Starting phenix.real_space_refine on Thu Sep 18 23:52:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e28_47443/09_2025/9e28_47443.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e28_47443/09_2025/9e28_47443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e28_47443/09_2025/9e28_47443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e28_47443/09_2025/9e28_47443.map" model { file = "/net/cci-nas-00/data/ceres_data/9e28_47443/09_2025/9e28_47443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e28_47443/09_2025/9e28_47443.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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: 3 Type Number sf(0) Gaussians C 11781 2.51 5 N 4734 2.21 5 O 4734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21249 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 756 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 136} Link IDs: {'PTRANS': 8, 'TRANS': 143} Chain breaks: 2 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 467 Unresolved non-hydrogen angles: 592 Unresolved non-hydrogen dihedrals: 384 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 5, 'ARG:plan': 6, 'GLU:plan': 14, 'ASP:plan': 6, 'PHE:plan': 6, 'TYR:plan': 4, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 229 Chain: "B" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 1604 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 291} Link IDs: {'PTRANS': 13, 'TRANS': 310} Chain breaks: 1 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1081 Unresolved non-hydrogen angles: 1381 Unresolved non-hydrogen dihedrals: 914 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLU:plan': 31, 'GLN:plan1': 10, 'TRP:plan': 5, 'ARG:plan': 13, 'ASN:plan1': 7, 'PHE:plan': 13, 'ASP:plan': 23, 'HIS:plan': 13, 'TYR:plan': 11} Unresolved non-hydrogen planarities: 584 Chain: "C" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 1604 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 291} Link IDs: {'PTRANS': 13, 'TRANS': 310} Chain breaks: 1 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1081 Unresolved non-hydrogen angles: 1381 Unresolved non-hydrogen dihedrals: 914 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLU:plan': 31, 'GLN:plan1': 10, 'TRP:plan': 5, 'ARG:plan': 13, 'ASN:plan1': 7, 'PHE:plan': 13, 'ASP:plan': 23, 'HIS:plan': 13, 'TYR:plan': 11} Unresolved non-hydrogen planarities: 584 Chain: "D" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 2054 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 355} Link IDs: {'PTRANS': 18, 'TRANS': 397} Chain breaks: 1 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1294 Unresolved non-hydrogen angles: 1681 Unresolved non-hydrogen dihedrals: 1105 Unresolved non-hydrogen chiralities: 103 Planarities with less than four sites: {'GLU:plan': 30, 'GLN:plan1': 14, 'HIS:plan': 18, 'PHE:plan': 17, 'ASP:plan': 22, 'ARG:plan': 18, 'ASN:plan1': 24, 'TRP:plan': 11, 'TYR:plan': 11} Unresolved non-hydrogen planarities: 772 Chain: "E" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 477 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 5, 'TRANS': 90} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 298 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 237 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 5, 'GLN:plan1': 6, 'ASN:plan1': 5, 'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 143 Chain: "F" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 477 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 5, 'TRANS': 90} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 298 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 237 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 5, 'GLN:plan1': 6, 'ASN:plan1': 5, 'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 143 Chain: "G" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 756 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 136} Link IDs: {'PTRANS': 8, 'TRANS': 143} Chain breaks: 2 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 467 Unresolved non-hydrogen angles: 592 Unresolved non-hydrogen dihedrals: 384 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 5, 'ARG:plan': 6, 'GLU:plan': 14, 'ASP:plan': 6, 'PHE:plan': 6, 'TYR:plan': 4, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 229 Chain: "H" Number of atoms: 2118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 2118 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 367} Link IDs: {'PTRANS': 18, 'TRANS': 410} Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1346 Unresolved non-hydrogen angles: 1748 Unresolved non-hydrogen dihedrals: 1149 Unresolved non-hydrogen chiralities: 105 Planarities with less than four sites: {'GLU:plan': 31, 'GLN:plan1': 15, 'HIS:plan': 18, 'PHE:plan': 19, 'ASP:plan': 24, 'ARG:plan': 19, 'ASN:plan1': 25, 'TYR:plan': 12, 'TRP:plan': 11} Unresolved non-hydrogen planarities: 813 Chain: "d" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 441 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 86} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 4, 'GLU:plan': 7, 'GLN:plan1': 4, 'TYR:plan': 5, 'HIS:plan': 4, 'PHE:plan': 5, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 175 Chain: "e" Number of atoms: 4608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1152, 4608 Classifications: {'peptide': 1152} Incomplete info: {'backbone_only': 1106} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 1117} Chain breaks: 2 Unresolved chain link angles: 34 Unresolved non-hydrogen bonds: 5064 Unresolved non-hydrogen angles: 7253 Unresolved non-hydrogen dihedrals: 3296 Unresolved non-hydrogen chiralities: 1439 Planarities with less than four sites: {'HIS:plan': 19, 'ASN:plan1': 48, 'GLN:plan1': 77, 'TYR:plan': 36, 'GLU:plan': 101, 'ARG:plan': 87, 'ASP:plan': 62, 'PHE:plan': 40, 'TRP:plan': 23} Unresolved non-hydrogen planarities: 2499 Chain: "f" Number of atoms: 4609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1151, 4609 Classifications: {'peptide': 1151} Incomplete info: {'backbone_only': 1100, 'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 1116} Chain breaks: 3 Unresolved chain link angles: 34 Unresolved non-hydrogen bonds: 5058 Unresolved non-hydrogen angles: 7241 Unresolved non-hydrogen dihedrals: 3296 Unresolved non-hydrogen chiralities: 1433 Planarities with less than four sites: {'HIS:plan': 19, 'ASN:plan1': 48, 'GLN:plan1': 77, 'TYR:plan': 36, 'GLU:plan': 101, 'ARG:plan': 87, 'ASP:plan': 62, 'PHE:plan': 40, 'TRP:plan': 23} Unresolved non-hydrogen planarities: 2497 Chain: "g" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 154 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 3, 'TRANS': 27} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "h" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 154 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 3, 'TRANS': 27} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "i" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 441 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 86} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 4, 'GLU:plan': 7, 'GLN:plan1': 4, 'TYR:plan': 5, 'HIS:plan': 4, 'PHE:plan': 5, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 175 Chain: "k" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 498 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 1, 'TRANS': 99} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 245 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 5, 'ASN:plan1': 6, 'TYR:plan': 3, 'GLN:plan1': 5, 'HIS:plan': 2, 'TRP:plan': 3, 'PHE:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 148 Chain: "v" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 498 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 1, 'TRANS': 99} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 245 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 5, 'ASN:plan1': 6, 'TYR:plan': 3, 'GLN:plan1': 5, 'HIS:plan': 2, 'TRP:plan': 3, 'PHE:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 148 Time building chain proxies: 6.01, per 1000 atoms: 0.28 Number of scatterers: 21249 At special positions: 0 Unit cell: (144.925, 152.405, 347.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 4734 8.00 N 4734 7.00 C 11781 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 953.7 nanoseconds 9356 Ramachandran restraints generated. 4678 Oldfield, 0 Emsley, 4678 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4626 Finding SS restraints... Secondary structure from input PDB file: 155 helices and 29 sheets defined 57.9% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 27 through 34 Processing helix chain 'A' and resid 37 through 41 removed outlier: 4.227A pdb=" N LEU A 41 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 57 Processing helix chain 'A' and resid 58 through 71 Processing helix chain 'A' and resid 144 through 156 removed outlier: 3.601A pdb=" N THR A 148 " --> pdb=" O SER A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 179 through 198 Processing helix chain 'B' and resid 28 through 48 Processing helix chain 'B' and resid 66 through 75 Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 115 through 120 Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 127 through 131 removed outlier: 4.289A pdb=" N THR B 131 " --> pdb=" O LEU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 164 removed outlier: 4.346A pdb=" N MET B 146 " --> pdb=" O PRO B 142 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N GLU B 147 " --> pdb=" O TRP B 143 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 183 Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 247 through 266 Processing helix chain 'B' and resid 279 through 293 Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.639A pdb=" N ALA B 307 " --> pdb=" O GLU B 304 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL B 308 " --> pdb=" O LYS B 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 304 through 308' Processing helix chain 'B' and resid 316 through 326 removed outlier: 3.961A pdb=" N ASN B 326 " --> pdb=" O ILE B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 373 Processing helix chain 'C' and resid 28 through 44 Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'C' and resid 66 through 76 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'C' and resid 118 through 123 removed outlier: 3.976A pdb=" N ALA C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 164 removed outlier: 3.554A pdb=" N MET C 163 " --> pdb=" O HIS C 159 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS C 164 " --> pdb=" O ILE C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 183 Processing helix chain 'C' and resid 233 through 235 No H-bonds generated for 'chain 'C' and resid 233 through 235' Processing helix chain 'C' and resid 236 through 243 Processing helix chain 'C' and resid 247 through 266 Processing helix chain 'C' and resid 279 through 291 Processing helix chain 'C' and resid 316 through 325 Processing helix chain 'C' and resid 335 through 340 removed outlier: 3.728A pdb=" N PHE C 339 " --> pdb=" O TYR C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 373 Processing helix chain 'D' and resid 185 through 192 Processing helix chain 'D' and resid 193 through 212 Processing helix chain 'D' and resid 581 through 609 Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 35 through 61 removed outlier: 4.537A pdb=" N THR E 39 " --> pdb=" O ASP E 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 12 Processing helix chain 'F' and resid 35 through 61 Processing helix chain 'G' and resid 28 through 38 Processing helix chain 'G' and resid 49 through 57 Processing helix chain 'G' and resid 58 through 71 Processing helix chain 'G' and resid 144 through 156 removed outlier: 4.527A pdb=" N THR G 148 " --> pdb=" O SER G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 168 Processing helix chain 'G' and resid 179 through 198 Processing helix chain 'H' and resid 185 through 193 Processing helix chain 'H' and resid 193 through 212 Processing helix chain 'H' and resid 225 through 232 removed outlier: 4.459A pdb=" N LYS H 229 " --> pdb=" O ASP H 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 236 removed outlier: 3.782A pdb=" N GLY H 236 " --> pdb=" O ILE H 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 233 through 236' Processing helix chain 'H' and resid 574 through 579 removed outlier: 3.969A pdb=" N VAL H 579 " --> pdb=" O GLU H 575 " (cutoff:3.500A) Processing helix chain 'H' and resid 583 through 609 Processing helix chain 'd' and resid 14 through 32 Processing helix chain 'd' and resid 34 through 50 Processing helix chain 'e' and resid 211 through 223 Processing helix chain 'e' and resid 233 through 238 removed outlier: 3.605A pdb=" N GLU e 237 " --> pdb=" O GLY e 233 " (cutoff:3.500A) Processing helix chain 'e' and resid 238 through 261 Processing helix chain 'e' and resid 270 through 294 Processing helix chain 'e' and resid 294 through 307 Processing helix chain 'e' and resid 309 through 319 Processing helix chain 'e' and resid 321 through 331 Processing helix chain 'e' and resid 340 through 347 Processing helix chain 'e' and resid 349 through 370 Processing helix chain 'e' and resid 373 through 400 Processing helix chain 'e' and resid 405 through 441 Processing helix chain 'e' and resid 456 through 483 Processing helix chain 'e' and resid 513 through 533 Processing helix chain 'e' and resid 539 through 575 Processing helix chain 'e' and resid 577 through 589 Processing helix chain 'e' and resid 590 through 592 No H-bonds generated for 'chain 'e' and resid 590 through 592' Processing helix chain 'e' and resid 596 through 625 removed outlier: 5.092A pdb=" N THR e 606 " --> pdb=" O ARG e 602 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLN e 607 " --> pdb=" O GLU e 603 " (cutoff:3.500A) Processing helix chain 'e' and resid 630 through 639 Processing helix chain 'e' and resid 642 through 670 Processing helix chain 'e' and resid 672 through 675 Processing helix chain 'e' and resid 676 through 693 Processing helix chain 'e' and resid 695 through 710 Processing helix chain 'e' and resid 740 through 757 removed outlier: 4.147A pdb=" N ILE e 744 " --> pdb=" O LEU e 740 " (cutoff:3.500A) Processing helix chain 'e' and resid 761 through 798 Proline residue: e 776 - end of helix Processing helix chain 'e' and resid 805 through 822 Processing helix chain 'e' and resid 828 through 867 Processing helix chain 'e' and resid 870 through 891 Processing helix chain 'e' and resid 895 through 927 Processing helix chain 'e' and resid 974 through 995 removed outlier: 3.901A pdb=" N VAL e 993 " --> pdb=" O TRP e 989 " (cutoff:3.500A) Processing helix chain 'e' and resid 999 through 1004 removed outlier: 4.446A pdb=" N GLN e1002 " --> pdb=" O ILE e 999 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG e1003 " --> pdb=" O GLN e1000 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR e1004 " --> pdb=" O SER e1001 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 999 through 1004' Processing helix chain 'e' and resid 1013 through 1018 Processing helix chain 'e' and resid 1020 through 1024 removed outlier: 3.538A pdb=" N LEU e1023 " --> pdb=" O ARG e1020 " (cutoff:3.500A) Processing helix chain 'e' and resid 1030 through 1055 Processing helix chain 'e' and resid 1057 through 1063 removed outlier: 4.177A pdb=" N TRP e1061 " --> pdb=" O TYR e1057 " (cutoff:3.500A) Processing helix chain 'e' and resid 1064 through 1073 Processing helix chain 'e' and resid 1075 through 1092 Processing helix chain 'e' and resid 1109 through 1156 Processing helix chain 'e' and resid 1162 through 1200 removed outlier: 4.157A pdb=" N GLN e1182 " --> pdb=" O ARG e1178 " (cutoff:3.500A) Processing helix chain 'e' and resid 1210 through 1264 removed outlier: 4.205A pdb=" N ALA e1237 " --> pdb=" O GLN e1233 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASN e1238 " --> pdb=" O GLN e1234 " (cutoff:3.500A) Processing helix chain 'e' and resid 1271 through 1305 removed outlier: 3.788A pdb=" N GLU e1275 " --> pdb=" O LEU e1271 " (cutoff:3.500A) Processing helix chain 'e' and resid 1313 through 1349 removed outlier: 3.855A pdb=" N GLN e1342 " --> pdb=" O LYS e1338 " (cutoff:3.500A) Processing helix chain 'e' and resid 1355 through 1371 Processing helix chain 'e' and resid 1374 through 1380 Processing helix chain 'e' and resid 1380 through 1404 removed outlier: 4.393A pdb=" N GLU e1384 " --> pdb=" O TYR e1380 " (cutoff:3.500A) Processing helix chain 'f' and resid 211 through 223 Processing helix chain 'f' and resid 228 through 233 Processing helix chain 'f' and resid 233 through 238 removed outlier: 3.797A pdb=" N GLU f 237 " --> pdb=" O GLY f 233 " (cutoff:3.500A) Processing helix chain 'f' and resid 238 through 262 removed outlier: 4.091A pdb=" N LEU f 262 " --> pdb=" O LYS f 258 " (cutoff:3.500A) Processing helix chain 'f' and resid 270 through 294 Processing helix chain 'f' and resid 294 through 307 Processing helix chain 'f' and resid 309 through 321 removed outlier: 3.773A pdb=" N GLY f 321 " --> pdb=" O ASP f 317 " (cutoff:3.500A) Processing helix chain 'f' and resid 321 through 333 Processing helix chain 'f' and resid 339 through 347 removed outlier: 3.501A pdb=" N ASP f 343 " --> pdb=" O PHE f 339 " (cutoff:3.500A) Processing helix chain 'f' and resid 349 through 370 Processing helix chain 'f' and resid 373 through 400 Processing helix chain 'f' and resid 405 through 441 Processing helix chain 'f' and resid 457 through 485 removed outlier: 3.653A pdb=" N ARG f 485 " --> pdb=" O VAL f 481 " (cutoff:3.500A) Processing helix chain 'f' and resid 513 through 533 Processing helix chain 'f' and resid 539 through 574 Processing helix chain 'f' and resid 577 through 589 Processing helix chain 'f' and resid 590 through 592 No H-bonds generated for 'chain 'f' and resid 590 through 592' Processing helix chain 'f' and resid 597 through 625 removed outlier: 4.555A pdb=" N THR f 606 " --> pdb=" O ARG f 602 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLN f 607 " --> pdb=" O GLU f 603 " (cutoff:3.500A) Processing helix chain 'f' and resid 630 through 639 Processing helix chain 'f' and resid 642 through 670 Processing helix chain 'f' and resid 676 through 693 Processing helix chain 'f' and resid 694 through 710 removed outlier: 3.874A pdb=" N ILE f 698 " --> pdb=" O ASN f 694 " (cutoff:3.500A) Processing helix chain 'f' and resid 740 through 757 Processing helix chain 'f' and resid 761 through 798 Proline residue: f 776 - end of helix removed outlier: 4.069A pdb=" N SER f 780 " --> pdb=" O PRO f 776 " (cutoff:3.500A) Processing helix chain 'f' and resid 800 through 804 removed outlier: 4.102A pdb=" N LEU f 803 " --> pdb=" O THR f 800 " (cutoff:3.500A) Processing helix chain 'f' and resid 805 through 822 Processing helix chain 'f' and resid 828 through 867 Processing helix chain 'f' and resid 870 through 891 Processing helix chain 'f' and resid 895 through 927 Processing helix chain 'f' and resid 974 through 995 removed outlier: 4.039A pdb=" N VAL f 993 " --> pdb=" O TRP f 989 " (cutoff:3.500A) Processing helix chain 'f' and resid 1000 through 1004 removed outlier: 3.642A pdb=" N TYR f1004 " --> pdb=" O SER f1001 " (cutoff:3.500A) Processing helix chain 'f' and resid 1013 through 1018 Processing helix chain 'f' and resid 1019 through 1023 removed outlier: 4.271A pdb=" N LEU f1023 " --> pdb=" O ARG f1020 " (cutoff:3.500A) Processing helix chain 'f' and resid 1030 through 1056 Processing helix chain 'f' and resid 1058 through 1063 Processing helix chain 'f' and resid 1064 through 1073 Processing helix chain 'f' and resid 1075 through 1093 Processing helix chain 'f' and resid 1109 through 1156 Processing helix chain 'f' and resid 1162 through 1200 removed outlier: 4.445A pdb=" N LYS f1181 " --> pdb=" O LYS f1177 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLN f1182 " --> pdb=" O ARG f1178 " (cutoff:3.500A) Processing helix chain 'f' and resid 1210 through 1231 Processing helix chain 'f' and resid 1232 through 1234 No H-bonds generated for 'chain 'f' and resid 1232 through 1234' Processing helix chain 'f' and resid 1235 through 1265 Processing helix chain 'f' and resid 1266 through 1269 removed outlier: 3.610A pdb=" N GLY f1269 " --> pdb=" O PRO f1266 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 1266 through 1269' Processing helix chain 'f' and resid 1272 through 1305 Processing helix chain 'f' and resid 1313 through 1348 Processing helix chain 'f' and resid 1355 through 1372 Processing helix chain 'f' and resid 1374 through 1380 Processing helix chain 'f' and resid 1380 through 1404 removed outlier: 5.158A pdb=" N MET f1398 " --> pdb=" O MET f1394 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU f1399 " --> pdb=" O LYS f1395 " (cutoff:3.500A) Processing helix chain 'i' and resid 14 through 32 Processing helix chain 'i' and resid 34 through 50 Processing helix chain 'k' and resid 14 through 29 Processing helix chain 'k' and resid 35 through 58 removed outlier: 4.622A pdb=" N ASN k 40 " --> pdb=" O HIS k 36 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLN k 41 " --> pdb=" O SER k 37 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY k 58 " --> pdb=" O LEU k 54 " (cutoff:3.500A) Processing helix chain 'v' and resid 14 through 29 Processing helix chain 'v' and resid 38 through 58 removed outlier: 4.001A pdb=" N GLY v 58 " --> pdb=" O LEU v 54 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 88 through 95 Processing sheet with id=AA2, first strand: chain 'C' and resid 87 through 95 removed outlier: 3.724A pdb=" N LEU C 132 " --> pdb=" O ASN C 56 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE C 60 " --> pdb=" O ILE C 134 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N LEU C 228 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL C 133 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N VAL C 230 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N PHE C 135 " --> pdb=" O VAL C 230 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA C 268 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU C 269 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 240 through 245 removed outlier: 5.619A pdb=" N ILE D 570 " --> pdb=" O ASN D 242 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN D 244 " --> pdb=" O ILE D 568 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ILE D 568 " --> pdb=" O GLN D 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 256 through 260 removed outlier: 4.454A pdb=" N CYS D 258 " --> pdb=" O SER D 272 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER D 272 " --> pdb=" O CYS D 258 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA D 271 " --> pdb=" O LEU D 288 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 309 through 314 removed outlier: 6.571A pdb=" N GLY D 325 " --> pdb=" O MET D 310 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ALA D 312 " --> pdb=" O VAL D 323 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL D 323 " --> pdb=" O ALA D 312 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N PHE D 314 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N LEU D 321 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 360 through 364 removed outlier: 4.240A pdb=" N CYS D 360 " --> pdb=" O ILE D 375 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE D 375 " --> pdb=" O CYS D 360 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 411 through 412 removed outlier: 4.088A pdb=" N VAL D 423 " --> pdb=" O TYR D 431 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR D 431 " --> pdb=" O VAL D 423 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N VAL D 430 " --> pdb=" O MET D 445 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N MET D 445 " --> pdb=" O VAL D 430 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N THR D 432 " --> pdb=" O SER D 443 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 470 through 472 removed outlier: 3.610A pdb=" N TRP D 483 " --> pdb=" O PHE D 471 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR D 492 " --> pdb=" O LEU D 482 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 513 through 518 removed outlier: 3.672A pdb=" N TRP D 526 " --> pdb=" O PHE D 514 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG D 522 " --> pdb=" O ASP D 518 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 22 through 24 removed outlier: 4.038A pdb=" N LEU E 88 " --> pdb=" O ALA E 81 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA E 81 " --> pdb=" O LEU E 88 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 19 through 23 removed outlier: 3.573A pdb=" N VAL F 80 " --> pdb=" O LEU F 69 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 83 through 84 removed outlier: 3.835A pdb=" N LEU G 84 " --> pdb=" O PHE G 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 240 through 244 removed outlier: 6.854A pdb=" N ILE H 570 " --> pdb=" O ASN H 242 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN H 244 " --> pdb=" O ILE H 568 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ILE H 568 " --> pdb=" O GLN H 244 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL H 561 " --> pdb=" O VAL H 569 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 268 through 272 Processing sheet with id=AB6, first strand: chain 'H' and resid 309 through 313 removed outlier: 3.596A pdb=" N SER H 311 " --> pdb=" O GLY H 325 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 358 through 361 Processing sheet with id=AB8, first strand: chain 'H' and resid 399 through 400 Processing sheet with id=AB9, first strand: chain 'H' and resid 408 through 412 removed outlier: 3.983A pdb=" N SER H 410 " --> pdb=" O GLY H 424 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 480 through 483 Processing sheet with id=AC2, first strand: chain 'H' and resid 501 through 506 removed outlier: 4.016A pdb=" N CYS H 516 " --> pdb=" O ASP H 524 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASP H 518 " --> pdb=" O ARG H 522 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ARG H 522 " --> pdb=" O ASP H 518 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'd' and resid 11 through 13 removed outlier: 4.019A pdb=" N ASP d 12 " --> pdb=" O PHE d 73 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE d 73 " --> pdb=" O ASP d 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'd' and resid 76 through 78 Processing sheet with id=AC5, first strand: chain 'e' and resid 722 through 725 removed outlier: 3.685A pdb=" N VAL e 725 " --> pdb=" O GLY e 730 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N GLY e 730 " --> pdb=" O VAL e 725 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'f' and resid 719 through 723 Processing sheet with id=AC7, first strand: chain 'g' and resid 129 through 132 removed outlier: 3.754A pdb=" N TYR g 130 " --> pdb=" O HIS i 68 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N HIS i 68 " --> pdb=" O TYR g 130 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'h' and resid 120 through 121 removed outlier: 3.878A pdb=" N VAL h 120 " --> pdb=" O THR v 79 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR v 79 " --> pdb=" O VAL h 120 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER k 107 " --> pdb=" O THR k 66 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL k 106 " --> pdb=" O VAL k 95 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL k 95 " --> pdb=" O VAL k 106 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA k 108 " --> pdb=" O CYS k 93 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N CYS k 93 " --> pdb=" O ALA k 108 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'h' and resid 120 through 121 removed outlier: 3.878A pdb=" N VAL h 120 " --> pdb=" O THR v 79 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR v 79 " --> pdb=" O VAL h 120 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'i' and resid 6 through 7 removed outlier: 3.912A pdb=" N PHE i 76 " --> pdb=" O ILE i 83 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL i 81 " --> pdb=" O LEU i 78 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'k' and resid 79 through 83 removed outlier: 4.021A pdb=" N LEU v 111 " --> pdb=" O LYS v 62 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL v 68 " --> pdb=" O ILE v 105 " (cutoff:3.500A) 2267 hydrogen bonds defined for protein. 6663 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: 5.38 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 4734 1.29 - 1.35: 4706 1.35 - 1.42: 0 1.42 - 1.48: 4733 1.48 - 1.55: 7048 Bond restraints: 21221 Sorted by residual: bond pdb=" C SER B 140 " pdb=" N ARG B 141 " ideal model delta sigma weight residual 1.332 1.316 0.016 1.22e-02 6.72e+03 1.65e+00 bond pdb=" C LYS f1242 " pdb=" O LYS f1242 " ideal model delta sigma weight residual 1.237 1.223 0.014 1.17e-02 7.31e+03 1.45e+00 bond pdb=" CA VAL f1244 " pdb=" C VAL f1244 " ideal model delta sigma weight residual 1.524 1.538 -0.015 1.30e-02 5.92e+03 1.27e+00 bond pdb=" CA THR A 139 " pdb=" CB THR A 139 " ideal model delta sigma weight residual 1.538 1.525 0.013 1.22e-02 6.72e+03 1.22e+00 bond pdb=" N ARG B 141 " pdb=" CA ARG B 141 " ideal model delta sigma weight residual 1.462 1.451 0.011 9.90e-03 1.02e+04 1.15e+00 ... (remaining 21216 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 27982 1.92 - 3.84: 213 3.84 - 5.76: 11 5.76 - 7.68: 4 7.68 - 9.60: 2 Bond angle restraints: 28212 Sorted by residual: angle pdb=" C VAL C 345 " pdb=" N ARG C 346 " pdb=" CA ARG C 346 " ideal model delta sigma weight residual 121.54 130.36 -8.82 1.91e+00 2.74e-01 2.13e+01 angle pdb=" N LEU A 42 " pdb=" CA LEU A 42 " pdb=" C LEU A 42 " ideal model delta sigma weight residual 110.80 120.40 -9.60 2.13e+00 2.20e-01 2.03e+01 angle pdb=" N VAL e 805 " pdb=" CA VAL e 805 " pdb=" C VAL e 805 " ideal model delta sigma weight residual 111.91 108.33 3.58 8.90e-01 1.26e+00 1.62e+01 angle pdb=" N GLY C 61 " pdb=" CA GLY C 61 " pdb=" C GLY C 61 " ideal model delta sigma weight residual 110.20 115.48 -5.28 1.32e+00 5.74e-01 1.60e+01 angle pdb=" N VAL f1236 " pdb=" CA VAL f1236 " pdb=" C VAL f1236 " ideal model delta sigma weight residual 109.34 116.85 -7.51 2.08e+00 2.31e-01 1.30e+01 ... (remaining 28207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.79: 8676 5.79 - 11.58: 583 11.58 - 17.36: 64 17.36 - 23.15: 6 23.15 - 28.94: 3 Dihedral angle restraints: 9332 sinusoidal: 0 harmonic: 9332 Sorted by residual: dihedral pdb=" CA ALA G 127 " pdb=" C ALA G 127 " pdb=" N ASP G 128 " pdb=" CA ASP G 128 " ideal model delta harmonic sigma weight residual -180.00 -151.06 -28.94 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA LYS A 129 " pdb=" C LYS A 129 " pdb=" N PRO A 130 " pdb=" CA PRO A 130 " ideal model delta harmonic sigma weight residual -180.00 -151.79 -28.21 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA SER G 132 " pdb=" C SER G 132 " pdb=" N SER G 133 " pdb=" CA SER G 133 " ideal model delta harmonic sigma weight residual 180.00 156.84 23.16 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 9329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1323 0.028 - 0.056: 566 0.056 - 0.084: 208 0.084 - 0.112: 183 0.112 - 0.140: 33 Chirality restraints: 2313 Sorted by residual: chirality pdb=" CA ILE d 74 " pdb=" N ILE d 74 " pdb=" C ILE d 74 " pdb=" CB ILE d 74 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA GLU A 43 " pdb=" N GLU A 43 " pdb=" C GLU A 43 " pdb=" CB GLU A 43 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA LEU A 42 " pdb=" N LEU A 42 " pdb=" C LEU A 42 " pdb=" CB LEU A 42 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.14 2.00e-01 2.50e+01 4.57e-01 ... (remaining 2310 not shown) Planarity restraints: 4706 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 129 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C LYS A 129 " -0.031 2.00e-02 2.50e+03 pdb=" O LYS A 129 " 0.012 2.00e-02 2.50e+03 pdb=" N PRO A 130 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 129 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.35e+00 pdb=" C LYS G 129 " 0.027 2.00e-02 2.50e+03 pdb=" O LYS G 129 " -0.010 2.00e-02 2.50e+03 pdb=" N PRO G 130 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU G 135 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.66e+00 pdb=" C LEU G 135 " 0.022 2.00e-02 2.50e+03 pdb=" O LEU G 135 " -0.008 2.00e-02 2.50e+03 pdb=" N ARG G 136 " -0.008 2.00e-02 2.50e+03 ... (remaining 4703 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 6419 2.80 - 3.32: 20234 3.32 - 3.85: 32754 3.85 - 4.37: 29409 4.37 - 4.90: 53013 Nonbonded interactions: 141829 Sorted by model distance: nonbonded pdb=" O ASP D 247 " pdb=" N SER D 251 " model vdw 2.269 3.120 nonbonded pdb=" O LYS A 129 " pdb=" N GLY G 45 " model vdw 2.277 3.120 nonbonded pdb=" N LEU A 42 " pdb=" O ASP G 126 " model vdw 2.286 3.120 nonbonded pdb=" N SER H 257 " pdb=" O SER H 272 " model vdw 2.294 3.120 nonbonded pdb=" O ALA H 308 " pdb=" N TYR H 327 " model vdw 2.304 3.120 ... (remaining 141824 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 184 through 212 or resid 226 through 612)) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'd' selection = chain 'i' } ncs_group { reference = (chain 'e' and (resid 210 through 454 or resid 456 through 1404)) selection = (chain 'f' and (name N or name CA or name C or name O )) } ncs_group { reference = chain 'g' selection = chain 'h' } ncs_group { reference = chain 'k' selection = chain 'v' } 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: 7.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 24.220 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 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 : 0.002 0.020 21221 Z= 0.166 Angle : 0.481 9.603 28212 Z= 0.314 Chirality : 0.044 0.140 2313 Planarity : 0.002 0.018 4706 Dihedral : 4.243 28.938 4706 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.50 % Favored : 92.39 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.04 % 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 (0.12), residues: 4678 helix: 2.48 (0.09), residues: 2587 sheet: -2.70 (0.26), residues: 359 loop : -2.36 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 101 PHE 0.000 0.000 PHE A 68 TRP 0.000 0.000 TRP B 36 Details of bonding type rmsd covalent geometry : bond 0.00221 (21221) covalent geometry : angle 0.48141 (28212) hydrogen bonds : bond 0.11925 ( 2265) hydrogen bonds : angle 5.62111 ( 6663) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9356 Ramachandran restraints generated. 4678 Oldfield, 0 Emsley, 4678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9356 Ramachandran restraints generated. 4678 Oldfield, 0 Emsley, 4678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.836 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.0871 time to fit residues: 18.7918 Evaluate side-chains 108 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 0.3980 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 0.1980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 50.0000 chunk 401 optimal weight: 5.9990 overall best weight: 2.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.117568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.071801 restraints weight = 180362.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.068353 restraints weight = 254992.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.067569 restraints weight = 273220.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.067717 restraints weight = 233115.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.067704 restraints weight = 200334.838| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.0631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.025 21221 Z= 0.112 Angle : 0.369 9.433 28212 Z= 0.232 Chirality : 0.044 0.154 2313 Planarity : 0.002 0.019 4706 Dihedral : 3.845 28.117 4706 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.54 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.04 % 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: 1.27 (0.13), residues: 4678 helix: 3.20 (0.09), residues: 2600 sheet: -2.94 (0.26), residues: 334 loop : -2.29 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 101 PHE 0.000 0.000 PHE A 68 TRP 0.000 0.000 TRP B 36 Details of bonding type rmsd covalent geometry : bond 0.00148 (21221) covalent geometry : angle 0.36866 (28212) hydrogen bonds : bond 0.03806 ( 2265) hydrogen bonds : angle 4.41953 ( 6663) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9356 Ramachandran restraints generated. 4678 Oldfield, 0 Emsley, 4678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9356 Ramachandran restraints generated. 4678 Oldfield, 0 Emsley, 4678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.779 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.0896 time to fit residues: 19.5668 Evaluate side-chains 108 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 44 optimal weight: 4.9990 chunk 186 optimal weight: 50.0000 chunk 403 optimal weight: 10.0000 chunk 293 optimal weight: 40.0000 chunk 288 optimal weight: 10.0000 chunk 169 optimal weight: 9.9990 chunk 415 optimal weight: 5.9990 chunk 70 optimal weight: 20.0000 chunk 266 optimal weight: 3.9990 chunk 129 optimal weight: 30.0000 chunk 107 optimal weight: 20.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.117129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.071400 restraints weight = 181657.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.067848 restraints weight = 274408.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.066994 restraints weight = 289611.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.067238 restraints weight = 256087.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.067141 restraints weight = 225490.067| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21221 Z= 0.203 Angle : 0.448 9.466 28212 Z= 0.292 Chirality : 0.044 0.144 2313 Planarity : 0.003 0.015 4706 Dihedral : 4.279 30.599 4706 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.06 % Favored : 90.87 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.05 (0.13), residues: 4678 helix: 3.02 (0.09), residues: 2603 sheet: -2.91 (0.27), residues: 320 loop : -2.43 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 101 PHE 0.000 0.000 PHE A 68 TRP 0.000 0.000 TRP B 36 Details of bonding type rmsd covalent geometry : bond 0.00273 (21221) covalent geometry : angle 0.44765 (28212) hydrogen bonds : bond 0.04382 ( 2265) hydrogen bonds : angle 4.67466 ( 6663) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9356 Ramachandran restraints generated. 4678 Oldfield, 0 Emsley, 4678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9356 Ramachandran restraints generated. 4678 Oldfield, 0 Emsley, 4678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.734 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.0886 time to fit residues: 19.2650 Evaluate side-chains 108 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 52 optimal weight: 30.0000 chunk 302 optimal weight: 9.9990 chunk 98 optimal weight: 20.0000 chunk 461 optimal weight: 20.0000 chunk 87 optimal weight: 9.9990 chunk 249 optimal weight: 0.3980 chunk 263 optimal weight: 5.9990 chunk 400 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 307 optimal weight: 6.9990 chunk 291 optimal weight: 6.9990 overall best weight: 6.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.117117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.071428 restraints weight = 181414.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.067901 restraints weight = 248368.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.067301 restraints weight = 276483.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.067378 restraints weight = 219127.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.067560 restraints weight = 202801.215| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21221 Z= 0.173 Angle : 0.415 9.724 28212 Z= 0.268 Chirality : 0.044 0.148 2313 Planarity : 0.002 0.013 4706 Dihedral : 4.186 30.620 4706 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.12 % Favored : 91.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.14 (0.13), residues: 4678 helix: 3.14 (0.09), residues: 2592 sheet: -2.78 (0.28), residues: 322 loop : -2.44 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 101 PHE 0.000 0.000 PHE A 68 TRP 0.000 0.000 TRP B 36 Details of bonding type rmsd covalent geometry : bond 0.00232 (21221) covalent geometry : angle 0.41510 (28212) hydrogen bonds : bond 0.04026 ( 2265) hydrogen bonds : angle 4.48138 ( 6663) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9356 Ramachandran restraints generated. 4678 Oldfield, 0 Emsley, 4678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9356 Ramachandran restraints generated. 4678 Oldfield, 0 Emsley, 4678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.838 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.0914 time to fit residues: 19.9272 Evaluate side-chains 108 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 279 optimal weight: 20.0000 chunk 450 optimal weight: 40.0000 chunk 281 optimal weight: 0.9980 chunk 285 optimal weight: 0.9990 chunk 190 optimal weight: 50.0000 chunk 355 optimal weight: 9.9990 chunk 222 optimal weight: 6.9990 chunk 308 optimal weight: 50.0000 chunk 239 optimal weight: 30.0000 chunk 292 optimal weight: 8.9990 chunk 288 optimal weight: 9.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.116992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.071748 restraints weight = 180866.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.068079 restraints weight = 222174.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.067683 restraints weight = 236197.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.067869 restraints weight = 215384.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.067631 restraints weight = 201411.381| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21221 Z= 0.168 Angle : 0.414 9.473 28212 Z= 0.265 Chirality : 0.044 0.145 2313 Planarity : 0.002 0.015 4706 Dihedral : 4.162 29.836 4706 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.32 % Favored : 90.59 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.04 % 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: 1.18 (0.13), residues: 4678 helix: 3.19 (0.09), residues: 2598 sheet: -2.71 (0.30), residues: 294 loop : -2.50 (0.15), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 101 PHE 0.000 0.000 PHE A 68 TRP 0.000 0.000 TRP B 36 Details of bonding type rmsd covalent geometry : bond 0.00225 (21221) covalent geometry : angle 0.41362 (28212) hydrogen bonds : bond 0.04006 ( 2265) hydrogen bonds : angle 4.42456 ( 6663) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9356 Ramachandran restraints generated. 4678 Oldfield, 0 Emsley, 4678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9356 Ramachandran restraints generated. 4678 Oldfield, 0 Emsley, 4678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.866 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.0874 time to fit residues: 19.0221 Evaluate side-chains 108 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 86 optimal weight: 4.9990 chunk 406 optimal weight: 5.9990 chunk 82 optimal weight: 40.0000 chunk 32 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 230 optimal weight: 40.0000 chunk 303 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 466 optimal weight: 50.0000 chunk 421 optimal weight: 9.9990 chunk 246 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.117060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.071580 restraints weight = 180534.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.067973 restraints weight = 237366.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.067337 restraints weight = 262179.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.067449 restraints weight = 238304.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.067465 restraints weight = 205176.146| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21221 Z= 0.154 Angle : 0.400 9.712 28212 Z= 0.255 Chirality : 0.044 0.149 2313 Planarity : 0.002 0.014 4706 Dihedral : 4.075 29.732 4706 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.74 % Favored : 92.15 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.04 % 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: 1.24 (0.13), residues: 4678 helix: 3.29 (0.09), residues: 2587 sheet: -2.76 (0.30), residues: 293 loop : -2.52 (0.15), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 101 PHE 0.000 0.000 PHE A 68 TRP 0.000 0.000 TRP B 36 Details of bonding type rmsd covalent geometry : bond 0.00207 (21221) covalent geometry : angle 0.39950 (28212) hydrogen bonds : bond 0.03828 ( 2265) hydrogen bonds : angle 4.33079 ( 6663) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9356 Ramachandran restraints generated. 4678 Oldfield, 0 Emsley, 4678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9356 Ramachandran restraints generated. 4678 Oldfield, 0 Emsley, 4678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.803 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.0869 time to fit residues: 18.8800 Evaluate side-chains 108 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 277 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 238 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 183 optimal weight: 20.0000 chunk 320 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 457 optimal weight: 120.0000 chunk 383 optimal weight: 0.4980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.117471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.071594 restraints weight = 179123.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.068425 restraints weight = 208087.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.067947 restraints weight = 249216.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.067965 restraints weight = 213897.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.067897 restraints weight = 192643.001| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.014 21221 Z= 0.086 Angle : 0.337 9.338 28212 Z= 0.209 Chirality : 0.043 0.147 2313 Planarity : 0.001 0.012 4706 Dihedral : 3.587 26.516 4706 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.31 % Favored : 93.63 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.04 % 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: 1.68 (0.13), residues: 4678 helix: 3.67 (0.09), residues: 2596 sheet: -2.95 (0.27), residues: 351 loop : -2.28 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 101 PHE 0.000 0.000 PHE A 68 TRP 0.000 0.000 TRP B 36 Details of bonding type rmsd covalent geometry : bond 0.00112 (21221) covalent geometry : angle 0.33735 (28212) hydrogen bonds : bond 0.03244 ( 2265) hydrogen bonds : angle 3.84077 ( 6663) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9356 Ramachandran restraints generated. 4678 Oldfield, 0 Emsley, 4678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9356 Ramachandran restraints generated. 4678 Oldfield, 0 Emsley, 4678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.875 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.0927 time to fit residues: 20.0544 Evaluate side-chains 108 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 68 optimal weight: 20.0000 chunk 225 optimal weight: 5.9990 chunk 354 optimal weight: 8.9990 chunk 429 optimal weight: 10.0000 chunk 431 optimal weight: 30.0000 chunk 357 optimal weight: 4.9990 chunk 102 optimal weight: 40.0000 chunk 403 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 406 optimal weight: 5.9990 chunk 211 optimal weight: 50.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.116806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.071415 restraints weight = 181339.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.068031 restraints weight = 213926.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.067422 restraints weight = 222194.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.067441 restraints weight = 231214.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.067421 restraints weight = 200378.185| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21221 Z= 0.197 Angle : 0.434 9.644 28212 Z= 0.281 Chirality : 0.044 0.151 2313 Planarity : 0.002 0.014 4706 Dihedral : 4.151 27.854 4706 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.51 % Favored : 90.38 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.04 % 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: 1.29 (0.13), residues: 4678 helix: 3.36 (0.09), residues: 2587 sheet: -2.81 (0.28), residues: 313 loop : -2.52 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 101 PHE 0.000 0.000 PHE A 68 TRP 0.000 0.000 TRP B 36 Details of bonding type rmsd covalent geometry : bond 0.00266 (21221) covalent geometry : angle 0.43399 (28212) hydrogen bonds : bond 0.04100 ( 2265) hydrogen bonds : angle 4.42719 ( 6663) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9356 Ramachandran restraints generated. 4678 Oldfield, 0 Emsley, 4678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9356 Ramachandran restraints generated. 4678 Oldfield, 0 Emsley, 4678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.883 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.0885 time to fit residues: 19.2961 Evaluate side-chains 108 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 216 optimal weight: 3.9990 chunk 162 optimal weight: 20.0000 chunk 58 optimal weight: 8.9990 chunk 165 optimal weight: 40.0000 chunk 183 optimal weight: 9.9990 chunk 455 optimal weight: 30.0000 chunk 319 optimal weight: 40.0000 chunk 369 optimal weight: 5.9990 chunk 206 optimal weight: 5.9990 chunk 239 optimal weight: 30.0000 chunk 217 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.116767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.072264 restraints weight = 181204.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.068359 restraints weight = 238569.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.067516 restraints weight = 269146.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.067756 restraints weight = 249335.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.067758 restraints weight = 213132.708| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21221 Z= 0.179 Angle : 0.425 9.800 28212 Z= 0.274 Chirality : 0.044 0.156 2313 Planarity : 0.002 0.012 4706 Dihedral : 4.269 29.068 4706 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.09 % Favored : 90.85 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.04 % 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: 1.12 (0.13), residues: 4678 helix: 3.18 (0.10), residues: 2599 sheet: -2.90 (0.28), residues: 320 loop : -2.56 (0.15), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 101 PHE 0.000 0.000 PHE A 68 TRP 0.000 0.000 TRP B 36 Details of bonding type rmsd covalent geometry : bond 0.00241 (21221) covalent geometry : angle 0.42528 (28212) hydrogen bonds : bond 0.03992 ( 2265) hydrogen bonds : angle 4.46431 ( 6663) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9356 Ramachandran restraints generated. 4678 Oldfield, 0 Emsley, 4678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9356 Ramachandran restraints generated. 4678 Oldfield, 0 Emsley, 4678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.822 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.0900 time to fit residues: 19.6643 Evaluate side-chains 108 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 456 optimal weight: 30.0000 chunk 26 optimal weight: 20.0000 chunk 269 optimal weight: 7.9990 chunk 200 optimal weight: 0.0870 chunk 11 optimal weight: 20.0000 chunk 349 optimal weight: 8.9990 chunk 102 optimal weight: 40.0000 chunk 218 optimal weight: 9.9990 chunk 45 optimal weight: 20.0000 chunk 412 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 overall best weight: 7.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.116442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.071845 restraints weight = 182508.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.068365 restraints weight = 243130.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.067517 restraints weight = 264099.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.067672 restraints weight = 246832.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.067752 restraints weight = 211509.576| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21221 Z= 0.211 Angle : 0.461 9.784 28212 Z= 0.299 Chirality : 0.044 0.157 2313 Planarity : 0.002 0.017 4706 Dihedral : 4.511 30.681 4706 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.75 % Favored : 89.12 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.85 (0.13), residues: 4678 helix: 2.99 (0.10), residues: 2595 sheet: -3.07 (0.27), residues: 320 loop : -2.70 (0.15), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 101 PHE 0.000 0.000 PHE A 68 TRP 0.000 0.000 TRP B 36 Details of bonding type rmsd covalent geometry : bond 0.00284 (21221) covalent geometry : angle 0.46086 (28212) hydrogen bonds : bond 0.04309 ( 2265) hydrogen bonds : angle 4.72644 ( 6663) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9356 Ramachandran restraints generated. 4678 Oldfield, 0 Emsley, 4678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9356 Ramachandran restraints generated. 4678 Oldfield, 0 Emsley, 4678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.768 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.0886 time to fit residues: 19.0740 Evaluate side-chains 108 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 317 optimal weight: 20.0000 chunk 390 optimal weight: 0.6980 chunk 328 optimal weight: 40.0000 chunk 31 optimal weight: 0.0570 chunk 159 optimal weight: 0.8980 chunk 293 optimal weight: 50.0000 chunk 84 optimal weight: 0.0470 chunk 67 optimal weight: 0.9980 chunk 306 optimal weight: 20.0000 chunk 232 optimal weight: 9.9990 chunk 34 optimal weight: 30.0000 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.117357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.072437 restraints weight = 180772.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.068968 restraints weight = 246744.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.068048 restraints weight = 282190.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.068156 restraints weight = 247126.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.068177 restraints weight = 213398.292| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.018 21221 Z= 0.092 Angle : 0.348 9.765 28212 Z= 0.217 Chirality : 0.043 0.160 2313 Planarity : 0.002 0.012 4706 Dihedral : 3.627 27.175 4706 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.45 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.04 % 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: 1.61 (0.13), residues: 4678 helix: 3.62 (0.09), residues: 2602 sheet: -2.85 (0.27), residues: 331 loop : -2.38 (0.15), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 101 PHE 0.000 0.000 PHE A 68 TRP 0.000 0.000 TRP B 36 Details of bonding type rmsd covalent geometry : bond 0.00118 (21221) covalent geometry : angle 0.34795 (28212) hydrogen bonds : bond 0.03253 ( 2265) hydrogen bonds : angle 3.83282 ( 6663) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5703.88 seconds wall clock time: 97 minutes 7.94 seconds (5827.94 seconds total)