Starting phenix.real_space_refine on Tue Jul 29 08:51:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r5h_18915/07_2025/8r5h_18915.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r5h_18915/07_2025/8r5h_18915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r5h_18915/07_2025/8r5h_18915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r5h_18915/07_2025/8r5h_18915.map" model { file = "/net/cci-nas-00/data/ceres_data/8r5h_18915/07_2025/8r5h_18915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r5h_18915/07_2025/8r5h_18915.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 S 71 5.16 5 Cl 1 4.86 5 C 7225 2.51 5 N 1926 2.21 5 O 2051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11277 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4918 Classifications: {'peptide': 631} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 17, 'TRANS': 613} Chain breaks: 3 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 323 Unresolved non-hydrogen dihedrals: 221 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 25, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 180 Chain: "R" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 587 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain breaks: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1396 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 16, 'TRANS': 170} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 80 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "U" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 759 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 93} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 862 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 104} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 816 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 95} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1205 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 13, 'TRANS': 135} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'SY8': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Classifications: {'peptide': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5105 SG CYS R 42 52.292 71.426 64.049 1.00 67.35 S ATOM 5121 SG CYS R 45 49.840 69.266 66.363 1.00 77.17 S ATOM 5339 SG CYS R 83 49.456 72.954 66.113 1.00 81.07 S ATOM 5268 SG CYS R 75 59.869 81.569 57.203 1.00 77.02 S ATOM 5424 SG CYS R 94 58.480 81.685 60.878 1.00 78.76 S ATOM 5177 SG CYS R 53 45.098 70.965 64.633 1.00104.29 S ATOM 5196 SG CYS R 56 41.358 70.236 64.534 1.00113.59 S ATOM 5222 SG CYS R 68 43.244 71.906 61.490 1.00 84.39 S Time building chain proxies: 7.61, per 1000 atoms: 0.67 Number of scatterers: 11277 At special positions: 0 Unit cell: (101.293, 125.978, 173.645, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 Cl 1 17.00 S 71 16.00 O 2051 8.00 N 1926 7.00 C 7225 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 additional links: simple=1, symmetry=0 Simple link: pdb=" C GLY U 75 " - pdb=" N SY8 C1101 " Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.91 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 45 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" ND1 HIS R 77 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 75 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb=" ZN R 203 " pdb="ZN ZN R 203 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 56 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 53 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 68 " Number of angles added : 6 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2800 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 22 sheets defined 48.5% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 12 through 19 Processing helix chain 'A' and resid 21 through 25 Processing helix chain 'A' and resid 33 through 46 removed outlier: 4.157A pdb=" N PHE A 39 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER A 40 " --> pdb=" O ASN A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 78 removed outlier: 5.180A pdb=" N LEU A 77 " --> pdb=" O HIS A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 104 removed outlier: 3.746A pdb=" N GLU A 93 " --> pdb=" O ARG A 89 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR A 94 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR A 100 " --> pdb=" O LYS A 96 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N CYS A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 104 " --> pdb=" O TYR A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 Processing helix chain 'A' and resid 139 through 152 removed outlier: 3.665A pdb=" N LEU A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 170 Processing helix chain 'A' and resid 178 through 189 removed outlier: 3.992A pdb=" N PHE A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 228 removed outlier: 3.784A pdb=" N GLN A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N SER A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Proline residue: A 210 - end of helix Processing helix chain 'A' and resid 235 through 251 removed outlier: 3.700A pdb=" N ARG A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 274 Processing helix chain 'A' and resid 278 through 285 removed outlier: 4.568A pdb=" N HIS A 283 " --> pdb=" O HIS A 279 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ASN A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 303 removed outlier: 4.183A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN A 296 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ALA A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 328 Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'A' and resid 362 through 376 Processing helix chain 'A' and resid 387 through 398 Processing helix chain 'A' and resid 410 through 424 removed outlier: 3.835A pdb=" N SER A 417 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TYR A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 444 Processing helix chain 'A' and resid 453 through 465 Processing helix chain 'A' and resid 470 through 496 removed outlier: 5.254A pdb=" N MET A 476 " --> pdb=" O LYS A 472 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ALA A 484 " --> pdb=" O MET A 480 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ASP A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LYS A 495 " --> pdb=" O ASN A 491 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ASN A 496 " --> pdb=" O ASN A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 547 removed outlier: 5.043A pdb=" N LYS A 535 " --> pdb=" O GLN A 531 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N SER A 536 " --> pdb=" O GLU A 532 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN A 538 " --> pdb=" O GLU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 589 removed outlier: 3.621A pdb=" N PHE A 588 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 603 Processing helix chain 'A' and resid 607 through 619 Processing helix chain 'C' and resid 9 through 22 removed outlier: 5.434A pdb=" N GLU C 22 " --> pdb=" O LYS C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 119 through 132 Processing helix chain 'C' and resid 142 through 154 Processing helix chain 'C' and resid 159 through 179 Processing helix chain 'D' and resid 33 through 38 removed outlier: 4.184A pdb=" N THR D 38 " --> pdb=" O GLU D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 47 Processing helix chain 'D' and resid 67 through 83 removed outlier: 4.099A pdb=" N LYS D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 110 removed outlier: 5.624A pdb=" N LEU D 101 " --> pdb=" O PRO D 97 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N GLU D 102 " --> pdb=" O GLU D 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 35 removed outlier: 5.234A pdb=" N ARG G 29 " --> pdb=" O PHE G 25 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE G 30 " --> pdb=" O GLU G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 41 No H-bonds generated for 'chain 'G' and resid 39 through 41' Processing helix chain 'G' and resid 57 through 60 No H-bonds generated for 'chain 'G' and resid 57 through 60' Processing helix chain 'A' and resid 538 through 547 Processing helix chain 'A' and resid 614 through 618 Processing helix chain 'R' and resid 54 through 57 No H-bonds generated for 'chain 'R' and resid 54 through 57' Processing helix chain 'R' and resid 81 through 90 removed outlier: 4.614A pdb=" N THR R 90 " --> pdb=" O ARG R 86 " (cutoff:3.500A) Processing helix chain 'U' and resid 23 through 34 Processing helix chain 'U' and resid 38 through 40 No H-bonds generated for 'chain 'U' and resid 38 through 40' Processing helix chain 'U' and resid 56 through 59 No H-bonds generated for 'chain 'U' and resid 56 through 59' Processing helix chain 'F' and resid 349 through 365 Processing helix chain 'F' and resid 375 through 377 No H-bonds generated for 'chain 'F' and resid 375 through 377' Processing helix chain 'F' and resid 381 through 386 Processing helix chain 'F' and resid 389 through 394 Processing helix chain 'F' and resid 399 through 409 removed outlier: 3.732A pdb=" N ALA F 409 " --> pdb=" O SER F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 433 removed outlier: 3.981A pdb=" N PHE F 418 " --> pdb=" O ASP F 414 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA F 429 " --> pdb=" O MET F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 456 Processing helix chain 'H' and resid 157 through 170 Processing helix chain 'H' and resid 172 through 178 removed outlier: 5.306A pdb=" N TYR H 175 " --> pdb=" O PRO H 172 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ARG H 176 " --> pdb=" O GLU H 173 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG H 177 " --> pdb=" O ASN H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 190 removed outlier: 4.060A pdb=" N GLU H 186 " --> pdb=" O ARG H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 208 Processing sheet with id=AA3, first strand: chain 'H' and resid 104 through 112 removed outlier: 3.857A pdb=" N THR H 105 " --> pdb=" O ASN H 78 " (cutoff:3.500A) removed outlier: 10.156A pdb=" N ILE H 147 " --> pdb=" O PRO H 71 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLN H 73 " --> pdb=" O ILE H 147 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ALA H 149 " --> pdb=" O GLN H 73 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE H 75 " --> pdb=" O ALA H 149 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE H 151 " --> pdb=" O ILE H 75 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N CYS H 77 " --> pdb=" O ILE H 151 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 95 through 97 removed outlier: 4.958A pdb=" N LEU H 116 " --> pdb=" O LEU H 89 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'C' and resid 40 through 46 No H-bonds generated for sheet with id=9 Processing sheet with id=10, first strand: chain 'C' and resid 57 through 64 No H-bonds generated for sheet with id=10 Processing sheet with id=11, first strand: chain 'C' and resid 74 through 78 No H-bonds generated for sheet with id=11 Processing sheet with id=12, first strand: chain 'U' and resid 2 through 6 No H-bonds generated for sheet with id=12 Processing sheet with id=13, first strand: chain 'U' and resid 12 through 16 No H-bonds generated for sheet with id=13 Processing sheet with id=14, first strand: chain 'U' and resid 42 through 44 No H-bonds generated for sheet with id=14 Processing sheet with id=15, first strand: chain 'U' and resid 66 through 70 No H-bonds generated for sheet with id=15 Processing sheet with id=20, first strand: chain 'A' and resid 507 through 512 No H-bonds generated for sheet with id=20 Processing sheet with id=22, first strand: chain 'A' and resid 552 through 556 No H-bonds generated for sheet with id=22 Processing sheet with id=A, first strand: chain 'A' and resid 561 through 566 removed outlier: 4.350A pdb=" N TYR A 573 " --> pdb=" O MET A 566 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 593 through 594 Processing sheet with id=23, first strand: chain 'R' and resid 70 through 72 No H-bonds generated for sheet with id=23 Processing sheet with id=24, first strand: chain 'R' and resid 78 through 80 No H-bonds generated for sheet with id=24 Processing sheet with id=8, first strand: chain 'C' and resid 28 through 32 No H-bonds generated for sheet with id=8 Processing sheet with id=1, first strand: chain 'G' and resid 42 through 45 No H-bonds generated for sheet with id=1 Processing sheet with id=2, first strand: chain 'G' and resid 73 through 79 No H-bonds generated for sheet with id=2 Processing sheet with id=3, first strand: chain 'G' and resid 2 through 9 No H-bonds generated for sheet with id=3 Processing sheet with id=4, first strand: chain 'G' and resid 12 through 19 No H-bonds generated for sheet with id=4 Processing sheet with id=6, first strand: chain 'D' and resid 18 through 23 No H-bonds generated for sheet with id=6 Processing sheet with id=7, first strand: chain 'D' and resid 59 through 62 No H-bonds generated for sheet with id=7 449 hydrogen bonds defined for protein. 1341 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.89 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3639 1.34 - 1.46: 2386 1.46 - 1.58: 5394 1.58 - 1.70: 0 1.70 - 1.82: 117 Bond restraints: 11536 Sorted by residual: bond pdb=" CBZ 759 H 301 " pdb=" NBI 759 H 301 " ideal model delta sigma weight residual 1.410 1.325 0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" CBX 759 H 301 " pdb=" CCI 759 H 301 " ideal model delta sigma weight residual 1.475 1.430 0.045 2.00e-02 2.50e+03 5.16e+00 bond pdb=" C LEU A 308 " pdb=" N PRO A 309 " ideal model delta sigma weight residual 1.334 1.362 -0.027 1.51e-02 4.39e+03 3.28e+00 bond pdb=" CBZ 759 H 301 " pdb=" CCH 759 H 301 " ideal model delta sigma weight residual 1.343 1.377 -0.034 2.00e-02 2.50e+03 2.95e+00 bond pdb=" C SER A 209 " pdb=" N PRO A 210 " ideal model delta sigma weight residual 1.335 1.359 -0.023 1.36e-02 5.41e+03 2.91e+00 ... (remaining 11531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 15044 1.55 - 3.09: 528 3.09 - 4.64: 79 4.64 - 6.18: 27 6.18 - 7.73: 7 Bond angle restraints: 15685 Sorted by residual: angle pdb=" N LEU A 473 " pdb=" CA LEU A 473 " pdb=" C LEU A 473 " ideal model delta sigma weight residual 113.18 106.05 7.13 1.33e+00 5.65e-01 2.87e+01 angle pdb=" N ARG H 177 " pdb=" CA ARG H 177 " pdb=" C ARG H 177 " ideal model delta sigma weight residual 114.09 106.57 7.52 1.55e+00 4.16e-01 2.35e+01 angle pdb=" C GLU D 54 " pdb=" CA GLU D 54 " pdb=" CB GLU D 54 " ideal model delta sigma weight residual 115.89 110.43 5.46 1.32e+00 5.74e-01 1.71e+01 angle pdb=" N GLU A 541 " pdb=" CA GLU A 541 " pdb=" CB GLU A 541 " ideal model delta sigma weight residual 110.12 115.68 -5.56 1.47e+00 4.63e-01 1.43e+01 angle pdb=" N PHE F 365 " pdb=" CA PHE F 365 " pdb=" C PHE F 365 " ideal model delta sigma weight residual 112.57 108.62 3.95 1.13e+00 7.83e-01 1.22e+01 ... (remaining 15680 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.36: 6676 27.36 - 54.73: 276 54.73 - 82.09: 16 82.09 - 109.45: 0 109.45 - 136.81: 3 Dihedral angle restraints: 6971 sinusoidal: 2676 harmonic: 4295 Sorted by residual: dihedral pdb=" CA HIS A 73 " pdb=" C HIS A 73 " pdb=" N LYS A 74 " pdb=" CA LYS A 74 " ideal model delta harmonic sigma weight residual 180.00 154.79 25.21 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA CYS F 368 " pdb=" C CYS F 368 " pdb=" N HIS F 369 " pdb=" CA HIS F 369 " ideal model delta harmonic sigma weight residual 180.00 155.70 24.30 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" C SY8 C1101 " pdb=" C1 SY8 C1101 " pdb=" C2 SY8 C1101 " pdb=" C3 SY8 C1101 " ideal model delta sinusoidal sigma weight residual 62.79 -160.40 -136.81 1 3.00e+01 1.11e-03 1.84e+01 ... (remaining 6968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1481 0.054 - 0.107: 261 0.107 - 0.161: 31 0.161 - 0.215: 0 0.215 - 0.269: 1 Chirality restraints: 1774 Sorted by residual: chirality pdb=" CCN 759 H 301 " pdb=" CBW 759 H 301 " pdb=" CCQ 759 H 301 " pdb=" NBN 759 H 301 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA VAL A 191 " pdb=" N VAL A 191 " pdb=" C VAL A 191 " pdb=" CB VAL A 191 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CA ARG A 75 " pdb=" N ARG A 75 " pdb=" C ARG A 75 " pdb=" CB ARG A 75 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.52e-01 ... (remaining 1771 not shown) Planarity restraints: 2007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 255 " -0.072 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO A 256 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO A 256 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 256 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" N 759 H 301 " 0.016 2.00e-02 2.50e+03 1.96e-02 5.76e+00 pdb=" CA 759 H 301 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 759 H 301 " -0.026 2.00e-02 2.50e+03 pdb=" CBW 759 H 301 " 0.013 2.00e-02 2.50e+03 pdb=" CCN 759 H 301 " 0.013 2.00e-02 2.50e+03 pdb=" OAK 759 H 301 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR H 98 " 0.036 5.00e-02 4.00e+02 5.41e-02 4.68e+00 pdb=" N PRO H 99 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO H 99 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO H 99 " 0.030 5.00e-02 4.00e+02 ... (remaining 2004 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 11 2.34 - 2.98: 5512 2.98 - 3.62: 15895 3.62 - 4.26: 22556 4.26 - 4.90: 38549 Nonbonded interactions: 82523 Sorted by model distance: nonbonded pdb=" SG CYS F 368 " pdb=" C SY8 C1101 " model vdw 1.705 3.820 nonbonded pdb=" OD2 ASP R 97 " pdb="ZN ZN R 202 " model vdw 1.992 2.230 nonbonded pdb=" OG1 THR A 520 " pdb=" OH TYR A 558 " model vdw 2.250 3.040 nonbonded pdb=" OD1 ASP A 633 " pdb=" OG SER A 636 " model vdw 2.252 3.040 nonbonded pdb=" NE2 GLN A 581 " pdb=" OG SER A 616 " model vdw 2.272 3.120 ... (remaining 82518 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.970 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.030 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 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 : 0.004 0.273 11550 Z= 0.195 Angle : 0.702 7.796 15693 Z= 0.402 Chirality : 0.041 0.269 1774 Planarity : 0.005 0.110 2006 Dihedral : 14.132 136.812 4170 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.23), residues: 1413 helix: 1.19 (0.21), residues: 652 sheet: -0.92 (0.49), residues: 116 loop : -1.97 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 374 HIS 0.007 0.001 HIS A 71 PHE 0.015 0.001 PHE D 52 TYR 0.017 0.001 TYR A 194 ARG 0.008 0.000 ARG A 442 Details of bonding type rmsd link_TRANS : bond 0.01047 ( 1) link_TRANS : angle 3.77714 ( 2) hydrogen bonds : bond 0.09552 ( 442) hydrogen bonds : angle 4.72389 ( 1341) metal coordination : bond 0.08425 ( 11) metal coordination : angle 4.60112 ( 6) covalent geometry : bond 0.00331 (11536) covalent geometry : angle 0.69533 (15685) Misc. bond : bond 0.04324 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 1.316 Fit side-chains REVERT: A 74 LYS cc_start: 0.7452 (ttpp) cc_final: 0.7219 (ttpp) REVERT: A 206 ILE cc_start: 0.8104 (tt) cc_final: 0.7880 (tt) REVERT: A 369 ASP cc_start: 0.6902 (m-30) cc_final: 0.6577 (m-30) REVERT: A 608 LYS cc_start: 0.8425 (ptpp) cc_final: 0.8223 (ptpp) REVERT: C 14 MET cc_start: 0.6235 (ptp) cc_final: 0.5834 (ptp) REVERT: F 364 MET cc_start: 0.5728 (ttm) cc_final: 0.5495 (ttm) REVERT: G 77 LEU cc_start: 0.7922 (tp) cc_final: 0.7581 (tp) REVERT: H 69 ARG cc_start: 0.7834 (mtm110) cc_final: 0.7634 (mtm110) REVERT: H 72 SER cc_start: 0.8067 (p) cc_final: 0.7831 (p) REVERT: H 136 PHE cc_start: 0.7730 (t80) cc_final: 0.7343 (t80) REVERT: H 202 THR cc_start: 0.6959 (m) cc_final: 0.6696 (m) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.2947 time to fit residues: 87.6722 Evaluate side-chains 209 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 255 HIS A 276 GLN A 463 GLN F 447 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.156388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.130849 restraints weight = 16634.689| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.64 r_work: 0.3587 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3587 r_free = 0.3587 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3587 r_free = 0.3587 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 11550 Z= 0.206 Angle : 0.636 9.137 15693 Z= 0.327 Chirality : 0.044 0.309 1774 Planarity : 0.006 0.101 2006 Dihedral : 9.565 172.554 1636 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 1.39 % Allowed : 8.81 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.22), residues: 1413 helix: 0.95 (0.20), residues: 661 sheet: -1.04 (0.48), residues: 119 loop : -2.10 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 374 HIS 0.009 0.002 HIS R 77 PHE 0.032 0.002 PHE A 350 TYR 0.014 0.002 TYR D 79 ARG 0.005 0.000 ARG H 177 Details of bonding type rmsd link_TRANS : bond 0.00050 ( 1) link_TRANS : angle 0.20869 ( 2) hydrogen bonds : bond 0.06325 ( 442) hydrogen bonds : angle 4.41613 ( 1341) metal coordination : bond 0.01745 ( 11) metal coordination : angle 2.91520 ( 6) covalent geometry : bond 0.00478 (11536) covalent geometry : angle 0.63328 (15685) Misc. bond : bond 0.00111 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 215 time to evaluate : 1.195 Fit side-chains revert: symmetry clash REVERT: A 41 ASP cc_start: 0.7889 (m-30) cc_final: 0.7676 (m-30) REVERT: A 74 LYS cc_start: 0.7823 (ttpp) cc_final: 0.7615 (ttpp) REVERT: A 206 ILE cc_start: 0.8203 (tt) cc_final: 0.7938 (tt) REVERT: A 389 GLU cc_start: 0.8024 (mp0) cc_final: 0.7776 (mp0) REVERT: A 620 VAL cc_start: 0.8530 (m) cc_final: 0.7961 (m) REVERT: A 622 MET cc_start: 0.7507 (mmm) cc_final: 0.6634 (mpp) REVERT: R 27 TRP cc_start: 0.7335 (t60) cc_final: 0.7104 (t60) REVERT: C 14 MET cc_start: 0.6700 (ptp) cc_final: 0.6320 (ptp) REVERT: D 17 MET cc_start: 0.6623 (tpp) cc_final: 0.6277 (tpp) REVERT: G 77 LEU cc_start: 0.8229 (tp) cc_final: 0.7906 (tp) REVERT: H 69 ARG cc_start: 0.8140 (mtm110) cc_final: 0.7841 (mtm110) REVERT: H 72 SER cc_start: 0.8148 (p) cc_final: 0.7935 (p) outliers start: 16 outliers final: 7 residues processed: 219 average time/residue: 0.2940 time to fit residues: 85.5698 Evaluate side-chains 211 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 204 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain H residue 152 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 125 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 97 optimal weight: 0.5980 chunk 114 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 0.3980 chunk 58 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 81 optimal weight: 0.1980 chunk 64 optimal weight: 0.3980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 255 HIS A 377 ASN A 463 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.158162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.132715 restraints weight = 16771.691| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.69 r_work: 0.3613 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3614 r_free = 0.3614 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3614 r_free = 0.3614 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11550 Z= 0.125 Angle : 0.555 7.305 15693 Z= 0.282 Chirality : 0.041 0.309 1774 Planarity : 0.005 0.091 2006 Dihedral : 9.439 177.664 1636 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 2.01 % Allowed : 11.42 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.22), residues: 1413 helix: 1.21 (0.21), residues: 660 sheet: -1.08 (0.48), residues: 119 loop : -2.00 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 374 HIS 0.007 0.001 HIS A 255 PHE 0.023 0.001 PHE A 490 TYR 0.019 0.001 TYR A 558 ARG 0.004 0.000 ARG H 200 Details of bonding type rmsd link_TRANS : bond 0.00021 ( 1) link_TRANS : angle 0.02134 ( 2) hydrogen bonds : bond 0.05014 ( 442) hydrogen bonds : angle 4.20575 ( 1341) metal coordination : bond 0.01686 ( 11) metal coordination : angle 2.79161 ( 6) covalent geometry : bond 0.00281 (11536) covalent geometry : angle 0.55195 (15685) Misc. bond : bond 0.00014 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 205 time to evaluate : 1.319 Fit side-chains revert: symmetry clash REVERT: A 206 ILE cc_start: 0.8166 (tt) cc_final: 0.7900 (tt) REVERT: A 389 GLU cc_start: 0.7954 (mp0) cc_final: 0.7644 (mp0) REVERT: R 27 TRP cc_start: 0.7306 (t60) cc_final: 0.7015 (t60) REVERT: C 14 MET cc_start: 0.6685 (ptp) cc_final: 0.6287 (ptp) REVERT: D 17 MET cc_start: 0.6560 (tpp) cc_final: 0.6249 (tpp) REVERT: G 77 LEU cc_start: 0.8230 (tp) cc_final: 0.7891 (tp) REVERT: H 69 ARG cc_start: 0.8126 (mtm110) cc_final: 0.7872 (mtm110) REVERT: H 72 SER cc_start: 0.8152 (p) cc_final: 0.7935 (p) REVERT: H 136 PHE cc_start: 0.7795 (t80) cc_final: 0.7379 (t80) outliers start: 23 outliers final: 15 residues processed: 214 average time/residue: 0.2968 time to fit residues: 84.5173 Evaluate side-chains 210 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 195 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 50 MET Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain H residue 152 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 109 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 72 optimal weight: 0.0970 chunk 50 optimal weight: 5.9990 chunk 116 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 117 optimal weight: 0.0030 chunk 130 optimal weight: 1.9990 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 109 ASN A 276 GLN A 377 ASN A 463 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.158896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.133286 restraints weight = 16559.283| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.41 r_work: 0.3627 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3463 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3463 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11550 Z= 0.118 Angle : 0.546 7.181 15693 Z= 0.275 Chirality : 0.040 0.309 1774 Planarity : 0.005 0.087 2006 Dihedral : 9.269 176.336 1636 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 2.35 % Allowed : 12.03 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.23), residues: 1413 helix: 1.36 (0.21), residues: 657 sheet: -1.12 (0.48), residues: 119 loop : -1.94 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 374 HIS 0.003 0.001 HIS A 71 PHE 0.026 0.001 PHE A 350 TYR 0.014 0.001 TYR D 79 ARG 0.005 0.000 ARG H 177 Details of bonding type rmsd link_TRANS : bond 0.00013 ( 1) link_TRANS : angle 0.03131 ( 2) hydrogen bonds : bond 0.04780 ( 442) hydrogen bonds : angle 4.10210 ( 1341) metal coordination : bond 0.01601 ( 11) metal coordination : angle 2.82703 ( 6) covalent geometry : bond 0.00266 (11536) covalent geometry : angle 0.54285 (15685) Misc. bond : bond 0.00017 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 204 time to evaluate : 1.307 Fit side-chains revert: symmetry clash REVERT: A 76 VAL cc_start: 0.8048 (t) cc_final: 0.7798 (t) REVERT: A 206 ILE cc_start: 0.8226 (tt) cc_final: 0.7952 (tt) REVERT: A 537 VAL cc_start: 0.6306 (OUTLIER) cc_final: 0.4688 (p) REVERT: R 27 TRP cc_start: 0.7413 (t60) cc_final: 0.7152 (t60) REVERT: C 14 MET cc_start: 0.6957 (ptp) cc_final: 0.6544 (ptp) REVERT: C 81 MET cc_start: 0.5978 (tpt) cc_final: 0.5124 (tpt) REVERT: C 118 GLN cc_start: 0.6918 (mm-40) cc_final: 0.6536 (mm-40) REVERT: G 77 LEU cc_start: 0.8317 (tp) cc_final: 0.7987 (tp) REVERT: H 69 ARG cc_start: 0.8229 (mtm110) cc_final: 0.7962 (mtm110) REVERT: H 136 PHE cc_start: 0.7784 (t80) cc_final: 0.7370 (t80) outliers start: 27 outliers final: 15 residues processed: 217 average time/residue: 0.2874 time to fit residues: 83.9463 Evaluate side-chains 213 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 197 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 168 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 39 optimal weight: 0.0770 chunk 119 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 77 optimal weight: 0.0020 chunk 30 optimal weight: 0.7980 overall best weight: 0.4946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 276 GLN A 463 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.159010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.134139 restraints weight = 16492.929| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.46 r_work: 0.3626 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11550 Z= 0.130 Angle : 0.563 9.496 15693 Z= 0.283 Chirality : 0.041 0.313 1774 Planarity : 0.005 0.084 2006 Dihedral : 9.244 176.951 1636 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.79 % Allowed : 12.90 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.23), residues: 1413 helix: 1.34 (0.21), residues: 657 sheet: -1.14 (0.48), residues: 119 loop : -1.91 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 374 HIS 0.004 0.001 HIS R 77 PHE 0.029 0.001 PHE A 350 TYR 0.018 0.001 TYR A 558 ARG 0.005 0.000 ARG H 177 Details of bonding type rmsd link_TRANS : bond 0.00008 ( 1) link_TRANS : angle 0.02606 ( 2) hydrogen bonds : bond 0.04942 ( 442) hydrogen bonds : angle 4.12053 ( 1341) metal coordination : bond 0.01632 ( 11) metal coordination : angle 2.87467 ( 6) covalent geometry : bond 0.00299 (11536) covalent geometry : angle 0.56041 (15685) Misc. bond : bond 0.00016 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 2.108 Fit side-chains revert: symmetry clash REVERT: A 76 VAL cc_start: 0.8087 (OUTLIER) cc_final: 0.7829 (t) REVERT: A 192 GLU cc_start: 0.8546 (pt0) cc_final: 0.8206 (pt0) REVERT: A 206 ILE cc_start: 0.8236 (tt) cc_final: 0.7965 (tt) REVERT: R 27 TRP cc_start: 0.7418 (t60) cc_final: 0.7157 (t60) REVERT: C 14 MET cc_start: 0.6958 (ptp) cc_final: 0.6549 (ptp) REVERT: C 81 MET cc_start: 0.5881 (tpt) cc_final: 0.5052 (tpt) REVERT: C 118 GLN cc_start: 0.6989 (mm-40) cc_final: 0.6568 (mm-40) REVERT: G 77 LEU cc_start: 0.8297 (tp) cc_final: 0.7963 (tp) REVERT: H 136 PHE cc_start: 0.7815 (t80) cc_final: 0.7387 (t80) outliers start: 32 outliers final: 20 residues processed: 218 average time/residue: 0.3202 time to fit residues: 94.2438 Evaluate side-chains 219 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 198 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 168 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 10 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 79 optimal weight: 0.2980 chunk 140 optimal weight: 0.0870 chunk 48 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 276 GLN A 463 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.158274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.133250 restraints weight = 16649.511| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.46 r_work: 0.3614 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3450 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3450 r_free = 0.3450 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3450 r_free = 0.3450 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3450 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11550 Z= 0.144 Angle : 0.574 8.869 15693 Z= 0.288 Chirality : 0.041 0.317 1774 Planarity : 0.005 0.082 2006 Dihedral : 9.254 176.926 1636 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 2.70 % Allowed : 13.34 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.23), residues: 1413 helix: 1.25 (0.21), residues: 667 sheet: -1.11 (0.50), residues: 114 loop : -1.97 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 374 HIS 0.006 0.001 HIS R 77 PHE 0.018 0.001 PHE A 543 TYR 0.015 0.001 TYR D 79 ARG 0.006 0.000 ARG H 177 Details of bonding type rmsd link_TRANS : bond 0.00001 ( 1) link_TRANS : angle 0.03391 ( 2) hydrogen bonds : bond 0.05247 ( 442) hydrogen bonds : angle 4.13290 ( 1341) metal coordination : bond 0.01792 ( 11) metal coordination : angle 3.03164 ( 6) covalent geometry : bond 0.00333 (11536) covalent geometry : angle 0.57124 (15685) Misc. bond : bond 0.00019 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 1.341 Fit side-chains revert: symmetry clash REVERT: A 76 VAL cc_start: 0.8109 (t) cc_final: 0.7843 (t) REVERT: A 192 GLU cc_start: 0.8565 (pt0) cc_final: 0.8197 (pt0) REVERT: A 206 ILE cc_start: 0.8251 (tt) cc_final: 0.7964 (tt) REVERT: A 265 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7465 (tm-30) REVERT: A 541 GLU cc_start: 0.6875 (mt-10) cc_final: 0.6544 (tt0) REVERT: R 27 TRP cc_start: 0.7452 (t60) cc_final: 0.7225 (t60) REVERT: C 14 MET cc_start: 0.6961 (ptp) cc_final: 0.6577 (ptp) REVERT: C 81 MET cc_start: 0.5830 (tpt) cc_final: 0.5040 (tpt) REVERT: C 118 GLN cc_start: 0.7073 (mm-40) cc_final: 0.6639 (mm-40) REVERT: G 77 LEU cc_start: 0.8292 (tp) cc_final: 0.7946 (tp) REVERT: H 69 ARG cc_start: 0.8196 (mtm110) cc_final: 0.7991 (mtm110) REVERT: H 136 PHE cc_start: 0.7799 (t80) cc_final: 0.7374 (t80) REVERT: H 155 VAL cc_start: 0.7046 (t) cc_final: 0.6742 (p) REVERT: H 203 GLN cc_start: 0.6724 (OUTLIER) cc_final: 0.6043 (mp10) outliers start: 31 outliers final: 22 residues processed: 225 average time/residue: 0.3326 time to fit residues: 101.9821 Evaluate side-chains 230 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 207 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 203 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 122 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 97 optimal weight: 0.3980 chunk 79 optimal weight: 0.0070 chunk 118 optimal weight: 0.5980 chunk 128 optimal weight: 0.8980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 276 GLN A 463 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.157950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.133092 restraints weight = 16704.743| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.49 r_work: 0.3618 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3455 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11550 Z= 0.136 Angle : 0.571 8.082 15693 Z= 0.287 Chirality : 0.041 0.318 1774 Planarity : 0.005 0.081 2006 Dihedral : 9.167 176.300 1636 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.79 % Allowed : 13.69 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.23), residues: 1413 helix: 1.26 (0.21), residues: 667 sheet: -1.12 (0.50), residues: 114 loop : -1.96 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 374 HIS 0.004 0.001 HIS R 77 PHE 0.033 0.001 PHE A 350 TYR 0.018 0.001 TYR A 558 ARG 0.006 0.000 ARG H 177 Details of bonding type rmsd link_TRANS : bond 0.00004 ( 1) link_TRANS : angle 0.03530 ( 2) hydrogen bonds : bond 0.05067 ( 442) hydrogen bonds : angle 4.13225 ( 1341) metal coordination : bond 0.01784 ( 11) metal coordination : angle 3.10353 ( 6) covalent geometry : bond 0.00313 (11536) covalent geometry : angle 0.56745 (15685) Misc. bond : bond 0.00018 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 211 time to evaluate : 1.315 Fit side-chains revert: symmetry clash REVERT: A 76 VAL cc_start: 0.8099 (t) cc_final: 0.7841 (t) REVERT: A 192 GLU cc_start: 0.8565 (pt0) cc_final: 0.8177 (pt0) REVERT: A 206 ILE cc_start: 0.8248 (tt) cc_final: 0.7965 (tt) REVERT: A 265 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7468 (tm-30) REVERT: A 361 ASP cc_start: 0.7455 (t0) cc_final: 0.7189 (m-30) REVERT: A 389 GLU cc_start: 0.8180 (mp0) cc_final: 0.7835 (mp0) REVERT: R 27 TRP cc_start: 0.7443 (t60) cc_final: 0.7221 (t60) REVERT: C 14 MET cc_start: 0.6966 (ptp) cc_final: 0.6582 (ptp) REVERT: C 81 MET cc_start: 0.5867 (tpt) cc_final: 0.5078 (tpt) REVERT: C 118 GLN cc_start: 0.7064 (mm-40) cc_final: 0.6629 (mm-40) REVERT: G 77 LEU cc_start: 0.8296 (tp) cc_final: 0.7961 (tp) REVERT: H 136 PHE cc_start: 0.7811 (t80) cc_final: 0.7225 (t80) REVERT: H 155 VAL cc_start: 0.7030 (t) cc_final: 0.6742 (p) REVERT: H 203 GLN cc_start: 0.6703 (OUTLIER) cc_final: 0.6053 (mp10) outliers start: 32 outliers final: 26 residues processed: 223 average time/residue: 0.3636 time to fit residues: 109.9854 Evaluate side-chains 231 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 204 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain U residue 69 LEU Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain F residue 407 LEU Chi-restraints excluded: chain F residue 453 ARG Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 203 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 129 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 125 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 11 optimal weight: 0.0030 chunk 7 optimal weight: 1.9990 chunk 68 optimal weight: 0.0670 overall best weight: 0.4528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 276 GLN A 463 GLN ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.157677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.132810 restraints weight = 16680.721| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.50 r_work: 0.3622 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3457 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11550 Z= 0.127 Angle : 0.578 8.799 15693 Z= 0.290 Chirality : 0.041 0.317 1774 Planarity : 0.005 0.079 2006 Dihedral : 9.101 176.583 1636 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 3.14 % Allowed : 13.69 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.23), residues: 1413 helix: 1.33 (0.21), residues: 659 sheet: -1.10 (0.50), residues: 114 loop : -1.92 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 374 HIS 0.004 0.001 HIS R 77 PHE 0.038 0.001 PHE A 350 TYR 0.016 0.001 TYR D 79 ARG 0.006 0.000 ARG H 177 Details of bonding type rmsd link_TRANS : bond 0.00003 ( 1) link_TRANS : angle 0.04668 ( 2) hydrogen bonds : bond 0.04923 ( 442) hydrogen bonds : angle 4.11451 ( 1341) metal coordination : bond 0.01712 ( 11) metal coordination : angle 3.05234 ( 6) covalent geometry : bond 0.00291 (11536) covalent geometry : angle 0.57484 (15685) Misc. bond : bond 0.00023 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 209 time to evaluate : 1.557 Fit side-chains revert: symmetry clash REVERT: A 76 VAL cc_start: 0.8086 (t) cc_final: 0.7832 (t) REVERT: A 192 GLU cc_start: 0.8552 (pt0) cc_final: 0.8124 (pt0) REVERT: A 206 ILE cc_start: 0.8231 (tt) cc_final: 0.7943 (tt) REVERT: A 265 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7522 (tm-30) REVERT: A 361 ASP cc_start: 0.7410 (t0) cc_final: 0.7156 (m-30) REVERT: A 389 GLU cc_start: 0.8180 (mp0) cc_final: 0.7833 (mp0) REVERT: R 27 TRP cc_start: 0.7430 (t60) cc_final: 0.7179 (t60) REVERT: C 14 MET cc_start: 0.6933 (ptp) cc_final: 0.6551 (ptp) REVERT: C 81 MET cc_start: 0.5913 (tpt) cc_final: 0.5126 (tpt) REVERT: C 118 GLN cc_start: 0.7053 (mm-40) cc_final: 0.6619 (mm-40) REVERT: G 77 LEU cc_start: 0.8296 (tp) cc_final: 0.7966 (tp) REVERT: H 136 PHE cc_start: 0.7805 (t80) cc_final: 0.7228 (t80) REVERT: H 155 VAL cc_start: 0.6999 (t) cc_final: 0.6686 (p) REVERT: H 203 GLN cc_start: 0.6684 (OUTLIER) cc_final: 0.6036 (mp10) outliers start: 36 outliers final: 28 residues processed: 225 average time/residue: 0.4240 time to fit residues: 133.0273 Evaluate side-chains 231 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 202 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 50 MET Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain U residue 69 LEU Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain F residue 368 CYS Chi-restraints excluded: chain F residue 453 ARG Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 203 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 50 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 104 optimal weight: 0.4980 chunk 107 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 18 optimal weight: 0.1980 chunk 131 optimal weight: 1.9990 chunk 74 optimal weight: 0.0370 chunk 117 optimal weight: 1.9990 chunk 108 optimal weight: 0.0010 chunk 25 optimal weight: 0.9980 overall best weight: 0.3464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 276 GLN A 463 GLN ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.159125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.134485 restraints weight = 16681.449| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.44 r_work: 0.3637 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11550 Z= 0.116 Angle : 0.581 10.896 15693 Z= 0.289 Chirality : 0.041 0.316 1774 Planarity : 0.005 0.079 2006 Dihedral : 8.970 177.790 1636 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 2.35 % Allowed : 14.04 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.23), residues: 1413 helix: 1.45 (0.21), residues: 655 sheet: -1.09 (0.50), residues: 114 loop : -1.86 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 35 HIS 0.003 0.001 HIS A 73 PHE 0.023 0.001 PHE A 543 TYR 0.015 0.001 TYR D 79 ARG 0.006 0.000 ARG H 177 Details of bonding type rmsd link_TRANS : bond 0.00005 ( 1) link_TRANS : angle 0.05024 ( 2) hydrogen bonds : bond 0.04595 ( 442) hydrogen bonds : angle 4.07249 ( 1341) metal coordination : bond 0.01567 ( 11) metal coordination : angle 2.90986 ( 6) covalent geometry : bond 0.00263 (11536) covalent geometry : angle 0.57801 (15685) Misc. bond : bond 0.00020 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 212 time to evaluate : 1.374 Fit side-chains revert: symmetry clash REVERT: A 76 VAL cc_start: 0.8046 (OUTLIER) cc_final: 0.7813 (t) REVERT: A 206 ILE cc_start: 0.8193 (tt) cc_final: 0.7905 (tt) REVERT: A 265 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7521 (tm-30) REVERT: A 389 GLU cc_start: 0.8157 (mp0) cc_final: 0.7784 (mp0) REVERT: R 27 TRP cc_start: 0.7404 (t60) cc_final: 0.7124 (t60) REVERT: C 14 MET cc_start: 0.6927 (ptp) cc_final: 0.6542 (ptp) REVERT: C 81 MET cc_start: 0.5904 (tpt) cc_final: 0.5087 (tpt) REVERT: C 118 GLN cc_start: 0.6988 (mm-40) cc_final: 0.6562 (mm-40) REVERT: G 77 LEU cc_start: 0.8301 (tp) cc_final: 0.7974 (tp) REVERT: H 136 PHE cc_start: 0.7808 (t80) cc_final: 0.7240 (t80) REVERT: H 155 VAL cc_start: 0.6985 (t) cc_final: 0.6663 (p) REVERT: H 203 GLN cc_start: 0.6673 (OUTLIER) cc_final: 0.6023 (mp10) outliers start: 27 outliers final: 22 residues processed: 223 average time/residue: 0.3088 time to fit residues: 92.2549 Evaluate side-chains 228 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 204 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 50 MET Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain F residue 453 ARG Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 203 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 70 optimal weight: 1.9990 chunk 85 optimal weight: 0.4980 chunk 88 optimal weight: 120.0000 chunk 102 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 101 optimal weight: 0.3980 chunk 51 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 204 GLN A 276 GLN A 463 GLN U 68 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.157863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.132383 restraints weight = 16568.251| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.39 r_work: 0.3614 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3450 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3450 r_free = 0.3450 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3450 r_free = 0.3450 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3450 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11550 Z= 0.148 Angle : 0.600 12.176 15693 Z= 0.302 Chirality : 0.042 0.320 1774 Planarity : 0.005 0.080 2006 Dihedral : 9.029 179.298 1636 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.35 % Allowed : 14.30 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.23), residues: 1413 helix: 1.31 (0.21), residues: 659 sheet: -1.12 (0.51), residues: 114 loop : -1.91 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 374 HIS 0.006 0.001 HIS A 73 PHE 0.021 0.001 PHE A 543 TYR 0.015 0.001 TYR D 79 ARG 0.005 0.000 ARG A 269 Details of bonding type rmsd link_TRANS : bond 0.00010 ( 1) link_TRANS : angle 0.07275 ( 2) hydrogen bonds : bond 0.05245 ( 442) hydrogen bonds : angle 4.08107 ( 1341) metal coordination : bond 0.01831 ( 11) metal coordination : angle 3.04442 ( 6) covalent geometry : bond 0.00344 (11536) covalent geometry : angle 0.59726 (15685) Misc. bond : bond 0.00023 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 212 time to evaluate : 1.263 Fit side-chains revert: symmetry clash REVERT: A 76 VAL cc_start: 0.8065 (t) cc_final: 0.7816 (t) REVERT: A 206 ILE cc_start: 0.8233 (tt) cc_final: 0.7943 (tt) REVERT: A 265 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7526 (tm-30) REVERT: A 361 ASP cc_start: 0.7382 (OUTLIER) cc_final: 0.7049 (m-30) REVERT: A 389 GLU cc_start: 0.8191 (mp0) cc_final: 0.7757 (mp0) REVERT: R 27 TRP cc_start: 0.7439 (t60) cc_final: 0.7191 (t60) REVERT: C 14 MET cc_start: 0.6945 (ptp) cc_final: 0.6551 (ptp) REVERT: C 81 MET cc_start: 0.5879 (tpt) cc_final: 0.5060 (tpt) REVERT: C 118 GLN cc_start: 0.7045 (mm-40) cc_final: 0.6592 (mm-40) REVERT: G 77 LEU cc_start: 0.8308 (tp) cc_final: 0.7969 (tp) REVERT: H 136 PHE cc_start: 0.7818 (t80) cc_final: 0.7199 (t80) REVERT: H 155 VAL cc_start: 0.6993 (t) cc_final: 0.6685 (p) REVERT: H 203 GLN cc_start: 0.6692 (OUTLIER) cc_final: 0.6044 (mp10) outliers start: 27 outliers final: 22 residues processed: 222 average time/residue: 0.2955 time to fit residues: 87.8188 Evaluate side-chains 230 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain F residue 453 ARG Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 203 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 68 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 56 optimal weight: 0.0970 chunk 96 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 276 GLN A 463 GLN ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 68 HIS G 70 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.157467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.132552 restraints weight = 16577.664| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.43 r_work: 0.3609 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3448 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3448 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11550 Z= 0.153 Angle : 0.611 11.914 15693 Z= 0.305 Chirality : 0.042 0.325 1774 Planarity : 0.005 0.080 2006 Dihedral : 8.999 179.360 1636 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.79 % Allowed : 14.21 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.23), residues: 1413 helix: 1.23 (0.21), residues: 664 sheet: -1.13 (0.51), residues: 114 loop : -1.92 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 374 HIS 0.005 0.001 HIS R 77 PHE 0.021 0.001 PHE A 543 TYR 0.015 0.001 TYR D 79 ARG 0.006 0.000 ARG H 177 Details of bonding type rmsd link_TRANS : bond 0.00028 ( 1) link_TRANS : angle 0.06731 ( 2) hydrogen bonds : bond 0.05323 ( 442) hydrogen bonds : angle 4.11780 ( 1341) metal coordination : bond 0.01828 ( 11) metal coordination : angle 3.09999 ( 6) covalent geometry : bond 0.00357 (11536) covalent geometry : angle 0.60774 (15685) Misc. bond : bond 0.00023 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6995.30 seconds wall clock time: 124 minutes 34.90 seconds (7474.90 seconds total)