Starting phenix.real_space_refine on Sat Oct 11 03:13:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r5h_18915/10_2025/8r5h_18915.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r5h_18915/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8r5h_18915/10_2025/8r5h_18915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r5h_18915/10_2025/8r5h_18915.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8r5h_18915/10_2025/8r5h_18915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r5h_18915/10_2025/8r5h_18915.map" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: {'ASP:plan': 8, 'GLU:plan': 25, 'ARG:plan': 4, 'GLN:plan1': 3, 'PHE:plan': 2, 'ASN:plan1': 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: {'ASP:plan': 1, 'ARG:plan': 3, 'HIS:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 2, 'ASN:plan1': 1} 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: {'GLU:plan': 7, 'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2, 'TYR: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: {'ASP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG: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: {'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 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: 3.05, per 1000 atoms: 0.27 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: 0.98 Conformation dependent library (CDL) restraints added in 659.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.38 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: 1.55 Time building geometry restraints manager: 1.26 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: 4.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.950 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.570 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (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 ARG 0.008 0.000 ARG A 442 TYR 0.017 0.001 TYR A 194 PHE 0.015 0.001 PHE D 52 TRP 0.010 0.001 TRP F 374 HIS 0.007 0.001 HIS A 71 Details of bonding type rmsd covalent geometry : bond 0.00331 (11536) covalent geometry : angle 0.69533 (15685) hydrogen bonds : bond 0.09552 ( 442) hydrogen bonds : angle 4.72389 ( 1341) metal coordination : bond 0.08425 ( 11) metal coordination : angle 4.60112 ( 6) Misc. bond : bond 0.04324 ( 2) link_TRANS : bond 0.01047 ( 1) link_TRANS : angle 3.77714 ( 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 : 0.396 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: 0.7832 (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: 0.1332 time to fit residues: 39.6693 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 : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 0.0870 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.0370 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.0470 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.1980 overall best weight: 0.1734 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.161547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.136476 restraints weight = 16862.497| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.55 r_work: 0.3670 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3671 r_free = 0.3671 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3671 r_free = 0.3671 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.0815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11550 Z= 0.104 Angle : 0.541 6.810 15693 Z= 0.273 Chirality : 0.040 0.298 1774 Planarity : 0.005 0.099 2006 Dihedral : 9.181 172.326 1636 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 0.96 % Allowed : 7.85 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.23), residues: 1413 helix: 1.39 (0.21), residues: 657 sheet: -0.83 (0.49), residues: 119 loop : -1.95 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 177 TYR 0.009 0.001 TYR D 79 PHE 0.023 0.001 PHE A 350 TRP 0.008 0.001 TRP F 374 HIS 0.007 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00223 (11536) covalent geometry : angle 0.53931 (15685) hydrogen bonds : bond 0.04293 ( 442) hydrogen bonds : angle 4.16519 ( 1341) metal coordination : bond 0.00990 ( 11) metal coordination : angle 2.02869 ( 6) Misc. bond : bond 0.00257 ( 2) link_TRANS : bond 0.00084 ( 1) link_TRANS : angle 0.25392 ( 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 218 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 207 time to evaluate : 0.433 Fit side-chains REVERT: A 147 TRP cc_start: 0.8024 (t-100) cc_final: 0.7493 (t-100) REVERT: A 206 ILE cc_start: 0.8102 (tt) cc_final: 0.7775 (tt) REVERT: A 369 ASP cc_start: 0.7039 (m-30) cc_final: 0.6765 (m-30) REVERT: A 377 ASN cc_start: 0.7588 (m-40) cc_final: 0.7018 (t0) REVERT: C 14 MET cc_start: 0.6648 (ptp) cc_final: 0.6255 (ptp) REVERT: U 1 MET cc_start: 0.6633 (ppp) cc_final: 0.6383 (ppp) REVERT: D 17 MET cc_start: 0.6481 (tpp) cc_final: 0.6200 (tpp) REVERT: G 77 LEU cc_start: 0.8233 (tp) cc_final: 0.7911 (tp) REVERT: H 72 SER cc_start: 0.8227 (p) cc_final: 0.8023 (p) REVERT: H 136 PHE cc_start: 0.7746 (t80) cc_final: 0.7394 (t80) outliers start: 11 outliers final: 7 residues processed: 209 average time/residue: 0.1394 time to fit residues: 38.8049 Evaluate side-chains 208 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 201 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain R residue 50 MET Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 168 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 86 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 F 447 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.155848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.130238 restraints weight = 16814.453| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.59 r_work: 0.3582 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 11550 Z= 0.210 Angle : 0.631 8.241 15693 Z= 0.325 Chirality : 0.044 0.316 1774 Planarity : 0.005 0.093 2006 Dihedral : 9.714 178.120 1636 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 2.44 % Allowed : 10.20 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.22), residues: 1413 helix: 1.03 (0.20), residues: 662 sheet: -1.01 (0.49), residues: 119 loop : -2.10 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 177 TYR 0.017 0.002 TYR A 259 PHE 0.032 0.002 PHE A 350 TRP 0.012 0.002 TRP R 27 HIS 0.010 0.002 HIS R 77 Details of bonding type rmsd covalent geometry : bond 0.00487 (11536) covalent geometry : angle 0.62805 (15685) hydrogen bonds : bond 0.06499 ( 442) hydrogen bonds : angle 4.35397 ( 1341) metal coordination : bond 0.02152 ( 11) metal coordination : angle 3.11889 ( 6) Misc. bond : bond 0.00041 ( 2) link_TRANS : bond 0.00048 ( 1) link_TRANS : angle 0.02615 ( 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 248 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 220 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 76 VAL cc_start: 0.8100 (t) cc_final: 0.7830 (t) REVERT: A 206 ILE cc_start: 0.8282 (tt) cc_final: 0.8007 (tt) REVERT: A 389 GLU cc_start: 0.8231 (mp0) cc_final: 0.7962 (mp0) REVERT: R 27 TRP cc_start: 0.7465 (t60) cc_final: 0.7260 (t60) REVERT: C 14 MET cc_start: 0.6980 (ptp) cc_final: 0.6597 (ptp) REVERT: D 17 MET cc_start: 0.7009 (tpp) cc_final: 0.6648 (tpp) REVERT: G 77 LEU cc_start: 0.8317 (tp) cc_final: 0.7985 (tp) REVERT: H 136 PHE cc_start: 0.7845 (t80) cc_final: 0.7397 (t80) REVERT: H 155 VAL cc_start: 0.7157 (t) cc_final: 0.6872 (p) outliers start: 28 outliers final: 13 residues processed: 228 average time/residue: 0.1356 time to fit residues: 41.2930 Evaluate side-chains 222 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 209 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 232 CYS Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 585 LEU 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 H residue 152 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 73 optimal weight: 4.9990 chunk 105 optimal weight: 0.3980 chunk 16 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 84 optimal weight: 0.0470 chunk 122 optimal weight: 0.0870 chunk 116 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 overall best weight: 0.2456 ------------------------------------------------------------------------------- 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 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 GLN G 70 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.159552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.134491 restraints weight = 16874.580| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.59 r_work: 0.3639 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3478 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3478 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11550 Z= 0.105 Angle : 0.540 7.299 15693 Z= 0.271 Chirality : 0.040 0.310 1774 Planarity : 0.005 0.087 2006 Dihedral : 9.199 174.851 1636 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.35 % Allowed : 12.55 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.23), residues: 1413 helix: 1.40 (0.21), residues: 657 sheet: -1.01 (0.49), residues: 119 loop : -1.96 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 69 TYR 0.017 0.001 TYR A 558 PHE 0.029 0.001 PHE A 490 TRP 0.011 0.001 TRP F 374 HIS 0.003 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00229 (11536) covalent geometry : angle 0.53724 (15685) hydrogen bonds : bond 0.04459 ( 442) hydrogen bonds : angle 4.10065 ( 1341) metal coordination : bond 0.01543 ( 11) metal coordination : angle 2.73151 ( 6) Misc. bond : bond 0.00013 ( 2) link_TRANS : bond 0.00016 ( 1) link_TRANS : angle 0.01947 ( 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 239 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 212 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 76 VAL cc_start: 0.8017 (OUTLIER) cc_final: 0.7765 (t) REVERT: A 206 ILE cc_start: 0.8195 (tt) cc_final: 0.7924 (tt) REVERT: A 265 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7488 (tm-30) REVERT: R 27 TRP cc_start: 0.7424 (t60) cc_final: 0.7133 (t60) REVERT: C 14 MET cc_start: 0.6902 (ptp) cc_final: 0.6491 (ptp) REVERT: C 81 MET cc_start: 0.5973 (tpt) cc_final: 0.5132 (tpt) REVERT: C 118 GLN cc_start: 0.6891 (mm-40) cc_final: 0.6524 (mm-40) REVERT: F 408 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.6435 (mp0) REVERT: G 77 LEU cc_start: 0.8313 (tp) cc_final: 0.7991 (tp) REVERT: H 136 PHE cc_start: 0.7781 (t80) cc_final: 0.7375 (t80) outliers start: 27 outliers final: 15 residues processed: 223 average time/residue: 0.1406 time to fit residues: 41.8839 Evaluate side-chains 219 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 220 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 642 MET 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 408 GLU Chi-restraints excluded: chain G residue 70 GLN Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 181 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 134 optimal weight: 0.0970 chunk 65 optimal weight: 1.9990 chunk 126 optimal weight: 0.0470 chunk 72 optimal weight: 0.0040 chunk 131 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 120 optimal weight: 0.0370 chunk 49 optimal weight: 0.3980 chunk 90 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 overall best weight: 0.1166 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 GLN ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.161126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.136311 restraints weight = 16749.960| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.56 r_work: 0.3669 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3510 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3510 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11550 Z= 0.098 Angle : 0.528 8.365 15693 Z= 0.262 Chirality : 0.039 0.306 1774 Planarity : 0.005 0.081 2006 Dihedral : 9.023 176.389 1636 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.09 % Allowed : 13.43 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.23), residues: 1413 helix: 1.56 (0.21), residues: 660 sheet: -0.88 (0.50), residues: 114 loop : -1.83 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 177 TYR 0.011 0.001 TYR A 235 PHE 0.025 0.001 PHE A 350 TRP 0.011 0.001 TRP A 35 HIS 0.003 0.000 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00213 (11536) covalent geometry : angle 0.52609 (15685) hydrogen bonds : bond 0.03950 ( 442) hydrogen bonds : angle 3.98534 ( 1341) metal coordination : bond 0.01248 ( 11) metal coordination : angle 2.64084 ( 6) Misc. bond : bond 0.00013 ( 2) link_TRANS : bond 0.00010 ( 1) link_TRANS : angle 0.01675 ( 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 237 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 206 ILE cc_start: 0.8148 (tt) cc_final: 0.7851 (tt) REVERT: A 265 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7516 (tm-30) REVERT: R 27 TRP cc_start: 0.7388 (t60) cc_final: 0.7044 (t60) REVERT: C 14 MET cc_start: 0.6864 (ptp) cc_final: 0.6487 (ptp) REVERT: C 81 MET cc_start: 0.5890 (tpt) cc_final: 0.5097 (tpt) REVERT: C 118 GLN cc_start: 0.6832 (mm-40) cc_final: 0.6402 (mm-40) REVERT: G 77 LEU cc_start: 0.8300 (tp) cc_final: 0.7989 (tp) REVERT: H 136 PHE cc_start: 0.7738 (t80) cc_final: 0.7356 (t80) REVERT: H 155 VAL cc_start: 0.7043 (t) cc_final: 0.6680 (p) outliers start: 24 outliers final: 16 residues processed: 220 average time/residue: 0.1276 time to fit residues: 37.6051 Evaluate side-chains 223 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 207 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 642 MET 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 10 optimal weight: 0.1980 chunk 102 optimal weight: 0.6980 chunk 125 optimal weight: 0.5980 chunk 87 optimal weight: 9.9990 chunk 25 optimal weight: 0.0570 chunk 122 optimal weight: 0.0570 chunk 44 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.3216 ------------------------------------------------------------------------------- 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 377 ASN A 463 GLN G 70 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.160236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.135306 restraints weight = 16910.334| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.59 r_work: 0.3648 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3652 r_free = 0.3652 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3652 r_free = 0.3652 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11550 Z= 0.107 Angle : 0.537 7.968 15693 Z= 0.266 Chirality : 0.040 0.317 1774 Planarity : 0.005 0.080 2006 Dihedral : 8.987 176.965 1636 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.27 % Allowed : 13.51 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.23), residues: 1413 helix: 1.61 (0.21), residues: 659 sheet: -0.93 (0.49), residues: 119 loop : -1.80 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 177 TYR 0.018 0.001 TYR A 558 PHE 0.026 0.001 PHE A 350 TRP 0.009 0.001 TRP F 374 HIS 0.003 0.001 HIS R 77 Details of bonding type rmsd covalent geometry : bond 0.00243 (11536) covalent geometry : angle 0.53478 (15685) hydrogen bonds : bond 0.04267 ( 442) hydrogen bonds : angle 3.96273 ( 1341) metal coordination : bond 0.01357 ( 11) metal coordination : angle 2.57161 ( 6) Misc. bond : bond 0.00016 ( 2) link_TRANS : bond 0.00010 ( 1) link_TRANS : angle 0.02810 ( 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 240 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 214 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 206 ILE cc_start: 0.8059 (tt) cc_final: 0.7741 (tt) REVERT: A 537 VAL cc_start: 0.6083 (OUTLIER) cc_final: 0.4543 (p) REVERT: R 27 TRP cc_start: 0.7284 (t60) cc_final: 0.6962 (t60) REVERT: C 14 MET cc_start: 0.6596 (ptp) cc_final: 0.6242 (ptp) REVERT: C 81 MET cc_start: 0.5728 (tpt) cc_final: 0.4958 (tpt) REVERT: C 118 GLN cc_start: 0.6727 (mm-40) cc_final: 0.6222 (mm-40) REVERT: F 442 MET cc_start: 0.6065 (ptp) cc_final: 0.5785 (mtm) REVERT: G 77 LEU cc_start: 0.8215 (tp) cc_final: 0.7896 (tp) REVERT: H 136 PHE cc_start: 0.7728 (t80) cc_final: 0.7306 (t80) REVERT: H 155 VAL cc_start: 0.7012 (t) cc_final: 0.6660 (p) REVERT: H 203 GLN cc_start: 0.6680 (OUTLIER) cc_final: 0.6005 (mp10) outliers start: 26 outliers final: 15 residues processed: 224 average time/residue: 0.1300 time to fit residues: 39.1813 Evaluate side-chains 224 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 207 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 232 CYS 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 537 VAL Chi-restraints excluded: chain A residue 642 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 80 optimal weight: 0.0070 chunk 58 optimal weight: 2.9990 chunk 49 optimal weight: 0.0670 chunk 86 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 123 optimal weight: 0.0040 chunk 13 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.2748 ------------------------------------------------------------------------------- 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 = 0.4094 r_free = 0.4094 target = 0.160475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.135349 restraints weight = 16965.678| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.64 r_work: 0.3647 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3647 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3647 r_free = 0.3647 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3647 r_free = 0.3647 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11550 Z= 0.104 Angle : 0.538 7.530 15693 Z= 0.268 Chirality : 0.040 0.319 1774 Planarity : 0.004 0.078 2006 Dihedral : 8.892 176.695 1636 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.18 % Allowed : 14.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.23), residues: 1413 helix: 1.61 (0.21), residues: 660 sheet: -0.86 (0.50), residues: 114 loop : -1.79 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 177 TYR 0.018 0.001 TYR D 79 PHE 0.009 0.001 PHE A 339 TRP 0.008 0.001 TRP F 374 HIS 0.004 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00233 (11536) covalent geometry : angle 0.53539 (15685) hydrogen bonds : bond 0.04146 ( 442) hydrogen bonds : angle 3.91679 ( 1341) metal coordination : bond 0.01372 ( 11) metal coordination : angle 2.65792 ( 6) Misc. bond : bond 0.00015 ( 2) link_TRANS : bond 0.00011 ( 1) link_TRANS : angle 0.03465 ( 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 238 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 213 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 206 ILE cc_start: 0.8048 (tt) cc_final: 0.7733 (tt) REVERT: A 361 ASP cc_start: 0.7226 (t0) cc_final: 0.6833 (m-30) REVERT: A 537 VAL cc_start: 0.5982 (OUTLIER) cc_final: 0.5743 (p) REVERT: R 27 TRP cc_start: 0.7279 (t60) cc_final: 0.6950 (t60) REVERT: C 14 MET cc_start: 0.6591 (ptp) cc_final: 0.6231 (ptp) REVERT: C 81 MET cc_start: 0.5771 (tpt) cc_final: 0.5002 (tpt) REVERT: C 118 GLN cc_start: 0.6739 (mm-40) cc_final: 0.6227 (mm-40) REVERT: F 442 MET cc_start: 0.6028 (ptp) cc_final: 0.5762 (mtm) REVERT: G 77 LEU cc_start: 0.8217 (tp) cc_final: 0.7904 (tp) REVERT: H 136 PHE cc_start: 0.7711 (t80) cc_final: 0.7296 (t80) REVERT: H 155 VAL cc_start: 0.6963 (t) cc_final: 0.6611 (p) REVERT: H 203 GLN cc_start: 0.6675 (OUTLIER) cc_final: 0.6027 (mp10) outliers start: 25 outliers final: 16 residues processed: 224 average time/residue: 0.1309 time to fit residues: 38.9895 Evaluate side-chains 226 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 208 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 232 CYS 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 529 ILE Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 642 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 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 136 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 92 optimal weight: 0.0370 chunk 129 optimal weight: 0.3980 chunk 38 optimal weight: 6.9990 chunk 137 optimal weight: 0.6980 chunk 66 optimal weight: 0.0010 chunk 11 optimal weight: 0.0970 chunk 112 optimal weight: 4.9990 chunk 0 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 overall best weight: 0.2462 ------------------------------------------------------------------------------- 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 = 0.4097 r_free = 0.4097 target = 0.160694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.135360 restraints weight = 16791.188| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.40 r_work: 0.3669 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11550 Z= 0.100 Angle : 0.531 7.982 15693 Z= 0.262 Chirality : 0.039 0.319 1774 Planarity : 0.004 0.076 2006 Dihedral : 8.772 176.250 1636 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.27 % Allowed : 14.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.23), residues: 1413 helix: 1.72 (0.21), residues: 654 sheet: -0.85 (0.50), residues: 114 loop : -1.78 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 177 TYR 0.017 0.001 TYR A 558 PHE 0.026 0.001 PHE A 350 TRP 0.008 0.001 TRP F 374 HIS 0.005 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00224 (11536) covalent geometry : angle 0.52844 (15685) hydrogen bonds : bond 0.03936 ( 442) hydrogen bonds : angle 3.78983 ( 1341) metal coordination : bond 0.01324 ( 11) metal coordination : angle 2.61139 ( 6) Misc. bond : bond 0.00017 ( 2) link_TRANS : bond 0.00006 ( 1) link_TRANS : angle 0.03670 ( 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 239 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 213 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 206 ILE cc_start: 0.8143 (tt) cc_final: 0.7827 (tt) REVERT: A 361 ASP cc_start: 0.7263 (t0) cc_final: 0.6940 (m-30) REVERT: A 537 VAL cc_start: 0.6076 (OUTLIER) cc_final: 0.5850 (p) REVERT: R 27 TRP cc_start: 0.7383 (t60) cc_final: 0.7036 (t60) REVERT: C 14 MET cc_start: 0.6889 (ptp) cc_final: 0.6518 (ptp) REVERT: C 81 MET cc_start: 0.5855 (tpt) cc_final: 0.5093 (tpt) REVERT: C 118 GLN cc_start: 0.6873 (mm-40) cc_final: 0.6387 (mm-40) REVERT: F 442 MET cc_start: 0.6265 (ptp) cc_final: 0.5977 (mtm) REVERT: G 77 LEU cc_start: 0.8275 (tp) cc_final: 0.7976 (tp) REVERT: H 136 PHE cc_start: 0.7732 (t80) cc_final: 0.7322 (t80) REVERT: H 155 VAL cc_start: 0.6977 (t) cc_final: 0.6584 (p) REVERT: H 203 GLN cc_start: 0.6664 (OUTLIER) cc_final: 0.6020 (mp10) outliers start: 26 outliers final: 15 residues processed: 223 average time/residue: 0.1317 time to fit residues: 39.2983 Evaluate side-chains 226 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 209 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 642 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 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 47 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 0.0870 chunk 10 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 chunk 39 optimal weight: 0.2980 chunk 121 optimal weight: 0.5980 chunk 99 optimal weight: 0.0970 chunk 79 optimal weight: 0.0670 overall best weight: 0.1894 ------------------------------------------------------------------------------- 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 = 0.4106 r_free = 0.4106 target = 0.161284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.136095 restraints weight = 16708.700| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.39 r_work: 0.3670 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3512 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3512 r_free = 0.3512 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3512 r_free = 0.3512 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3512 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11550 Z= 0.098 Angle : 0.540 9.001 15693 Z= 0.264 Chirality : 0.039 0.318 1774 Planarity : 0.004 0.075 2006 Dihedral : 8.703 175.832 1636 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 1.66 % Allowed : 15.08 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.23), residues: 1413 helix: 1.76 (0.21), residues: 655 sheet: -0.85 (0.50), residues: 114 loop : -1.73 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 437 TYR 0.018 0.001 TYR A 558 PHE 0.025 0.001 PHE A 350 TRP 0.008 0.001 TRP F 374 HIS 0.004 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00220 (11536) covalent geometry : angle 0.53740 (15685) hydrogen bonds : bond 0.03780 ( 442) hydrogen bonds : angle 3.75469 ( 1341) metal coordination : bond 0.01348 ( 11) metal coordination : angle 2.69748 ( 6) Misc. bond : bond 0.00015 ( 2) link_TRANS : bond 0.00013 ( 1) link_TRANS : angle 0.04703 ( 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 238 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 219 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: A 148 ARG cc_start: 0.8195 (ttt-90) cc_final: 0.6702 (mpt180) REVERT: A 206 ILE cc_start: 0.8111 (tt) cc_final: 0.7802 (tt) REVERT: A 249 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7746 (ttp-110) REVERT: A 361 ASP cc_start: 0.7252 (t0) cc_final: 0.7035 (m-30) REVERT: A 487 ASN cc_start: 0.7190 (m-40) cc_final: 0.6982 (m-40) REVERT: A 537 VAL cc_start: 0.6196 (OUTLIER) cc_final: 0.5989 (p) REVERT: A 582 MET cc_start: 0.7777 (tpt) cc_final: 0.7537 (tpp) REVERT: R 27 TRP cc_start: 0.7371 (t60) cc_final: 0.7055 (t60) REVERT: C 14 MET cc_start: 0.6860 (ptp) cc_final: 0.6490 (ptp) REVERT: C 81 MET cc_start: 0.5775 (tpt) cc_final: 0.5003 (tpt) REVERT: C 118 GLN cc_start: 0.6852 (mm-40) cc_final: 0.6361 (mm-40) REVERT: G 77 LEU cc_start: 0.8277 (tp) cc_final: 0.7987 (tp) REVERT: H 136 PHE cc_start: 0.7742 (t80) cc_final: 0.7332 (t80) REVERT: H 155 VAL cc_start: 0.6954 (t) cc_final: 0.6542 (p) REVERT: H 203 GLN cc_start: 0.6656 (OUTLIER) cc_final: 0.6041 (mp10) outliers start: 19 outliers final: 13 residues processed: 228 average time/residue: 0.1342 time to fit residues: 40.9427 Evaluate side-chains 225 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 209 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 75 ARG 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 423 LYS Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 642 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 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 93 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 0.0030 chunk 19 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.159755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.134629 restraints weight = 16579.010| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.51 r_work: 0.3625 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3465 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 11550 Z= 0.138 Angle : 0.585 9.037 15693 Z= 0.289 Chirality : 0.041 0.326 1774 Planarity : 0.005 0.077 2006 Dihedral : 8.855 175.597 1636 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 1.83 % Allowed : 15.08 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.23), residues: 1413 helix: 1.63 (0.21), residues: 655 sheet: -0.93 (0.51), residues: 114 loop : -1.81 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 437 TYR 0.014 0.001 TYR D 79 PHE 0.022 0.001 PHE A 350 TRP 0.008 0.001 TRP F 374 HIS 0.005 0.001 HIS R 77 Details of bonding type rmsd covalent geometry : bond 0.00326 (11536) covalent geometry : angle 0.58222 (15685) hydrogen bonds : bond 0.04843 ( 442) hydrogen bonds : angle 3.85592 ( 1341) metal coordination : bond 0.01798 ( 11) metal coordination : angle 2.99169 ( 6) Misc. bond : bond 0.00024 ( 2) link_TRANS : bond 0.00009 ( 1) link_TRANS : angle 0.04717 ( 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 240 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 219 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 76 VAL cc_start: 0.8121 (t) cc_final: 0.7857 (t) REVERT: A 192 GLU cc_start: 0.8510 (pt0) cc_final: 0.8284 (pt0) REVERT: A 206 ILE cc_start: 0.8194 (tt) cc_final: 0.7884 (tt) REVERT: A 235 TYR cc_start: 0.7778 (t80) cc_final: 0.7520 (t80) REVERT: A 487 ASN cc_start: 0.7215 (m-40) cc_final: 0.6983 (m-40) REVERT: R 27 TRP cc_start: 0.7408 (t60) cc_final: 0.7098 (t60) REVERT: C 14 MET cc_start: 0.6921 (ptp) cc_final: 0.6529 (ptp) REVERT: C 81 MET cc_start: 0.5823 (tpt) cc_final: 0.5069 (tpt) REVERT: C 118 GLN cc_start: 0.6942 (mm-40) cc_final: 0.6631 (mm-40) REVERT: G 77 LEU cc_start: 0.8284 (tp) cc_final: 0.7979 (tp) REVERT: H 136 PHE cc_start: 0.7795 (t80) cc_final: 0.7351 (t80) REVERT: H 155 VAL cc_start: 0.6968 (t) cc_final: 0.6630 (p) REVERT: H 203 GLN cc_start: 0.6691 (OUTLIER) cc_final: 0.6056 (mp10) outliers start: 21 outliers final: 16 residues processed: 227 average time/residue: 0.1406 time to fit residues: 42.1025 Evaluate side-chains 230 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 213 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 75 ARG 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 328 SER Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 642 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 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 42 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 90 optimal weight: 0.0030 chunk 15 optimal weight: 0.0060 chunk 128 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 0.0980 overall best weight: 0.2806 ------------------------------------------------------------------------------- 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 = 0.4095 r_free = 0.4095 target = 0.160666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.135778 restraints weight = 16787.791| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.55 r_work: 0.3648 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 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 = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11550 Z= 0.108 Angle : 0.564 9.067 15693 Z= 0.276 Chirality : 0.040 0.321 1774 Planarity : 0.005 0.077 2006 Dihedral : 8.741 175.429 1636 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 1.48 % Allowed : 15.87 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.23), residues: 1413 helix: 1.78 (0.21), residues: 648 sheet: -0.91 (0.51), residues: 114 loop : -1.76 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 437 TYR 0.022 0.001 TYR A 558 PHE 0.025 0.001 PHE A 10 TRP 0.008 0.001 TRP F 374 HIS 0.003 0.001 HIS F 369 Details of bonding type rmsd covalent geometry : bond 0.00247 (11536) covalent geometry : angle 0.56146 (15685) hydrogen bonds : bond 0.04178 ( 442) hydrogen bonds : angle 3.83440 ( 1341) metal coordination : bond 0.01665 ( 11) metal coordination : angle 2.88136 ( 6) Misc. bond : bond 0.00022 ( 2) link_TRANS : bond 0.00009 ( 1) link_TRANS : angle 0.03622 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3104.73 seconds wall clock time: 53 minutes 47.09 seconds (3227.09 seconds total)