue: 0.1809 time to fit residues: 164.6468 Evaluate side-chains 425 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 425 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 234 optimal weight: 6.9990 chunk 305 optimal weight: 0.6980 chunk 306 optimal weight: 3.9990 chunk 381 optimal weight: 7.9990 chunk 235 optimal weight: 0.7980 chunk 240 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 359 optimal weight: 50.0000 chunk 172 optimal weight: 0.7980 chunk 173 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 GLN ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1081 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.151013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.131436 restraints weight = 108974.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.131617 restraints weight = 138399.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.132949 restraints weight = 115711.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.133065 restraints weight = 85958.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.133835 restraints weight = 78066.283| |-----------------------------------------------------------------------------| r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 31881 Z= 0.145 Angle : 0.627 12.531 43091 Z= 0.329 Chirality : 0.043 0.231 4778 Planarity : 0.005 0.138 5408 Dihedral : 7.023 101.205 4421 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.19 % Favored : 94.65 % Rotamer: Outliers : 0.06 % Allowed : 2.96 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.13), residues: 3910 helix: 0.42 (0.12), residues: 1836 sheet: -1.10 (0.27), residues: 324 loop : -1.20 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 30 TYR 0.026 0.002 TYR G1127 PHE 0.027 0.002 PHE H1141 TRP 0.052 0.002 TRP D 606 HIS 0.009 0.001 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00308 (31855) covalent geometry : angle 0.62454 (43061) SS BOND : bond 0.00384 ( 15) SS BOND : angle 2.18001 ( 30) hydrogen bonds : bond 0.03824 ( 1467) hydrogen bonds : angle 5.11122 ( 4188) Misc. bond : bond 0.01321 ( 11) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 547 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 PHE cc_start: 0.8330 (p90) cc_final: 0.8080 (p90) REVERT: A 193 ILE cc_start: 0.8485 (mt) cc_final: 0.8193 (tt) REVERT: A 249 ASP cc_start: 0.8019 (t0) cc_final: 0.7004 (t0) REVERT: A 458 LYS cc_start: 0.8068 (mmmt) cc_final: 0.6943 (mmmt) REVERT: A 722 LYS cc_start: 0.7794 (pttt) cc_final: 0.7571 (ptmt) REVERT: A 787 LEU cc_start: 0.7923 (tp) cc_final: 0.7665 (tp) REVERT: B 25 GLU cc_start: 0.8539 (mp0) cc_final: 0.8169 (mp0) REVERT: B 77 TYR cc_start: 0.7813 (p90) cc_final: 0.7479 (p90) REVERT: B 79 LYS cc_start: 0.7905 (tttt) cc_final: 0.7187 (tppt) REVERT: B 330 GLU cc_start: 0.7786 (tt0) cc_final: 0.7437 (tp30) REVERT: B 404 PRO cc_start: 0.6164 (Cg_endo) cc_final: 0.5443 (Cg_exo) REVERT: B 578 TRP cc_start: 0.7415 (t-100) cc_final: 0.6951 (t-100) REVERT: B 629 MET cc_start: 0.5798 (mmp) cc_final: 0.4641 (tpt) REVERT: B 807 MET cc_start: 0.7134 (mtm) cc_final: 0.6624 (mmp) REVERT: C 13 GLN cc_start: 0.5955 (mp10) cc_final: 0.5286 (tp-100) REVERT: C 27 SER cc_start: 0.8422 (m) cc_final: 0.8181 (p) REVERT: C 104 ASP cc_start: 0.7350 (m-30) cc_final: 0.6802 (t0) REVERT: C 170 ASN cc_start: 0.8091 (m-40) cc_final: 0.7711 (p0) REVERT: C 370 LYS cc_start: 0.7934 (ttmt) cc_final: 0.7346 (ttmt) REVERT: C 408 MET cc_start: 0.8012 (mtm) cc_final: 0.7613 (mtm) REVERT: C 674 MET cc_start: 0.8644 (mmp) cc_final: 0.7868 (mmm) REVERT: D 25 GLU cc_start: 0.8397 (mp0) cc_final: 0.8098 (mp0) REVERT: D 147 GLN cc_start: 0.6994 (pp30) cc_final: 0.6693 (pp30) REVERT: D 151 ASP cc_start: 0.7887 (m-30) cc_final: 0.7408 (t0) REVERT: D 193 ILE cc_start: 0.9134 (mt) cc_final: 0.8620 (tt) REVERT: D 330 GLU cc_start: 0.7868 (tt0) cc_final: 0.7380 (tm-30) REVERT: D 380 MET cc_start: 0.5931 (ptm) cc_final: 0.5441 (ptm) REVERT: D 527 MET cc_start: 0.7814 (mmp) cc_final: 0.7423 (mmp) REVERT: E 1089 GLU cc_start: 0.4301 (tp30) cc_final: 0.4026 (pt0) REVERT: E 1155 TYR cc_start: 0.6533 (t80) cc_final: 0.6124 (t80) REVERT: E 1175 TYR cc_start: 0.3284 (m-10) cc_final: 0.2966 (m-10) REVERT: G 1155 TYR cc_start: 0.7138 (t80) cc_final: 0.6816 (t80) REVERT: G 1191 MET cc_start: 0.9070 (mmm) cc_final: 0.8665 (mmm) REVERT: G 1195 LEU cc_start: 0.8810 (mt) cc_final: 0.8542 (tt) REVERT: G 1199 MET cc_start: 0.8560 (ppp) cc_final: 0.8315 (ppp) outliers start: 2 outliers final: 0 residues processed: 548 average time/residue: 0.1730 time to fit residues: 153.6847 Evaluate side-chains 415 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 320 optimal weight: 40.0000 chunk 124 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 283 optimal weight: 9.9990 chunk 296 optimal weight: 0.0970 chunk 150 optimal weight: 2.9990 chunk 300 optimal weight: 5.9990 chunk 114 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 250 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN D 344 ASN ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.148853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.123509 restraints weight = 102791.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.122940 restraints weight = 75394.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.124655 restraints weight = 68026.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.124587 restraints weight = 53828.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.125363 restraints weight = 49690.252| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31881 Z= 0.145 Angle : 0.620 9.089 43091 Z= 0.325 Chirality : 0.043 0.234 4778 Planarity : 0.005 0.120 5408 Dihedral : 6.842 98.859 4421 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.45 % Favored : 94.40 % Rotamer: Outliers : 0.06 % Allowed : 1.83 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.13), residues: 3910 helix: 0.60 (0.12), residues: 1828 sheet: -1.11 (0.29), residues: 303 loop : -1.21 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 309 TYR 0.021 0.001 TYR H1127 PHE 0.027 0.002 PHE H1141 TRP 0.060 0.002 TRP D 606 HIS 0.013 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00306 (31855) covalent geometry : angle 0.61810 (43061) SS BOND : bond 0.00288 ( 15) SS BOND : angle 1.89032 ( 30) hydrogen bonds : bond 0.03681 ( 1467) hydrogen bonds : angle 5.02773 ( 4188) Misc. bond : bond 0.01295 ( 11) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 547 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 PHE cc_start: 0.8329 (p90) cc_final: 0.8108 (p90) REVERT: A 147 GLN cc_start: 0.7700 (mt0) cc_final: 0.7146 (mp10) REVERT: A 193 ILE cc_start: 0.8273 (mt) cc_final: 0.7978 (tt) REVERT: A 249 ASP cc_start: 0.8200 (t0) cc_final: 0.7180 (t0) REVERT: A 407 MET cc_start: 0.5974 (mtt) cc_final: 0.4967 (mtt) REVERT: A 458 LYS cc_start: 0.8149 (mmmt) cc_final: 0.6986 (mmmt) REVERT: A 463 MET cc_start: 0.4259 (tpp) cc_final: 0.4057 (tpp) REVERT: A 495 PHE cc_start: 0.5928 (p90) cc_final: 0.5263 (p90) REVERT: A 722 LYS cc_start: 0.7879 (pttt) cc_final: 0.7473 (pttt) REVERT: A 787 LEU cc_start: 0.8094 (tp) cc_final: 0.7766 (tp) REVERT: B 25 GLU cc_start: 0.8630 (mp0) cc_final: 0.8269 (mp0) REVERT: B 79 LYS cc_start: 0.7931 (tttt) cc_final: 0.7158 (tppt) REVERT: B 330 GLU cc_start: 0.7935 (tt0) cc_final: 0.7513 (tp30) REVERT: B 404 PRO cc_start: 0.6517 (Cg_endo) cc_final: 0.5962 (Cg_exo) REVERT: B 414 MET cc_start: 0.8894 (ptp) cc_final: 0.8314 (ppp) REVERT: B 629 MET cc_start: 0.6498 (mmp) cc_final: 0.4545 (tpp) REVERT: B 807 MET cc_start: 0.7446 (mtm) cc_final: 0.6950 (mmp) REVERT: C 13 GLN cc_start: 0.6343 (mp10) cc_final: 0.5310 (tp-100) REVERT: C 104 ASP cc_start: 0.7444 (m-30) cc_final: 0.6882 (t0) REVERT: C 147 GLN cc_start: 0.8105 (mt0) cc_final: 0.7560 (mp10) REVERT: C 170 ASN cc_start: 0.8358 (m-40) cc_final: 0.7873 (p0) REVERT: C 193 ILE cc_start: 0.8028 (mt) cc_final: 0.7620 (tt) REVERT: C 408 MET cc_start: 0.8261 (mtm) cc_final: 0.7995 (mtm) REVERT: C 473 ASP cc_start: 0.7917 (m-30) cc_final: 0.7230 (t0) REVERT: C 527 MET cc_start: 0.7951 (ptt) cc_final: 0.6629 (ptt) REVERT: C 606 TRP cc_start: 0.6800 (m100) cc_final: 0.6380 (m100) REVERT: C 674 MET cc_start: 0.8927 (mmp) cc_final: 0.6923 (mmm) REVERT: D 25 GLU cc_start: 0.8574 (mp0) cc_final: 0.8277 (mp0) REVERT: D 147 GLN cc_start: 0.6742 (pp30) cc_final: 0.6387 (pp30) REVERT: D 151 ASP cc_start: 0.7605 (m-30) cc_final: 0.7094 (t0) REVERT: D 188 LYS cc_start: 0.9065 (mppt) cc_final: 0.8860 (mmtt) REVERT: D 193 ILE cc_start: 0.8886 (mt) cc_final: 0.8258 (tt) REVERT: D 265 LEU cc_start: 0.7124 (mt) cc_final: 0.6889 (mt) REVERT: D 330 GLU cc_start: 0.8041 (tt0) cc_final: 0.7498 (tm-30) REVERT: D 380 MET cc_start: 0.5982 (ptm) cc_final: 0.5574 (ptm) REVERT: D 527 MET cc_start: 0.7754 (mmp) cc_final: 0.7313 (mmp) REVERT: D 721 MET cc_start: 0.7923 (ptt) cc_final: 0.7678 (ptt) REVERT: E 1012 THR cc_start: 0.8374 (p) cc_final: 0.8149 (p) REVERT: E 1155 TYR cc_start: 0.7218 (t80) cc_final: 0.6729 (t80) REVERT: F 1203 ARG cc_start: 0.7387 (mtt180) cc_final: 0.7035 (mtt-85) REVERT: G 1155 TYR cc_start: 0.7527 (t80) cc_final: 0.7301 (t80) REVERT: G 1191 MET cc_start: 0.9205 (mmm) cc_final: 0.8812 (mmm) REVERT: G 1195 LEU cc_start: 0.9081 (mt) cc_final: 0.8755 (tt) REVERT: G 1199 MET cc_start: 0.8975 (ppp) cc_final: 0.8765 (ppp) outliers start: 2 outliers final: 2 residues processed: 548 average time/residue: 0.1731 time to fit residues: 153.7337 Evaluate side-chains 424 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 422 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 94 optimal weight: 3.9990 chunk 342 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 50 optimal weight: 0.2980 chunk 282 optimal weight: 0.9980 chunk 44 optimal weight: 0.2980 chunk 1 optimal weight: 2.9990 chunk 78 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 chunk 210 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 GLN C 83 ASN ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 587 GLN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.149169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.124499 restraints weight = 101942.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.125335 restraints weight = 85090.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.126527 restraints weight = 70472.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.126390 restraints weight = 55655.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.127169 restraints weight = 50877.076| |-----------------------------------------------------------------------------| r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31881 Z= 0.134 Angle : 0.610 13.861 43091 Z= 0.318 Chirality : 0.042 0.245 4778 Planarity : 0.005 0.143 5408 Dihedral : 6.711 97.309 4421 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.86 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.13), residues: 3910 helix: 0.65 (0.12), residues: 1846 sheet: -1.11 (0.27), residues: 324 loop : -1.22 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 420 TYR 0.017 0.001 TYR E1175 PHE 0.032 0.002 PHE G1141 TRP 0.063 0.002 TRP D 606 HIS 0.010 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00284 (31855) covalent geometry : angle 0.60817 (43061) SS BOND : bond 0.00693 ( 15) SS BOND : angle 1.79164 ( 30) hydrogen bonds : bond 0.03596 ( 1467) hydrogen bonds : angle 4.94224 ( 4188) Misc. bond : bond 0.01305 ( 11) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 535 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 PHE cc_start: 0.8268 (p90) cc_final: 0.8000 (p90) REVERT: A 147 GLN cc_start: 0.7578 (mt0) cc_final: 0.7047 (mp10) REVERT: A 193 ILE cc_start: 0.8309 (mt) cc_final: 0.8067 (tt) REVERT: A 249 ASP cc_start: 0.8190 (t0) cc_final: 0.7149 (t0) REVERT: A 303 ARG cc_start: 0.8764 (mpp-170) cc_final: 0.8437 (mpp-170) REVERT: A 361 MET cc_start: 0.5009 (mmp) cc_final: 0.4742 (mmp) REVERT: A 458 LYS cc_start: 0.8157 (mmmt) cc_final: 0.7016 (mmmt) REVERT: A 527 MET cc_start: 0.7275 (ptt) cc_final: 0.7017 (ppp) REVERT: A 714 GLN cc_start: 0.7088 (pt0) cc_final: 0.6530 (pp30) REVERT: A 722 LYS cc_start: 0.7870 (pttt) cc_final: 0.7477 (pttt) REVERT: A 787 LEU cc_start: 0.8052 (tp) cc_final: 0.7726 (tp) REVERT: B 25 GLU cc_start: 0.8618 (mp0) cc_final: 0.8286 (mp0) REVERT: B 330 GLU cc_start: 0.7906 (tt0) cc_final: 0.7538 (tp30) REVERT: B 404 PRO cc_start: 0.6330 (Cg_endo) cc_final: 0.5763 (Cg_exo) REVERT: B 414 MET cc_start: 0.8754 (ptp) cc_final: 0.8252 (ppp) REVERT: B 578 TRP cc_start: 0.7361 (t-100) cc_final: 0.7105 (t-100) REVERT: B 629 MET cc_start: 0.6360 (mmp) cc_final: 0.4492 (tpp) REVERT: B 807 MET cc_start: 0.7558 (mtm) cc_final: 0.6966 (mmp) REVERT: C 13 GLN cc_start: 0.6363 (mp10) cc_final: 0.5283 (tp-100) REVERT: C 104 ASP cc_start: 0.7388 (m-30) cc_final: 0.6816 (t0) REVERT: C 147 GLN cc_start: 0.8069 (mt0) cc_final: 0.7515 (mp10) REVERT: C 170 ASN cc_start: 0.8327 (m-40) cc_final: 0.7791 (p0) REVERT: C 193 ILE cc_start: 0.8057 (mt) cc_final: 0.7676 (tt) REVERT: C 408 MET cc_start: 0.8287 (mtm) cc_final: 0.7988 (mtm) REVERT: C 473 ASP cc_start: 0.7823 (m-30) cc_final: 0.7239 (t0) REVERT: C 527 MET cc_start: 0.7881 (ptt) cc_final: 0.6574 (ptt) REVERT: C 606 TRP cc_start: 0.6564 (m-10) cc_final: 0.6226 (m100) REVERT: C 674 MET cc_start: 0.8640 (mmp) cc_final: 0.7879 (mmm) REVERT: D 25 GLU cc_start: 0.8551 (mp0) cc_final: 0.8150 (mp0) REVERT: D 147 GLN cc_start: 0.6712 (pp30) cc_final: 0.6405 (pp30) REVERT: D 151 ASP cc_start: 0.7429 (m-30) cc_final: 0.7056 (t0) REVERT: D 193 ILE cc_start: 0.8869 (mt) cc_final: 0.8317 (tt) REVERT: D 209 ILE cc_start: 0.9098 (mt) cc_final: 0.8680 (mm) REVERT: D 265 LEU cc_start: 0.7021 (mt) cc_final: 0.6820 (mt) REVERT: D 330 GLU cc_start: 0.7950 (tt0) cc_final: 0.7441 (tm-30) REVERT: D 366 ASN cc_start: 0.7351 (p0) cc_final: 0.7010 (m-40) REVERT: D 380 MET cc_start: 0.5841 (ptm) cc_final: 0.5534 (ptm) REVERT: D 463 MET cc_start: 0.7980 (mpp) cc_final: 0.7117 (mpp) REVERT: D 527 MET cc_start: 0.7645 (mmp) cc_final: 0.7319 (mmp) REVERT: E 1155 TYR cc_start: 0.7046 (t80) cc_final: 0.6581 (t80) REVERT: F 1203 ARG cc_start: 0.7220 (mtt180) cc_final: 0.7019 (mtt-85) REVERT: G 1073 LYS cc_start: 0.7365 (mmpt) cc_final: 0.7115 (mmpt) REVERT: G 1191 MET cc_start: 0.9171 (mmm) cc_final: 0.8776 (mmm) REVERT: G 1195 LEU cc_start: 0.9011 (mt) cc_final: 0.8639 (tt) REVERT: G 1199 MET cc_start: 0.8873 (ppp) cc_final: 0.8637 (ppp) REVERT: H 1009 MET cc_start: 0.6069 (tpp) cc_final: 0.5447 (mtt) outliers start: 0 outliers final: 0 residues processed: 535 average time/residue: 0.1720 time to fit residues: 148.2609 Evaluate side-chains 427 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 427 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 323 optimal weight: 20.0000 chunk 144 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 342 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 145 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 chunk 252 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN B 714 GLN ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1059 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 = 0.4413 r_free = 0.4413 target = 0.146921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.121689 restraints weight = 101990.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.121360 restraints weight = 79399.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.122457 restraints weight = 75073.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.122562 restraints weight = 57423.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.123278 restraints weight = 50443.454| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31881 Z= 0.175 Angle : 0.646 11.622 43091 Z= 0.337 Chirality : 0.043 0.226 4778 Planarity : 0.005 0.127 5408 Dihedral : 6.697 95.402 4421 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.60 % Favored : 94.25 % Rotamer: Outliers : 0.06 % Allowed : 1.14 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.13), residues: 3910 helix: 0.65 (0.12), residues: 1814 sheet: -1.15 (0.28), residues: 309 loop : -1.30 (0.14), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 369 TYR 0.024 0.002 TYR A 616 PHE 0.027 0.002 PHE H1141 TRP 0.065 0.002 TRP D 606 HIS 0.007 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00381 (31855) covalent geometry : angle 0.64543 (43061) SS BOND : bond 0.00369 ( 15) SS BOND : angle 1.52186 ( 30) hydrogen bonds : bond 0.03775 ( 1467) hydrogen bonds : angle 5.04657 ( 4188) Misc. bond : bond 0.01294 ( 11) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 521 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 PHE cc_start: 0.8317 (p90) cc_final: 0.8081 (p90) REVERT: A 147 GLN cc_start: 0.7742 (mt0) cc_final: 0.7233 (mp10) REVERT: A 249 ASP cc_start: 0.8276 (t0) cc_final: 0.7255 (t0) REVERT: A 303 ARG cc_start: 0.8853 (mpp-170) cc_final: 0.8513 (mtm-85) REVERT: A 458 LYS cc_start: 0.8240 (mmmt) cc_final: 0.7017 (mmmt) REVERT: A 473 ASP cc_start: 0.8184 (m-30) cc_final: 0.7829 (t70) REVERT: A 479 LEU cc_start: 0.7338 (tp) cc_final: 0.6791 (tp) REVERT: A 527 MET cc_start: 0.7205 (ptt) cc_final: 0.6996 (ppp) REVERT: A 722 LYS cc_start: 0.7836 (pttt) cc_final: 0.7409 (pttt) REVERT: B 25 GLU cc_start: 0.8563 (mp0) cc_final: 0.8231 (mp0) REVERT: B 330 GLU cc_start: 0.7864 (tt0) cc_final: 0.7641 (tm-30) REVERT: B 414 MET cc_start: 0.8820 (ptp) cc_final: 0.8290 (ppp) REVERT: B 629 MET cc_start: 0.6433 (mmp) cc_final: 0.4462 (tpp) REVERT: B 807 MET cc_start: 0.7498 (mtm) cc_final: 0.7019 (mmp) REVERT: C 13 GLN cc_start: 0.6419 (mp10) cc_final: 0.5345 (tp-100) REVERT: C 104 ASP cc_start: 0.7589 (m-30) cc_final: 0.6906 (t0) REVERT: C 127 TYR cc_start: 0.7956 (t80) cc_final: 0.7716 (t80) REVERT: C 147 GLN cc_start: 0.8057 (mt0) cc_final: 0.7547 (mp10) REVERT: C 170 ASN cc_start: 0.8344 (m-40) cc_final: 0.7761 (p0) REVERT: C 380 MET cc_start: 0.7908 (tmm) cc_final: 0.7332 (tpt) REVERT: C 408 MET cc_start: 0.8297 (mtm) cc_final: 0.7985 (mtm) REVERT: C 473 ASP cc_start: 0.7781 (m-30) cc_final: 0.7181 (t70) REVERT: C 606 TRP cc_start: 0.6838 (m-10) cc_final: 0.6375 (m100) REVERT: C 674 MET cc_start: 0.8700 (mmp) cc_final: 0.7912 (mmm) REVERT: D 25 GLU cc_start: 0.8394 (mp0) cc_final: 0.8062 (mp0) REVERT: D 330 GLU cc_start: 0.8003 (tt0) cc_final: 0.7501 (tm-30) REVERT: D 380 MET cc_start: 0.5824 (ptm) cc_final: 0.5523 (ptm) REVERT: D 463 MET cc_start: 0.8062 (mpp) cc_final: 0.7312 (mpp) REVERT: D 527 MET cc_start: 0.7736 (mmp) cc_final: 0.7402 (mmp) REVERT: E 1155 TYR cc_start: 0.7112 (t80) cc_final: 0.6641 (t80) REVERT: E 1175 TYR cc_start: 0.3718 (m-10) cc_final: 0.3479 (m-10) REVERT: F 1203 ARG cc_start: 0.7692 (mtt180) cc_final: 0.7377 (mtt-85) REVERT: G 1009 MET cc_start: 0.9146 (ptp) cc_final: 0.8663 (mpp) REVERT: G 1073 LYS cc_start: 0.7453 (mmpt) cc_final: 0.7024 (mmpt) REVERT: G 1155 TYR cc_start: 0.7487 (t80) cc_final: 0.7188 (t80) REVERT: G 1191 MET cc_start: 0.9179 (mmm) cc_final: 0.8757 (mmm) REVERT: G 1195 LEU cc_start: 0.9033 (mt) cc_final: 0.8679 (tt) REVERT: G 1199 MET cc_start: 0.8890 (ppp) cc_final: 0.8662 (ppp) REVERT: H 1009 MET cc_start: 0.5520 (tpp) cc_final: 0.4940 (mmm) REVERT: H 1012 THR cc_start: 0.8562 (p) cc_final: 0.8321 (t) REVERT: H 1098 ARG cc_start: 0.8822 (mpt-90) cc_final: 0.8488 (mtt90) outliers start: 2 outliers final: 1 residues processed: 523 average time/residue: 0.1701 time to fit residues: 144.7328 Evaluate side-chains 396 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 395 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 34 optimal weight: 3.9990 chunk 264 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 chunk 361 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 133 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 chunk 296 optimal weight: 3.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 HIS ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.148159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.122765 restraints weight = 102080.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.122605 restraints weight = 77465.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.123961 restraints weight = 67897.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.123903 restraints weight = 53309.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.124651 restraints weight = 48878.346| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31881 Z= 0.147 Angle : 0.638 18.033 43091 Z= 0.329 Chirality : 0.043 0.298 4778 Planarity : 0.005 0.159 5408 Dihedral : 6.667 95.208 4421 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.24 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.13), residues: 3910 helix: 0.68 (0.12), residues: 1830 sheet: -1.34 (0.27), residues: 324 loop : -1.33 (0.15), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 675 TYR 0.026 0.001 TYR A 177 PHE 0.027 0.002 PHE H1141 TRP 0.078 0.002 TRP D 606 HIS 0.007 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00315 (31855) covalent geometry : angle 0.63688 (43061) SS BOND : bond 0.00482 ( 15) SS BOND : angle 1.61512 ( 30) hydrogen bonds : bond 0.03601 ( 1467) hydrogen bonds : angle 4.93463 ( 4188) Misc. bond : bond 0.01312 ( 11) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 502 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 SER cc_start: 0.8454 (m) cc_final: 0.8253 (p) REVERT: A 101 PHE cc_start: 0.8274 (p90) cc_final: 0.8048 (p90) REVERT: A 147 GLN cc_start: 0.7663 (mt0) cc_final: 0.7147 (mp10) REVERT: A 249 ASP cc_start: 0.8310 (t0) cc_final: 0.7298 (t0) REVERT: A 258 PHE cc_start: 0.7947 (m-80) cc_final: 0.7715 (m-80) REVERT: A 303 ARG cc_start: 0.8782 (mpp-170) cc_final: 0.8479 (mtm-85) REVERT: A 458 LYS cc_start: 0.8249 (mmmt) cc_final: 0.7047 (mmmt) REVERT: A 463 MET cc_start: 0.4118 (tpp) cc_final: 0.3677 (tpp) REVERT: A 473 ASP cc_start: 0.8062 (m-30) cc_final: 0.7717 (t70) REVERT: A 629 MET cc_start: 0.1451 (ptp) cc_final: 0.0818 (pmm) REVERT: A 722 LYS cc_start: 0.7758 (pttt) cc_final: 0.7254 (pttt) REVERT: B 25 GLU cc_start: 0.8500 (mp0) cc_final: 0.8088 (mp0) REVERT: B 330 GLU cc_start: 0.7890 (tt0) cc_final: 0.7550 (tp30) REVERT: B 414 MET cc_start: 0.8897 (ptp) cc_final: 0.8370 (ppp) REVERT: B 463 MET cc_start: 0.7418 (mmm) cc_final: 0.7112 (mmt) REVERT: B 629 MET cc_start: 0.6410 (mmp) cc_final: 0.4476 (tpp) REVERT: B 796 PHE cc_start: 0.8891 (m-10) cc_final: 0.8672 (m-80) REVERT: B 807 MET cc_start: 0.7512 (mtm) cc_final: 0.7072 (mmp) REVERT: C 13 GLN cc_start: 0.6482 (mp10) cc_final: 0.5342 (tp-100) REVERT: C 104 ASP cc_start: 0.7529 (m-30) cc_final: 0.6964 (t0) REVERT: C 170 ASN cc_start: 0.8271 (m-40) cc_final: 0.7686 (p0) REVERT: C 193 ILE cc_start: 0.8169 (mt) cc_final: 0.7774 (tt) REVERT: C 408 MET cc_start: 0.8223 (mtm) cc_final: 0.7905 (mtm) REVERT: C 473 ASP cc_start: 0.7783 (m-30) cc_final: 0.7158 (t70) REVERT: C 606 TRP cc_start: 0.6840 (m-10) cc_final: 0.6497 (m100) REVERT: C 674 MET cc_start: 0.8637 (mmp) cc_final: 0.7914 (mmm) REVERT: D 25 GLU cc_start: 0.8396 (mp0) cc_final: 0.8070 (mp0) REVERT: D 147 GLN cc_start: 0.6885 (pp30) cc_final: 0.6506 (pp30) REVERT: D 330 GLU cc_start: 0.7993 (tt0) cc_final: 0.7491 (tm-30) REVERT: D 366 ASN cc_start: 0.7553 (p0) cc_final: 0.7136 (m-40) REVERT: D 380 MET cc_start: 0.5902 (ptm) cc_final: 0.5571 (ptm) REVERT: D 463 MET cc_start: 0.8185 (mpp) cc_final: 0.7523 (mpp) REVERT: D 527 MET cc_start: 0.7637 (mmp) cc_final: 0.7336 (mmp) REVERT: E 1155 TYR cc_start: 0.7015 (t80) cc_final: 0.6571 (t80) REVERT: E 1175 TYR cc_start: 0.3828 (m-10) cc_final: 0.3496 (m-10) REVERT: F 1203 ARG cc_start: 0.7584 (mtt180) cc_final: 0.7296 (mtt-85) REVERT: G 1073 LYS cc_start: 0.7280 (mmpt) cc_final: 0.6817 (mmpt) REVERT: G 1155 TYR cc_start: 0.7361 (t80) cc_final: 0.7118 (t80) REVERT: G 1191 MET cc_start: 0.9188 (mmm) cc_final: 0.8927 (mmm) REVERT: G 1195 LEU cc_start: 0.9040 (mt) cc_final: 0.8677 (tt) REVERT: H 1009 MET cc_start: 0.5574 (tpp) cc_final: 0.4909 (mmm) outliers start: 0 outliers final: 0 residues processed: 502 average time/residue: 0.1691 time to fit residues: 138.3611 Evaluate side-chains 408 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 119 optimal weight: 9.9990 chunk 156 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 329 optimal weight: 0.9980 chunk 287 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 275 optimal weight: 1.9990 chunk 389 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN B 344 ASN ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 ASN ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 709 ASN ** G1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.145499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.120539 restraints weight = 102634.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.121014 restraints weight = 96404.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.122054 restraints weight = 75907.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.122203 restraints weight = 54833.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.123587 restraints weight = 52978.389| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31881 Z= 0.197 Angle : 0.679 14.928 43091 Z= 0.354 Chirality : 0.044 0.244 4778 Planarity : 0.005 0.145 5408 Dihedral : 6.726 93.984 4421 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.39 % Favored : 93.48 % Rotamer: Outliers : 0.03 % Allowed : 0.72 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.13), residues: 3910 helix: 0.63 (0.12), residues: 1807 sheet: -1.38 (0.28), residues: 303 loop : -1.36 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G1101 TYR 0.026 0.002 TYR A 616 PHE 0.054 0.002 PHE A 541 TRP 0.090 0.003 TRP D 606 HIS 0.008 0.002 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00432 (31855) covalent geometry : angle 0.67831 (43061) SS BOND : bond 0.00338 ( 15) SS BOND : angle 1.45414 ( 30) hydrogen bonds : bond 0.03912 ( 1467) hydrogen bonds : angle 5.08780 ( 4188) Misc. bond : bond 0.01331 ( 11) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 495 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 101 PHE cc_start: 0.8289 (p90) cc_final: 0.8036 (p90) REVERT: A 147 GLN cc_start: 0.7868 (mt0) cc_final: 0.7402 (mp10) REVERT: A 249 ASP cc_start: 0.8304 (t0) cc_final: 0.7340 (t0) REVERT: A 258 PHE cc_start: 0.8043 (m-80) cc_final: 0.7717 (m-80) REVERT: A 303 ARG cc_start: 0.8742 (mpp-170) cc_final: 0.8445 (mtm-85) REVERT: A 401 LEU cc_start: 0.5307 (tt) cc_final: 0.5028 (tp) REVERT: A 463 MET cc_start: 0.4179 (tpp) cc_final: 0.3771 (tpp) REVERT: A 473 ASP cc_start: 0.8126 (m-30) cc_final: 0.7774 (t70) REVERT: A 605 TRP cc_start: 0.7168 (t-100) cc_final: 0.6513 (t-100) REVERT: A 688 GLU cc_start: 0.8374 (tp30) cc_final: 0.8123 (tp30) REVERT: A 722 LYS cc_start: 0.7750 (pttt) cc_final: 0.7404 (pttt) REVERT: B 25 GLU cc_start: 0.8465 (mp0) cc_final: 0.8052 (mp0) REVERT: B 330 GLU cc_start: 0.7877 (tt0) cc_final: 0.7591 (tm-30) REVERT: B 414 MET cc_start: 0.8708 (ptp) cc_final: 0.8295 (ppp) REVERT: B 442 LEU cc_start: 0.8889 (mt) cc_final: 0.8614 (mt) REVERT: B 629 MET cc_start: 0.6425 (mmp) cc_final: 0.4471 (tpp) REVERT: B 807 MET cc_start: 0.7514 (mtm) cc_final: 0.7152 (mmm) REVERT: C 13 GLN cc_start: 0.6440 (mp10) cc_final: 0.5340 (tp-100) REVERT: C 104 ASP cc_start: 0.7542 (m-30) cc_final: 0.6975 (t0) REVERT: C 147 GLN cc_start: 0.7950 (mt0) cc_final: 0.7615 (mp10) REVERT: C 170 ASN cc_start: 0.8263 (m-40) cc_final: 0.7722 (p0) REVERT: C 408 MET cc_start: 0.8195 (mtm) cc_final: 0.7707 (mtm) REVERT: C 458 LYS cc_start: 0.7143 (mmpt) cc_final: 0.4423 (tmtt) REVERT: C 527 MET cc_start: 0.7714 (ptt) cc_final: 0.7090 (ptt) REVERT: C 606 TRP cc_start: 0.6959 (m-10) cc_final: 0.6540 (m100) REVERT: C 674 MET cc_start: 0.8684 (mmp) cc_final: 0.8116 (mmm) REVERT: D 25 GLU cc_start: 0.8373 (mp0) cc_final: 0.7956 (mp0) REVERT: D 211 ILE cc_start: 0.9099 (pt) cc_final: 0.8782 (mt) REVERT: D 330 GLU cc_start: 0.8021 (tt0) cc_final: 0.7459 (tm-30) REVERT: D 380 MET cc_start: 0.5785 (ptm) cc_final: 0.5572 (ptm) REVERT: D 463 MET cc_start: 0.8049 (mpp) cc_final: 0.7413 (mpp) REVERT: D 527 MET cc_start: 0.7674 (mmp) cc_final: 0.7408 (mmp) REVERT: E 1155 TYR cc_start: 0.6992 (t80) cc_final: 0.6552 (t80) REVERT: F 1199 MET cc_start: 0.5392 (mtm) cc_final: 0.5021 (mtt) REVERT: G 1009 MET cc_start: 0.9073 (ptp) cc_final: 0.8861 (mpp) REVERT: G 1073 LYS cc_start: 0.7360 (mmpt) cc_final: 0.6887 (mmpt) REVERT: G 1155 TYR cc_start: 0.7443 (t80) cc_final: 0.7167 (t80) REVERT: G 1191 MET cc_start: 0.9212 (mmm) cc_final: 0.8792 (mmm) REVERT: G 1195 LEU cc_start: 0.8982 (mt) cc_final: 0.8633 (tt) REVERT: H 1009 MET cc_start: 0.5362 (tpp) cc_final: 0.4760 (mmm) REVERT: H 1012 THR cc_start: 0.8514 (t) cc_final: 0.7980 (t) outliers start: 1 outliers final: 0 residues processed: 496 average time/residue: 0.1761 time to fit residues: 142.5446 Evaluate side-chains 386 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 386 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 179 optimal weight: 0.0170 chunk 228 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 248 optimal weight: 0.9980 chunk 178 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 150 optimal weight: 0.8980 chunk 168 optimal weight: 0.8980 chunk 347 optimal weight: 0.0970 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 ASN ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.149034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.124461 restraints weight = 102836.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.124487 restraints weight = 85991.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.126225 restraints weight = 70703.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.126011 restraints weight = 54280.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.126978 restraints weight = 51061.896| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31881 Z= 0.135 Angle : 0.649 14.315 43091 Z= 0.332 Chirality : 0.043 0.265 4778 Planarity : 0.005 0.136 5408 Dihedral : 6.645 94.549 4421 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.06 % Favored : 94.81 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.13), residues: 3910 helix: 0.74 (0.12), residues: 1836 sheet: -1.39 (0.28), residues: 315 loop : -1.36 (0.15), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G1101 TYR 0.021 0.001 TYR C 127 PHE 0.039 0.002 PHE A 541 TRP 0.094 0.002 TRP D 606 HIS 0.009 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00285 (31855) covalent geometry : angle 0.64819 (43061) SS BOND : bond 0.00239 ( 15) SS BOND : angle 1.55066 ( 30) hydrogen bonds : bond 0.03558 ( 1467) hydrogen bonds : angle 4.87050 ( 4188) Misc. bond : bond 0.01335 ( 11) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 490 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 PHE cc_start: 0.8117 (p90) cc_final: 0.7847 (p90) REVERT: A 147 GLN cc_start: 0.7597 (mt0) cc_final: 0.7138 (mp10) REVERT: A 249 ASP cc_start: 0.8236 (t0) cc_final: 0.7297 (t0) REVERT: A 258 PHE cc_start: 0.7834 (m-80) cc_final: 0.7579 (m-80) REVERT: A 303 ARG cc_start: 0.8618 (mpp-170) cc_final: 0.8348 (mtm-85) REVERT: A 458 LYS cc_start: 0.8169 (mmmt) cc_final: 0.6988 (mmmt) REVERT: A 473 ASP cc_start: 0.8028 (m-30) cc_final: 0.7650 (t70) REVERT: A 523 TYR cc_start: 0.7671 (t80) cc_final: 0.7463 (t80) REVERT: A 688 GLU cc_start: 0.8400 (tp30) cc_final: 0.8146 (tp30) REVERT: A 722 LYS cc_start: 0.7681 (pttt) cc_final: 0.7301 (pttt) REVERT: B 25 GLU cc_start: 0.8456 (mp0) cc_final: 0.8074 (mp0) REVERT: B 151 ASP cc_start: 0.7499 (m-30) cc_final: 0.7020 (t0) REVERT: B 330 GLU cc_start: 0.7824 (tt0) cc_final: 0.7544 (tp30) REVERT: B 414 MET cc_start: 0.8842 (ptp) cc_final: 0.8404 (ppp) REVERT: B 463 MET cc_start: 0.7138 (mmm) cc_final: 0.6884 (mmp) REVERT: B 629 MET cc_start: 0.6439 (mmp) cc_final: 0.4575 (tpp) REVERT: B 807 MET cc_start: 0.7420 (mtm) cc_final: 0.7195 (mmm) REVERT: C 13 GLN cc_start: 0.6379 (mp10) cc_final: 0.5366 (tp-100) REVERT: C 104 ASP cc_start: 0.7305 (m-30) cc_final: 0.6768 (t0) REVERT: C 122 LEU cc_start: 0.8271 (mt) cc_final: 0.7403 (tt) REVERT: C 127 TYR cc_start: 0.7812 (t80) cc_final: 0.7588 (t80) REVERT: C 147 GLN cc_start: 0.7847 (mt0) cc_final: 0.7510 (mp10) REVERT: C 170 ASN cc_start: 0.8171 (m-40) cc_final: 0.7642 (p0) REVERT: C 193 ILE cc_start: 0.8130 (mt) cc_final: 0.7772 (tt) REVERT: C 361 MET cc_start: 0.4457 (mmp) cc_final: 0.4100 (mmp) REVERT: C 408 MET cc_start: 0.8234 (mtm) cc_final: 0.7881 (mtm) REVERT: C 473 ASP cc_start: 0.7653 (m-30) cc_final: 0.6965 (t0) REVERT: C 527 MET cc_start: 0.7599 (ptt) cc_final: 0.6891 (ptt) REVERT: C 674 MET cc_start: 0.8590 (mmp) cc_final: 0.7918 (mmm) REVERT: D 25 GLU cc_start: 0.8424 (mp0) cc_final: 0.8128 (mp0) REVERT: D 124 LEU cc_start: 0.7984 (tp) cc_final: 0.7724 (tp) REVERT: D 193 ILE cc_start: 0.8797 (mt) cc_final: 0.8196 (tt) REVERT: D 211 ILE cc_start: 0.9021 (pt) cc_final: 0.8729 (mt) REVERT: D 330 GLU cc_start: 0.7946 (tt0) cc_final: 0.7482 (tm-30) REVERT: D 366 ASN cc_start: 0.7485 (p0) cc_final: 0.7158 (m-40) REVERT: D 463 MET cc_start: 0.8077 (mpp) cc_final: 0.7363 (mpp) REVERT: D 519 ASP cc_start: 0.8674 (m-30) cc_final: 0.8400 (t70) REVERT: D 527 MET cc_start: 0.7464 (mmp) cc_final: 0.7230 (mmp) REVERT: D 758 VAL cc_start: 0.9288 (t) cc_final: 0.8958 (t) REVERT: E 1155 TYR cc_start: 0.6931 (t80) cc_final: 0.6511 (t80) REVERT: F 1199 MET cc_start: 0.5223 (mtm) cc_final: 0.4606 (mtt) REVERT: G 1009 MET cc_start: 0.9059 (ptp) cc_final: 0.8833 (mpp) REVERT: G 1155 TYR cc_start: 0.7368 (t80) cc_final: 0.7106 (t80) REVERT: G 1191 MET cc_start: 0.9224 (mmm) cc_final: 0.8819 (mmm) REVERT: G 1195 LEU cc_start: 0.8977 (mt) cc_final: 0.8629 (tt) REVERT: H 1009 MET cc_start: 0.4763 (tpp) cc_final: 0.4263 (mtt) REVERT: H 1012 THR cc_start: 0.8506 (t) cc_final: 0.8222 (p) outliers start: 0 outliers final: 0 residues processed: 490 average time/residue: 0.1813 time to fit residues: 145.0960 Evaluate side-chains 386 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 386 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 281 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 379 optimal weight: 0.9980 chunk 386 optimal weight: 9.9990 chunk 151 optimal weight: 0.8980 chunk 310 optimal weight: 1.9990 chunk 362 optimal weight: 0.0570 chunk 318 optimal weight: 20.0000 chunk 277 optimal weight: 20.0000 chunk 333 optimal weight: 1.9990 chunk 304 optimal weight: 9.9990 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN B 169 ASN ** C 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 ASN ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.147915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.122995 restraints weight = 102989.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.122859 restraints weight = 80151.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.124374 restraints weight = 68553.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.124203 restraints weight = 54331.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.125023 restraints weight = 49215.169| |-----------------------------------------------------------------------------| r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31881 Z= 0.148 Angle : 0.647 13.643 43091 Z= 0.335 Chirality : 0.043 0.241 4778 Planarity : 0.005 0.130 5408 Dihedral : 6.552 93.819 4421 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.88 % Favored : 93.99 % Rotamer: Outliers : 0.06 % Allowed : 0.48 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.13), residues: 3910 helix: 0.83 (0.12), residues: 1825 sheet: -1.48 (0.27), residues: 325 loop : -1.37 (0.15), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G1101 TYR 0.018 0.002 TYR A 616 PHE 0.042 0.002 PHE F1186 TRP 0.088 0.003 TRP D 606 HIS 0.006 0.001 HIS F1059 Details of bonding type rmsd covalent geometry : bond 0.00322 (31855) covalent geometry : angle 0.64604 (43061) SS BOND : bond 0.00293 ( 15) SS BOND : angle 1.37095 ( 30) hydrogen bonds : bond 0.03536 ( 1467) hydrogen bonds : angle 4.91139 ( 4188) Misc. bond : bond 0.01322 ( 11) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4822.64 seconds wall clock time: 84 minutes 36.45 seconds (5076.45 seconds total)