Starting phenix.real_space_refine on Mon Jul 6 08:11:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7o1v_12697/07_2026/7o1v_12697.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o1v_12697/07_2026/7o1v_12697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7o1v_12697/07_2026/7o1v_12697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o1v_12697/07_2026/7o1v_12697.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7o1v_12697/07_2026/7o1v_12697.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7o1v_12697/07_2026/7o1v_12697.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7o1v_12697/07_2026/7o1v_12697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o1v_12697/07_2026/7o1v_12697.map" } resolution = 4.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14030 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Fe 12 7.16 5 P 5 5.49 5 Mg 88 5.21 5 S 77 5.16 5 C 14809 2.51 5 N 2821 2.21 5 O 3102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20914 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 739, 5787 Classifications: {'peptide': 739} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 706} Chain: "B" Number of atoms: 5770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5770 Classifications: {'peptide': 729} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 699} Chain: "C" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 600 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "D" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1102 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 130} Chain: "E" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 543 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "K" Number of atoms: 579 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 80, 573 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 76} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 80, 573 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 76} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 577 Chain: "M" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 238 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "A" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 2915 Unusual residues: {'BCR': 7, 'CLA': 44, 'LHG': 2, 'LMG': 1, 'PQN': 1, 'SF4': 1} Classifications: {'undetermined': 56} Link IDs: {None: 55} Unresolved non-hydrogen bonds: 419 Unresolved non-hydrogen angles: 505 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'CLA:plan-5': 9} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 3049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 3049 Unusual residues: {'BCR': 7, 'CLA': 42, 'ECH': 1, 'LHG': 2, 'LMG': 2, 'PQN': 1, 'SQD': 1} Classifications: {'undetermined': 56} Link IDs: {None: 55} Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 348 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'CLA:plan-5': 5} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 225 Unusual residues: {'BCR': 1, 'CLA': 2, 'LMG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "M" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'ECH': 1, 'LHG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10172 SG CYS B 565 52.260 54.264 69.749 1.00 76.47 S ATOM 4460 SG CYS A 583 55.090 51.432 65.757 1.00 76.47 S ATOM 4405 SG CYS A 574 51.382 53.937 62.737 1.00 76.47 S ATOM 10117 SG CYS B 556 49.046 49.708 66.761 1.00 76.47 S ATOM 11924 SG CYS C 51 46.989 46.605 55.869 1.00 76.47 S ATOM 11705 SG CYS C 21 43.836 44.434 52.400 1.00 84.93 S ATOM 11950 SG CYS C 54 41.602 45.907 55.559 1.00 80.98 S ATOM 11907 SG CYS C 48 44.453 40.300 57.240 1.00 86.60 S ATOM 11977 SG CYS C 58 32.877 51.403 57.772 1.00 80.34 S ATOM 11676 SG CYS C 17 35.764 47.099 54.893 1.00 95.90 S ATOM 11654 SG CYS C 14 32.602 52.201 52.888 1.00 99.11 S ATOM 11636 SG CYS C 11 29.055 46.822 54.499 1.00 94.23 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ACYS K 27 " occ=0.25 ... (10 atoms not shown) pdb=" SG BCYS K 27 " occ=0.75 Time building chain proxies: 3.67, per 1000 atoms: 0.18 Number of scatterers: 20914 At special positions: 0 Unit cell: (124.92, 124.087, 149.071, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 12 26.01 S 77 16.00 P 5 15.00 Mg 88 11.99 O 3102 8.00 N 2821 7.00 C 14809 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 915.0 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A3001 " pdb="FE2 SF4 A3001 " - pdb=" SG CYS A 583 " pdb="FE4 SF4 A3001 " - pdb=" SG CYS B 556 " pdb="FE3 SF4 A3001 " - pdb=" SG CYS A 574 " pdb="FE1 SF4 A3001 " - pdb=" SG CYS B 565 " pdb=" SF4 C3002 " pdb="FE2 SF4 C3002 " - pdb=" SG CYS C 21 " pdb="FE1 SF4 C3002 " - pdb=" SG CYS C 51 " pdb="FE3 SF4 C3002 " - pdb=" SG CYS C 54 " pdb="FE4 SF4 C3002 " - pdb=" SG CYS C 48 " pdb=" SF4 C3003 " pdb="FE4 SF4 C3003 " - pdb=" SG CYS C 11 " pdb="FE1 SF4 C3003 " - pdb=" SG CYS C 58 " pdb="FE3 SF4 C3003 " - pdb=" SG CYS C 14 " pdb="FE2 SF4 C3003 " - pdb=" SG CYS C 17 " Number of angles added : 36 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3382 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 9 sheets defined 59.2% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.940A pdb=" N TRP A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 97 removed outlier: 4.225A pdb=" N VAL A 68 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 97 " --> pdb=" O HIS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 105 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 142 through 151 removed outlier: 3.524A pdb=" N LEU A 146 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 182 removed outlier: 3.711A pdb=" N LEU A 158 " --> pdb=" O ASP A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 203 Processing helix chain 'A' and resid 203 through 219 removed outlier: 3.819A pdb=" N GLY A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 228 Processing helix chain 'A' and resid 238 through 245 removed outlier: 3.757A pdb=" N PHE A 242 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 253 removed outlier: 4.432A pdb=" N MET A 249 " --> pdb=" O GLU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 259 Processing helix chain 'A' and resid 260 through 265 Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 289 through 308 Processing helix chain 'A' and resid 320 through 327 Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 347 through 371 removed outlier: 4.077A pdb=" N GLN A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 414 removed outlier: 4.180A pdb=" N GLN A 386 " --> pdb=" O ASP A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 432 Processing helix chain 'A' and resid 432 through 450 Processing helix chain 'A' and resid 451 through 464 removed outlier: 3.615A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 470 removed outlier: 3.823A pdb=" N ASP A 469 " --> pdb=" O ARG A 466 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET A 470 " --> pdb=" O PRO A 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 466 through 470' Processing helix chain 'A' and resid 480 through 497 Proline residue: A 494 - end of helix Processing helix chain 'A' and resid 528 through 555 Processing helix chain 'A' and resid 564 through 569 removed outlier: 3.891A pdb=" N LEU A 568 " --> pdb=" O ASP A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 616 removed outlier: 4.161A pdb=" N PHE A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 639 Processing helix chain 'A' and resid 642 through 649 removed outlier: 3.733A pdb=" N PHE A 649 " --> pdb=" O TRP A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 659 removed outlier: 3.825A pdb=" N ALA A 655 " --> pdb=" O TRP A 651 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASN A 656 " --> pdb=" O ALA A 652 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL A 657 " --> pdb=" O GLN A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 688 removed outlier: 3.900A pdb=" N GLY A 669 " --> pdb=" O LEU A 665 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 683 " --> pdb=" O PHE A 679 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N MET A 684 " --> pdb=" O ALA A 680 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N PHE A 685 " --> pdb=" O PHE A 681 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER A 688 " --> pdb=" O MET A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 708 removed outlier: 3.569A pdb=" N LEU A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 749 removed outlier: 3.797A pdb=" N SER A 749 " --> pdb=" O ALA A 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 13 Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 38 through 71 Processing helix chain 'B' and resid 73 through 80 removed outlier: 3.813A pdb=" N ASP B 80 " --> pdb=" O GLN B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 105 Processing helix chain 'B' and resid 119 through 128 removed outlier: 3.886A pdb=" N TRP B 123 " --> pdb=" O GLY B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 156 Processing helix chain 'B' and resid 157 through 162 removed outlier: 6.315A pdb=" N LYS B 160 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG B 162 " --> pdb=" O PRO B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 170 removed outlier: 3.709A pdb=" N PHE B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 181 removed outlier: 3.677A pdb=" N ARG B 174 " --> pdb=" O ASN B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 197 Processing helix chain 'B' and resid 197 through 204 Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'B' and resid 229 through 233 removed outlier: 4.065A pdb=" N VAL B 232 " --> pdb=" O ASN B 229 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR B 233 " --> pdb=" O TRP B 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 229 through 233' Processing helix chain 'B' and resid 269 through 288 Processing helix chain 'B' and resid 300 through 308 removed outlier: 3.685A pdb=" N HIS B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 325 Processing helix chain 'B' and resid 327 through 351 removed outlier: 3.779A pdb=" N GLN B 331 " --> pdb=" O SER B 327 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 395 removed outlier: 3.552A pdb=" N GLN B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 444 removed outlier: 5.657A pdb=" N GLU B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ALA B 415 " --> pdb=" O GLU B 411 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE B 444 " --> pdb=" O VAL B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 450 removed outlier: 6.260A pdb=" N GLU B 448 " --> pdb=" O GLY B 445 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 449 " --> pdb=" O THR B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 465 Processing helix chain 'B' and resid 490 through 499 removed outlier: 3.649A pdb=" N ASN B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 537 Processing helix chain 'B' and resid 546 through 551 removed outlier: 3.520A pdb=" N PHE B 550 " --> pdb=" O ASP B 546 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY B 551 " --> pdb=" O LYS B 547 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 546 through 551' Processing helix chain 'B' and resid 568 through 601 removed outlier: 4.455A pdb=" N PHE B 578 " --> pdb=" O TYR B 574 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TRP B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 610 removed outlier: 4.398A pdb=" N PHE B 606 " --> pdb=" O ASN B 602 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 610 " --> pdb=" O PHE B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 619 removed outlier: 4.241A pdb=" N TRP B 616 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 624 No H-bonds generated for 'chain 'B' and resid 622 through 624' Processing helix chain 'B' and resid 625 through 630 removed outlier: 3.666A pdb=" N ASN B 630 " --> pdb=" O ALA B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 663 removed outlier: 3.533A pdb=" N ALA B 644 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N PHE B 660 " --> pdb=" O THR B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 682 removed outlier: 4.361A pdb=" N TRP B 668 " --> pdb=" O TRP B 664 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR B 682 " --> pdb=" O ALA B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 730 Processing helix chain 'C' and resid 15 through 21 removed outlier: 3.539A pdb=" N ARG C 19 " --> pdb=" O THR C 15 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N CYS C 21 " --> pdb=" O CYS C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 48 removed outlier: 3.650A pdb=" N CYS C 48 " --> pdb=" O THR C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 58 removed outlier: 3.923A pdb=" N CYS C 58 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 78 removed outlier: 3.857A pdb=" N GLY C 78 " --> pdb=" O THR C 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 25 removed outlier: 4.201A pdb=" N ASN D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 74 Processing helix chain 'D' and resid 121 through 125 removed outlier: 3.561A pdb=" N ASN D 125 " --> pdb=" O ILE D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'K' and resid 26 through 39 Processing helix chain 'K' and resid 62 through 85 Processing helix chain 'M' and resid 4 through 29 removed outlier: 4.754A pdb=" N LEU M 17 " --> pdb=" O VAL M 13 " (cutoff:3.500A) Proline residue: M 18 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 18 Processing sheet with id=AA2, first strand: chain 'A' and resid 113 through 115 removed outlier: 4.360A pdb=" N GLN A 115 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 137 " --> pdb=" O GLN A 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 514 through 515 removed outlier: 3.510A pdb=" N MET A 522 " --> pdb=" O ILE A 514 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 620 through 621 Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA6, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AA7, first strand: chain 'D' and resid 53 through 59 removed outlier: 3.519A pdb=" N TRP D 32 " --> pdb=" O ASN D 55 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE D 85 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 39 through 41 Processing sheet with id=AA9, first strand: chain 'E' and resid 58 through 61 removed outlier: 3.581A pdb=" N ASN E 59 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE E 38 " --> pdb=" O ALA E 26 " (cutoff:3.500A) 780 hydrogen bonds defined for protein. 2268 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 9159 1.42 - 1.64: 12454 1.64 - 1.86: 110 1.86 - 2.08: 176 2.08 - 2.30: 212 Bond restraints: 22111 Sorted by residual: bond pdb=" C42 LMG B5002 " pdb=" C43 LMG B5002 " ideal model delta sigma weight residual 1.526 1.327 0.199 2.00e-02 2.50e+03 9.87e+01 bond pdb=" C36 LMG K5009 " pdb=" C37 LMG K5009 " ideal model delta sigma weight residual 1.526 1.329 0.197 2.00e-02 2.50e+03 9.75e+01 bond pdb=" C42 LMG K5009 " pdb=" C43 LMG K5009 " ideal model delta sigma weight residual 1.526 1.329 0.197 2.00e-02 2.50e+03 9.66e+01 bond pdb=" C39 LMG B5002 " pdb=" C40 LMG B5002 " ideal model delta sigma weight residual 1.523 1.327 0.196 2.00e-02 2.50e+03 9.61e+01 bond pdb=" C36 LMG B5002 " pdb=" C37 LMG B5002 " ideal model delta sigma weight residual 1.526 1.330 0.196 2.00e-02 2.50e+03 9.59e+01 ... (remaining 22106 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.45: 31185 11.45 - 22.90: 111 22.90 - 34.35: 35 34.35 - 45.81: 12 45.81 - 57.26: 15 Bond angle restraints: 31358 Sorted by residual: angle pdb=" C10 BCR B4017 " pdb=" C11 BCR B4017 " pdb=" C12 BCR B4017 " ideal model delta sigma weight residual 122.66 179.92 -57.26 3.00e+00 1.11e-01 3.64e+02 angle pdb=" C10 BCR A4008 " pdb=" C11 BCR A4008 " pdb=" C12 BCR A4008 " ideal model delta sigma weight residual 122.66 178.84 -56.18 3.00e+00 1.11e-01 3.51e+02 angle pdb=" C10 BCR A4001 " pdb=" C11 BCR A4001 " pdb=" C12 BCR A4001 " ideal model delta sigma weight residual 122.66 178.50 -55.84 3.00e+00 1.11e-01 3.46e+02 angle pdb=" C10 BCR B4011 " pdb=" C11 BCR B4011 " pdb=" C12 BCR B4011 " ideal model delta sigma weight residual 122.66 178.09 -55.43 3.00e+00 1.11e-01 3.41e+02 angle pdb=" C10 BCR A4019 " pdb=" C11 BCR A4019 " pdb=" C12 BCR A4019 " ideal model delta sigma weight residual 122.66 177.90 -55.24 3.00e+00 1.11e-01 3.39e+02 ... (remaining 31353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.15: 8469 21.15 - 42.29: 1129 42.29 - 63.44: 398 63.44 - 84.58: 58 84.58 - 105.73: 5 Dihedral angle restraints: 10059 sinusoidal: 4748 harmonic: 5311 Sorted by residual: dihedral pdb=" CA TRP B 664 " pdb=" C TRP B 664 " pdb=" N ARG B 665 " pdb=" CA ARG B 665 " ideal model delta harmonic sigma weight residual -180.00 -150.31 -29.69 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA ARG A 560 " pdb=" C ARG A 560 " pdb=" N LEU A 561 " pdb=" CA LEU A 561 " ideal model delta harmonic sigma weight residual 180.00 152.53 27.47 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA MET A 310 " pdb=" C MET A 310 " pdb=" N TYR A 311 " pdb=" CA TYR A 311 " ideal model delta harmonic sigma weight residual -180.00 -154.93 -25.07 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 10056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.177: 2521 0.177 - 0.355: 45 0.355 - 0.532: 10 0.532 - 0.710: 65 0.710 - 0.887: 13 Chirality restraints: 2654 Sorted by residual: chirality pdb=" C3A CLA A1139 " pdb=" C2A CLA A1139 " pdb=" C4A CLA A1139 " pdb=" CMA CLA A1139 " both_signs ideal model delta sigma weight residual False -2.76 -1.88 -0.89 2.00e-01 2.50e+01 1.97e+01 chirality pdb=" C3A CLA B1223 " pdb=" C2A CLA B1223 " pdb=" C4A CLA B1223 " pdb=" CMA CLA B1223 " both_signs ideal model delta sigma weight residual False -2.76 -1.97 -0.80 2.00e-01 2.50e+01 1.58e+01 chirality pdb=" C3A CLA A1113 " pdb=" C2A CLA A1113 " pdb=" C4A CLA A1113 " pdb=" CMA CLA A1113 " both_signs ideal model delta sigma weight residual False -2.76 -2.00 -0.76 2.00e-01 2.50e+01 1.45e+01 ... (remaining 2651 not shown) Planarity restraints: 4080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 BCR B4017 " -0.349 2.00e-02 2.50e+03 2.00e-01 5.01e+02 pdb=" C11 BCR B4017 " 0.235 2.00e-02 2.50e+03 pdb=" C34 BCR B4017 " 0.088 2.00e-02 2.50e+03 pdb=" C8 BCR B4017 " 0.100 2.00e-02 2.50e+03 pdb=" C9 BCR B4017 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BCR A4003 " -0.345 2.00e-02 2.50e+03 1.98e-01 4.92e+02 pdb=" C11 BCR A4003 " 0.234 2.00e-02 2.50e+03 pdb=" C34 BCR A4003 " 0.043 2.00e-02 2.50e+03 pdb=" C8 BCR A4003 " 0.131 2.00e-02 2.50e+03 pdb=" C9 BCR A4003 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BCR B4004 " -0.343 2.00e-02 2.50e+03 1.95e-01 4.76e+02 pdb=" C11 BCR B4004 " 0.228 2.00e-02 2.50e+03 pdb=" C34 BCR B4004 " 0.086 2.00e-02 2.50e+03 pdb=" C8 BCR B4004 " 0.096 2.00e-02 2.50e+03 pdb=" C9 BCR B4004 " -0.067 2.00e-02 2.50e+03 ... (remaining 4077 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1668 2.75 - 3.28: 18144 3.28 - 3.82: 36985 3.82 - 4.36: 40372 4.36 - 4.90: 69019 Nonbonded interactions: 166188 Sorted by model distance: nonbonded pdb=" O GLN A 351 " pdb=" ND2 ASN A 355 " model vdw 2.207 3.120 nonbonded pdb=" OD2 ASP C 61 " pdb=" OG SER E 16 " model vdw 2.228 3.040 nonbonded pdb=" O GLY B 558 " pdb=" OG1 THR B 564 " model vdw 2.241 3.040 nonbonded pdb=" OG SER A 719 " pdb=" OG SER E 50 " model vdw 2.267 3.040 nonbonded pdb=" O GLU A 342 " pdb=" OG1 THR A 346 " model vdw 2.290 3.040 ... (remaining 166183 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=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 19.290 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 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 : 0.025 0.199 22123 Z= 1.240 Angle : 2.855 65.401 31394 Z= 0.980 Chirality : 0.132 0.887 2654 Planarity : 0.016 0.200 4080 Dihedral : 20.578 105.726 6677 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.39 % Favored : 94.56 % Rotamer: Outliers : 0.07 % Allowed : 0.80 % Favored : 99.13 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: -1.67 (0.18), residues: 1858 helix: -0.38 (0.15), residues: 1000 sheet: -0.69 (0.71), residues: 61 loop : -2.06 (0.20), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 121 TYR 0.056 0.003 TYR A 661 PHE 0.035 0.003 PHE B 589 TRP 0.038 0.002 TRP B 668 HIS 0.030 0.002 HIS A 608 Details of bonding type rmsd/Z covalent geometry : bond 0.02488 / 1.24 (22111) covalent geometry : angle 2.76916 / 0.98 (31358) hydrogen bonds : bond 0.14622 / 9.86 ( 780) hydrogen bonds : angle 6.14354 / 4.52 ( 2268) metal coordination : bond 0.01695 / 0.70 ( 12) metal coordination : angle 20.68809 / 13.33 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 368 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7225 (tp30) cc_final: 0.6722 (mm-30) REVERT: A 192 ASN cc_start: 0.8504 (t0) cc_final: 0.8050 (t0) REVERT: A 241 GLU cc_start: 0.7584 (pp20) cc_final: 0.6507 (tp30) REVERT: A 244 LEU cc_start: 0.8787 (tt) cc_final: 0.8307 (mt) REVERT: A 338 LYS cc_start: 0.8089 (ttpt) cc_final: 0.7483 (pttp) REVERT: A 606 ILE cc_start: 0.9159 (pt) cc_final: 0.8947 (pt) REVERT: A 613 MET cc_start: 0.8693 (mtp) cc_final: 0.8333 (mtm) REVERT: A 684 MET cc_start: 0.6888 (tpp) cc_final: 0.5531 (tpp) REVERT: B 169 LYS cc_start: 0.7613 (tppt) cc_final: 0.7317 (tppt) REVERT: B 589 PHE cc_start: 0.8791 (m-80) cc_final: 0.8580 (m-80) REVERT: C 39 ILE cc_start: 0.8711 (tt) cc_final: 0.8378 (tt) REVERT: D 1 MET cc_start: 0.5212 (tmm) cc_final: 0.4452 (tmm) REVERT: D 49 ILE cc_start: 0.8630 (mt) cc_final: 0.8347 (tp) REVERT: D 57 LEU cc_start: 0.7822 (tt) cc_final: 0.7613 (tt) REVERT: E 7 ASP cc_start: 0.5964 (m-30) cc_final: 0.5296 (t0) REVERT: E 8 LYS cc_start: 0.7714 (ttmm) cc_final: 0.6979 (ttmt) REVERT: K 38 TYR cc_start: 0.5462 (t80) cc_final: 0.5030 (t80) REVERT: K 70 MET cc_start: 0.7122 (ttt) cc_final: 0.6712 (ttp) REVERT: M 9 LEU cc_start: 0.8693 (mm) cc_final: 0.7969 (tt) outliers start: 1 outliers final: 0 residues processed: 368 average time/residue: 0.1268 time to fit residues: 75.9929 Evaluate side-chains 300 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 ASN A 543 HIS A 600 ASN ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN B 374 GLN ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 679 HIS K 74 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.109805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.091799 restraints weight = 41876.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.094575 restraints weight = 21042.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.096436 restraints weight = 13474.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.097603 restraints weight = 10087.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.098393 restraints weight = 8316.016| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22123 Z= 0.158 Angle : 0.925 65.498 31394 Z= 0.306 Chirality : 0.044 0.193 2654 Planarity : 0.004 0.067 4080 Dihedral : 20.267 89.545 3544 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.72 % Favored : 96.23 % Rotamer: Outliers : 0.13 % Allowed : 5.99 % Favored : 93.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: -0.65 (0.19), residues: 1858 helix: 0.61 (0.16), residues: 1014 sheet: -1.41 (0.59), residues: 82 loop : -1.76 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 112 TYR 0.020 0.001 TYR B 574 PHE 0.024 0.002 PHE A 84 TRP 0.025 0.001 TRP B 190 HIS 0.006 0.001 HIS B 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (22111) covalent geometry : angle 0.68584 / 0.30 (31358) hydrogen bonds : bond 0.05093 / 3.45 ( 780) hydrogen bonds : angle 4.63451 / 3.39 ( 2268) metal coordination : bond 0.01112 / 0.54 ( 12) metal coordination : angle 18.34062 / 12.29 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 367 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7092 (tp30) cc_final: 0.6803 (tp30) REVERT: A 197 MET cc_start: 0.8422 (mmm) cc_final: 0.8060 (tmm) REVERT: A 244 LEU cc_start: 0.8760 (tt) cc_final: 0.8335 (mt) REVERT: A 300 ILE cc_start: 0.9181 (tp) cc_final: 0.8970 (tp) REVERT: A 352 LEU cc_start: 0.8824 (tt) cc_final: 0.8524 (tt) REVERT: A 434 ASP cc_start: 0.8651 (p0) cc_final: 0.8078 (p0) REVERT: A 603 SER cc_start: 0.8825 (m) cc_final: 0.8610 (m) REVERT: A 719 SER cc_start: 0.9000 (t) cc_final: 0.8604 (m) REVERT: B 290 MET cc_start: 0.7618 (mmp) cc_final: 0.7400 (ttp) REVERT: B 326 ASN cc_start: 0.7940 (m-40) cc_final: 0.7469 (t0) REVERT: C 39 ILE cc_start: 0.8740 (tt) cc_final: 0.8486 (tt) REVERT: D 49 ILE cc_start: 0.8461 (mt) cc_final: 0.8181 (tp) REVERT: D 55 ASN cc_start: 0.8517 (m-40) cc_final: 0.8280 (m-40) REVERT: D 122 ILE cc_start: 0.6684 (mm) cc_final: 0.6338 (tp) REVERT: E 7 ASP cc_start: 0.5766 (m-30) cc_final: 0.5172 (t70) REVERT: E 8 LYS cc_start: 0.7627 (ttmm) cc_final: 0.7055 (ttmt) REVERT: E 43 ARG cc_start: 0.8376 (mtm180) cc_final: 0.8154 (mtm180) REVERT: E 58 THR cc_start: 0.7822 (m) cc_final: 0.7609 (m) REVERT: K 38 TYR cc_start: 0.5227 (t80) cc_final: 0.4767 (t80) REVERT: K 70 MET cc_start: 0.7133 (ttt) cc_final: 0.6698 (ttp) REVERT: M 5 ASP cc_start: 0.5644 (t70) cc_final: 0.5040 (t70) outliers start: 2 outliers final: 1 residues processed: 367 average time/residue: 0.1250 time to fit residues: 74.9396 Evaluate side-chains 294 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 293 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 140 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 101 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 chunk 177 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 HIS A 543 HIS B 156 HIS ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN B 372 HIS ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS B 582 ASN ** B 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.105629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.087511 restraints weight = 43085.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.090381 restraints weight = 20443.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.092193 restraints weight = 12641.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.093523 restraints weight = 9334.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.094199 restraints weight = 7642.690| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 22123 Z= 0.215 Angle : 0.948 72.788 31394 Z= 0.324 Chirality : 0.046 0.211 2654 Planarity : 0.005 0.062 4080 Dihedral : 19.599 89.131 3544 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.74 % Favored : 95.20 % Rotamer: Outliers : 0.13 % Allowed : 5.59 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: -0.45 (0.19), residues: 1858 helix: 0.74 (0.16), residues: 1019 sheet: -1.51 (0.58), residues: 84 loop : -1.59 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 312 TYR 0.029 0.002 TYR B 291 PHE 0.043 0.002 PHE C 62 TRP 0.024 0.002 TRP A 693 HIS 0.012 0.001 HIS A 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.21 (22111) covalent geometry : angle 0.71366 / 0.32 (31358) hydrogen bonds : bond 0.05630 / 3.84 ( 780) hydrogen bonds : angle 4.67584 / 3.41 ( 2268) metal coordination : bond 0.01711 / 0.83 ( 12) metal coordination : angle 18.42953 / 12.53 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 356 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7317 (tp30) cc_final: 0.6800 (tp30) REVERT: A 168 MET cc_start: 0.8541 (ppp) cc_final: 0.8323 (ppp) REVERT: A 241 GLU cc_start: 0.7822 (pp20) cc_final: 0.7595 (pp20) REVERT: A 244 LEU cc_start: 0.8769 (tt) cc_final: 0.8427 (mt) REVERT: A 310 MET cc_start: 0.8988 (tpp) cc_final: 0.8203 (mmm) REVERT: A 311 TYR cc_start: 0.8857 (m-80) cc_final: 0.8580 (m-10) REVERT: A 352 LEU cc_start: 0.8814 (tt) cc_final: 0.8472 (tt) REVERT: A 394 MET cc_start: 0.9022 (tpp) cc_final: 0.8774 (tpp) REVERT: A 434 ASP cc_start: 0.8658 (p0) cc_final: 0.7920 (p0) REVERT: A 598 MET cc_start: 0.8856 (tmm) cc_final: 0.8462 (tmm) REVERT: A 603 SER cc_start: 0.8783 (m) cc_final: 0.8539 (m) REVERT: A 684 MET cc_start: 0.9133 (tpp) cc_final: 0.8403 (tpp) REVERT: B 37 MET cc_start: 0.7688 (tpt) cc_final: 0.7364 (tpt) REVERT: B 326 ASN cc_start: 0.7987 (m-40) cc_final: 0.7530 (t0) REVERT: B 582 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.7988 (t0) REVERT: C 41 SER cc_start: 0.8911 (p) cc_final: 0.8630 (m) REVERT: C 42 SER cc_start: 0.9178 (p) cc_final: 0.8975 (p) REVERT: C 47 ASP cc_start: 0.8288 (m-30) cc_final: 0.8007 (m-30) REVERT: C 75 ARG cc_start: 0.8118 (tpt-90) cc_final: 0.7914 (tpt-90) REVERT: D 49 ILE cc_start: 0.8597 (mt) cc_final: 0.8170 (tp) REVERT: D 55 ASN cc_start: 0.8537 (m-40) cc_final: 0.8257 (m-40) REVERT: D 72 LEU cc_start: 0.8578 (mp) cc_final: 0.8316 (mp) REVERT: D 122 ILE cc_start: 0.6769 (mm) cc_final: 0.6514 (tp) REVERT: E 3 LEU cc_start: 0.6961 (mt) cc_final: 0.6711 (mt) REVERT: E 7 ASP cc_start: 0.6133 (m-30) cc_final: 0.5447 (t0) REVERT: E 8 LYS cc_start: 0.7696 (ttmm) cc_final: 0.6777 (ttmt) REVERT: E 13 ARG cc_start: 0.7147 (ttm170) cc_final: 0.6799 (ttm-80) REVERT: E 15 GLU cc_start: 0.7071 (mp0) cc_final: 0.6742 (mp0) REVERT: E 44 VAL cc_start: 0.9319 (p) cc_final: 0.9095 (t) REVERT: E 58 THR cc_start: 0.7790 (m) cc_final: 0.7581 (m) REVERT: K 38 TYR cc_start: 0.5197 (t80) cc_final: 0.4700 (t80) REVERT: K 58 LYS cc_start: 0.4760 (ptpp) cc_final: 0.3977 (mtmm) REVERT: M 5 ASP cc_start: 0.5811 (t70) cc_final: 0.5318 (t70) outliers start: 2 outliers final: 1 residues processed: 358 average time/residue: 0.1301 time to fit residues: 74.4374 Evaluate side-chains 293 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 291 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 36 optimal weight: 7.9990 chunk 153 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 168 optimal weight: 10.0000 chunk 177 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS A 218 HIS A 224 ASN ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN A 457 HIS ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 HIS ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.105646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.087481 restraints weight = 43109.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.090440 restraints weight = 20493.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.092281 restraints weight = 12604.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.093637 restraints weight = 9281.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.094354 restraints weight = 7554.524| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22123 Z= 0.189 Angle : 0.922 72.739 31394 Z= 0.306 Chirality : 0.045 0.274 2654 Planarity : 0.004 0.059 4080 Dihedral : 19.181 89.319 3544 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.10 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: -0.25 (0.20), residues: 1858 helix: 0.88 (0.16), residues: 1022 sheet: -1.27 (0.58), residues: 88 loop : -1.50 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 112 TYR 0.022 0.002 TYR B 574 PHE 0.021 0.002 PHE B 647 TRP 0.038 0.001 TRP A 693 HIS 0.011 0.001 HIS B 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (22111) covalent geometry : angle 0.67337 / 0.30 (31358) hydrogen bonds : bond 0.05200 / 3.55 ( 780) hydrogen bonds : angle 4.52006 / 3.28 ( 2268) metal coordination : bond 0.01272 / 0.65 ( 12) metal coordination : angle 18.60362 / 12.70 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.8471 (mmm) cc_final: 0.7814 (tmm) REVERT: A 241 GLU cc_start: 0.7657 (pp20) cc_final: 0.7354 (pp20) REVERT: A 244 LEU cc_start: 0.8749 (tt) cc_final: 0.8405 (mt) REVERT: A 352 LEU cc_start: 0.8830 (tt) cc_final: 0.8483 (tt) REVERT: A 434 ASP cc_start: 0.8697 (p0) cc_final: 0.7985 (p0) REVERT: A 598 MET cc_start: 0.8950 (tmm) cc_final: 0.8553 (tmm) REVERT: A 603 SER cc_start: 0.8754 (m) cc_final: 0.8524 (m) REVERT: A 613 MET cc_start: 0.8739 (mtp) cc_final: 0.8507 (mtm) REVERT: A 684 MET cc_start: 0.9096 (tpp) cc_final: 0.8483 (tpp) REVERT: B 142 LEU cc_start: 0.9417 (mp) cc_final: 0.9068 (tp) REVERT: B 262 HIS cc_start: 0.8274 (t70) cc_final: 0.7538 (t70) REVERT: B 290 MET cc_start: 0.8744 (mmm) cc_final: 0.8505 (tpt) REVERT: B 427 LEU cc_start: 0.8702 (tp) cc_final: 0.8383 (tp) REVERT: B 659 MET cc_start: 0.8119 (ttp) cc_final: 0.7769 (ttp) REVERT: C 39 ILE cc_start: 0.8863 (tt) cc_final: 0.8663 (tt) REVERT: C 41 SER cc_start: 0.8927 (p) cc_final: 0.8572 (m) REVERT: C 47 ASP cc_start: 0.8392 (m-30) cc_final: 0.8084 (m-30) REVERT: C 75 ARG cc_start: 0.8127 (tpt-90) cc_final: 0.7780 (tpt-90) REVERT: D 1 MET cc_start: 0.4010 (tpp) cc_final: 0.3581 (tpt) REVERT: D 57 LEU cc_start: 0.7756 (tt) cc_final: 0.7402 (tt) REVERT: D 72 LEU cc_start: 0.8641 (mp) cc_final: 0.8371 (mp) REVERT: E 3 LEU cc_start: 0.6811 (mt) cc_final: 0.6501 (mt) REVERT: E 5 ARG cc_start: 0.6645 (mtt180) cc_final: 0.5838 (mmp80) REVERT: E 7 ASP cc_start: 0.6249 (m-30) cc_final: 0.5373 (t0) REVERT: E 8 LYS cc_start: 0.7692 (ttmm) cc_final: 0.6742 (mttm) REVERT: E 15 GLU cc_start: 0.7279 (mp0) cc_final: 0.7068 (mp0) REVERT: E 18 TRP cc_start: 0.8257 (m-10) cc_final: 0.7699 (m-10) REVERT: E 52 SER cc_start: 0.8644 (m) cc_final: 0.8421 (m) REVERT: E 58 THR cc_start: 0.7709 (m) cc_final: 0.7502 (m) REVERT: K 38 TYR cc_start: 0.5202 (t80) cc_final: 0.4723 (t80) REVERT: K 43 LYS cc_start: 0.7444 (ptpp) cc_final: 0.6495 (ptmt) REVERT: M 5 ASP cc_start: 0.5747 (t70) cc_final: 0.5253 (t70) outliers start: 0 outliers final: 0 residues processed: 365 average time/residue: 0.1293 time to fit residues: 76.0074 Evaluate side-chains 285 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 18 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 139 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 26 optimal weight: 20.0000 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN A 458 ASN ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 HIS ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN B 106 GLN ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 ASN ** B 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 ASN E 60 ASN K 74 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.100204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.082844 restraints weight = 43387.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.085495 restraints weight = 21730.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.087238 restraints weight = 13839.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.088207 restraints weight = 10381.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.089044 restraints weight = 8781.735| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 22123 Z= 0.270 Angle : 1.037 78.998 31394 Z= 0.348 Chirality : 0.049 0.261 2654 Planarity : 0.005 0.059 4080 Dihedral : 19.207 88.742 3544 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.28 % Favored : 94.66 % Rotamer: Outliers : 0.13 % Allowed : 4.19 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: -0.40 (0.19), residues: 1858 helix: 0.72 (0.16), residues: 1022 sheet: -1.39 (0.58), residues: 89 loop : -1.49 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 560 TYR 0.033 0.002 TYR A 692 PHE 0.028 0.002 PHE C 62 TRP 0.023 0.002 TRP A 645 HIS 0.010 0.002 HIS B 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.27 (22111) covalent geometry : angle 0.76832 / 0.34 (31358) hydrogen bonds : bond 0.05926 / 4.02 ( 780) hydrogen bonds : angle 4.81845 / 3.51 ( 2268) metal coordination : bond 0.01966 / 0.96 ( 12) metal coordination : angle 20.60263 / 13.61 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 352 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.8549 (mmm) cc_final: 0.8072 (tpt) REVERT: A 244 LEU cc_start: 0.8743 (tt) cc_final: 0.8423 (mt) REVERT: A 352 LEU cc_start: 0.8903 (tt) cc_final: 0.8577 (tt) REVERT: A 434 ASP cc_start: 0.8750 (p0) cc_final: 0.8035 (p0) REVERT: A 598 MET cc_start: 0.9116 (tmm) cc_final: 0.8667 (tmm) REVERT: A 613 MET cc_start: 0.8768 (mtp) cc_final: 0.8417 (mtm) REVERT: A 684 MET cc_start: 0.9198 (tpp) cc_final: 0.8506 (tpp) REVERT: B 190 TRP cc_start: 0.8730 (t-100) cc_final: 0.8528 (t-100) REVERT: B 262 HIS cc_start: 0.8408 (t70) cc_final: 0.7854 (t70) REVERT: B 582 ASN cc_start: 0.8340 (OUTLIER) cc_final: 0.8056 (t0) REVERT: B 614 MET cc_start: 0.7545 (tpp) cc_final: 0.7258 (tpt) REVERT: B 659 MET cc_start: 0.8213 (ttp) cc_final: 0.7789 (ttp) REVERT: C 39 ILE cc_start: 0.8917 (tt) cc_final: 0.8707 (tt) REVERT: C 41 SER cc_start: 0.8946 (p) cc_final: 0.8507 (m) REVERT: C 47 ASP cc_start: 0.8666 (m-30) cc_final: 0.8367 (m-30) REVERT: D 72 LEU cc_start: 0.8767 (mp) cc_final: 0.8526 (mp) REVERT: E 8 LYS cc_start: 0.7828 (ttmm) cc_final: 0.7409 (mttm) REVERT: E 18 TRP cc_start: 0.8202 (m-10) cc_final: 0.7513 (m-10) REVERT: E 52 SER cc_start: 0.8742 (m) cc_final: 0.8509 (m) REVERT: K 38 TYR cc_start: 0.5240 (t80) cc_final: 0.4675 (t80) REVERT: K 43 LYS cc_start: 0.7918 (ptpp) cc_final: 0.7698 (ptpp) REVERT: M 5 ASP cc_start: 0.5746 (t70) cc_final: 0.5280 (t70) outliers start: 2 outliers final: 0 residues processed: 353 average time/residue: 0.1229 time to fit residues: 69.4815 Evaluate side-chains 282 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 281 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 49 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 GLN A 224 ASN ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 HIS ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.102337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.084842 restraints weight = 42996.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.087520 restraints weight = 21481.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.089305 restraints weight = 13637.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.090288 restraints weight = 10208.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.091083 restraints weight = 8641.192| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 22123 Z= 0.199 Angle : 0.948 67.071 31394 Z= 0.317 Chirality : 0.046 0.235 2654 Planarity : 0.004 0.056 4080 Dihedral : 18.735 86.535 3544 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.26 % Favored : 95.69 % Rotamer: Outliers : 0.07 % Allowed : 3.60 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: -0.16 (0.20), residues: 1858 helix: 0.92 (0.16), residues: 1007 sheet: -1.45 (0.57), residues: 89 loop : -1.31 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 5 TYR 0.021 0.002 TYR B 574 PHE 0.020 0.002 PHE B 647 TRP 0.029 0.001 TRP A 693 HIS 0.007 0.001 HIS B 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.20 (22111) covalent geometry : angle 0.69592 / 0.31 (31358) hydrogen bonds : bond 0.05350 / 3.62 ( 780) hydrogen bonds : angle 4.67804 / 3.39 ( 2268) metal coordination : bond 0.01445 / 0.77 ( 12) metal coordination : angle 19.04133 / 12.54 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 361 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.8435 (mmm) cc_final: 0.7899 (tmm) REVERT: A 244 LEU cc_start: 0.8685 (tt) cc_final: 0.8385 (mt) REVERT: A 352 LEU cc_start: 0.8834 (tt) cc_final: 0.8498 (tt) REVERT: A 461 MET cc_start: 0.8256 (mmm) cc_final: 0.8053 (mmm) REVERT: A 560 ARG cc_start: 0.7586 (ptt-90) cc_final: 0.7050 (ptt-90) REVERT: A 598 MET cc_start: 0.9079 (tmm) cc_final: 0.8624 (tmm) REVERT: A 613 MET cc_start: 0.8839 (mtp) cc_final: 0.8391 (mtm) REVERT: B 262 HIS cc_start: 0.8322 (t70) cc_final: 0.7807 (t70) REVERT: B 659 MET cc_start: 0.8315 (ttp) cc_final: 0.7880 (ttp) REVERT: B 673 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8711 (tm-30) REVERT: C 41 SER cc_start: 0.8863 (p) cc_final: 0.8472 (m) REVERT: C 47 ASP cc_start: 0.8726 (m-30) cc_final: 0.8323 (m-30) REVERT: D 57 LEU cc_start: 0.7539 (tt) cc_final: 0.7321 (tt) REVERT: D 72 LEU cc_start: 0.8710 (mp) cc_final: 0.8423 (mp) REVERT: E 8 LYS cc_start: 0.7828 (ttmm) cc_final: 0.7309 (mttm) REVERT: E 18 TRP cc_start: 0.8236 (m-10) cc_final: 0.7663 (m-10) REVERT: E 52 SER cc_start: 0.8755 (m) cc_final: 0.8476 (m) REVERT: E 58 THR cc_start: 0.7812 (m) cc_final: 0.7606 (m) REVERT: K 38 TYR cc_start: 0.5336 (t80) cc_final: 0.4721 (t80) REVERT: M 5 ASP cc_start: 0.5836 (t70) cc_final: 0.5348 (t70) outliers start: 1 outliers final: 0 residues processed: 361 average time/residue: 0.1282 time to fit residues: 74.8377 Evaluate side-chains 282 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 24 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 119 optimal weight: 20.0000 chunk 92 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 141 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN A 458 ASN ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 GLN ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN K 74 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.106864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.089543 restraints weight = 42365.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.092375 restraints weight = 20808.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.094191 restraints weight = 13045.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.095411 restraints weight = 9617.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.096277 restraints weight = 7870.559| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22123 Z= 0.130 Angle : 0.866 61.569 31394 Z= 0.287 Chirality : 0.043 0.212 2654 Planarity : 0.004 0.052 4080 Dihedral : 18.120 87.945 3544 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.37 % Favored : 95.58 % Rotamer: Outliers : 0.07 % Allowed : 2.13 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: 0.01 (0.20), residues: 1858 helix: 1.08 (0.16), residues: 1019 sheet: -1.44 (0.57), residues: 89 loop : -1.31 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 560 TYR 0.017 0.001 TYR B 574 PHE 0.021 0.002 PHE A 84 TRP 0.035 0.001 TRP A 693 HIS 0.006 0.001 HIS K 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (22111) covalent geometry : angle 0.63162 / 0.28 (31358) hydrogen bonds : bond 0.04573 / 3.07 ( 780) hydrogen bonds : angle 4.40360 / 3.19 ( 2268) metal coordination : bond 0.01138 / 0.44 ( 12) metal coordination : angle 17.52181 / 11.80 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 365 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7234 (tp30) cc_final: 0.6421 (mm-30) REVERT: A 197 MET cc_start: 0.8341 (mmm) cc_final: 0.8036 (tmm) REVERT: A 242 PHE cc_start: 0.6916 (m-80) cc_final: 0.6698 (m-80) REVERT: A 244 LEU cc_start: 0.8713 (tt) cc_final: 0.8370 (mt) REVERT: A 352 LEU cc_start: 0.8728 (tt) cc_final: 0.8361 (tt) REVERT: A 454 LEU cc_start: 0.9069 (mt) cc_final: 0.8861 (mt) REVERT: A 461 MET cc_start: 0.8213 (mmm) cc_final: 0.8010 (mmm) REVERT: A 584 GLN cc_start: 0.8677 (mt0) cc_final: 0.8260 (mp10) REVERT: A 598 MET cc_start: 0.8877 (tmm) cc_final: 0.8391 (tmm) REVERT: A 613 MET cc_start: 0.8778 (mtp) cc_final: 0.8313 (mtm) REVERT: A 719 SER cc_start: 0.8801 (t) cc_final: 0.8574 (m) REVERT: B 142 LEU cc_start: 0.9364 (mp) cc_final: 0.9052 (tp) REVERT: B 290 MET cc_start: 0.8519 (tpt) cc_final: 0.7139 (tpp) REVERT: B 542 LYS cc_start: 0.8106 (mmmm) cc_final: 0.7634 (mttt) REVERT: C 41 SER cc_start: 0.8768 (p) cc_final: 0.8444 (m) REVERT: C 47 ASP cc_start: 0.8512 (m-30) cc_final: 0.7994 (m-30) REVERT: D 28 TYR cc_start: 0.8045 (m-80) cc_final: 0.7783 (m-10) REVERT: D 57 LEU cc_start: 0.7566 (tt) cc_final: 0.7268 (tt) REVERT: D 72 LEU cc_start: 0.8619 (mp) cc_final: 0.8330 (mp) REVERT: E 5 ARG cc_start: 0.6915 (mtt180) cc_final: 0.5779 (mmp80) REVERT: E 8 LYS cc_start: 0.7696 (ttmm) cc_final: 0.7265 (mttm) REVERT: E 18 TRP cc_start: 0.8238 (m-10) cc_final: 0.7600 (m-10) REVERT: E 52 SER cc_start: 0.8629 (m) cc_final: 0.8336 (m) REVERT: K 38 TYR cc_start: 0.5198 (t80) cc_final: 0.4705 (t80) REVERT: M 5 ASP cc_start: 0.5659 (t70) cc_final: 0.5279 (t70) outliers start: 1 outliers final: 0 residues processed: 365 average time/residue: 0.1308 time to fit residues: 76.9484 Evaluate side-chains 290 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 72 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 122 optimal weight: 0.0070 chunk 67 optimal weight: 1.9990 chunk 169 optimal weight: 30.0000 chunk 117 optimal weight: 0.9990 chunk 113 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN A 458 ASN ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 74 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.109745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.092451 restraints weight = 41741.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.095338 restraints weight = 20438.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.097267 restraints weight = 12765.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.098319 restraints weight = 9351.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.099238 restraints weight = 7780.917| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22123 Z= 0.114 Angle : 0.853 62.876 31394 Z= 0.279 Chirality : 0.042 0.216 2654 Planarity : 0.004 0.056 4080 Dihedral : 17.717 85.706 3544 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.88 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: 0.17 (0.20), residues: 1858 helix: 1.23 (0.16), residues: 1014 sheet: -1.40 (0.57), residues: 89 loop : -1.24 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 73 TYR 0.024 0.001 TYR B 125 PHE 0.024 0.002 PHE A 92 TRP 0.027 0.001 TRP A 693 HIS 0.015 0.001 HIS A 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (22111) covalent geometry : angle 0.61339 / 0.27 (31358) hydrogen bonds : bond 0.04263 / 2.86 ( 780) hydrogen bonds : angle 4.26723 / 3.09 ( 2268) metal coordination : bond 0.01596 / 0.72 ( 12) metal coordination : angle 17.50819 / 11.91 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7125 (tp30) cc_final: 0.6237 (mm-30) REVERT: A 197 MET cc_start: 0.8237 (mmm) cc_final: 0.8028 (tmm) REVERT: A 244 LEU cc_start: 0.8661 (tt) cc_final: 0.8288 (mt) REVERT: A 352 LEU cc_start: 0.8704 (tt) cc_final: 0.8352 (tt) REVERT: A 461 MET cc_start: 0.8123 (mmm) cc_final: 0.7895 (mmm) REVERT: A 544 VAL cc_start: 0.8628 (t) cc_final: 0.8385 (t) REVERT: A 584 GLN cc_start: 0.8555 (mt0) cc_final: 0.8112 (mp10) REVERT: A 598 MET cc_start: 0.8722 (tmm) cc_final: 0.8146 (tmm) REVERT: A 613 MET cc_start: 0.8773 (mtp) cc_final: 0.8254 (mtm) REVERT: A 698 GLU cc_start: 0.8274 (tm-30) cc_final: 0.8017 (tm-30) REVERT: A 719 SER cc_start: 0.8815 (t) cc_final: 0.8539 (m) REVERT: B 142 LEU cc_start: 0.9368 (mp) cc_final: 0.9107 (tp) REVERT: B 262 HIS cc_start: 0.7901 (t-170) cc_final: 0.7411 (t70) REVERT: B 290 MET cc_start: 0.8262 (tpt) cc_final: 0.7652 (tpp) REVERT: B 542 LYS cc_start: 0.7946 (mmmm) cc_final: 0.7566 (mttt) REVERT: B 582 ASN cc_start: 0.7501 (t0) cc_final: 0.7099 (t0) REVERT: B 659 MET cc_start: 0.7530 (ttp) cc_final: 0.7301 (ttp) REVERT: C 41 SER cc_start: 0.8701 (p) cc_final: 0.8440 (m) REVERT: D 28 TYR cc_start: 0.8069 (m-80) cc_final: 0.7864 (m-10) REVERT: D 49 ILE cc_start: 0.8527 (mt) cc_final: 0.8288 (tp) REVERT: D 72 LEU cc_start: 0.8569 (mp) cc_final: 0.8289 (mp) REVERT: E 18 TRP cc_start: 0.8272 (m-10) cc_final: 0.7656 (m-10) REVERT: E 52 SER cc_start: 0.8542 (m) cc_final: 0.8240 (m) REVERT: E 58 THR cc_start: 0.7852 (m) cc_final: 0.7547 (m) REVERT: K 38 TYR cc_start: 0.5107 (t80) cc_final: 0.4711 (t80) REVERT: M 5 ASP cc_start: 0.5591 (t70) cc_final: 0.5241 (t70) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.1288 time to fit residues: 79.0130 Evaluate side-chains 298 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 183 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 160 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN K 74 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.100520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.082521 restraints weight = 43486.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.085333 restraints weight = 20679.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.087187 restraints weight = 12813.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.088316 restraints weight = 9466.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.089122 restraints weight = 7811.921| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 22123 Z= 0.278 Angle : 1.020 72.525 31394 Z= 0.357 Chirality : 0.050 0.283 2654 Planarity : 0.005 0.058 4080 Dihedral : 18.478 85.977 3544 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.07 % Favored : 94.88 % Rotamer: Outliers : 0.07 % Allowed : 1.00 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: -0.12 (0.20), residues: 1858 helix: 0.92 (0.16), residues: 1005 sheet: -1.25 (0.59), residues: 87 loop : -1.28 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 73 TYR 0.024 0.002 TYR A 692 PHE 0.034 0.002 PHE B 385 TRP 0.029 0.002 TRP B 295 HIS 0.010 0.002 HIS B 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00614 / 0.28 (22111) covalent geometry : angle 0.78327 / 0.35 (31358) hydrogen bonds : bond 0.05924 / 4.00 ( 780) hydrogen bonds : angle 4.82075 / 3.49 ( 2268) metal coordination : bond 0.01495 / 0.70 ( 12) metal coordination : angle 19.32379 / 12.97 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 346 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.8445 (mmm) cc_final: 0.7835 (tmm) REVERT: A 241 GLU cc_start: 0.8193 (pp20) cc_final: 0.7950 (pp20) REVERT: A 244 LEU cc_start: 0.8734 (tt) cc_final: 0.8373 (mt) REVERT: A 352 LEU cc_start: 0.8772 (tt) cc_final: 0.8499 (tt) REVERT: A 434 ASP cc_start: 0.8762 (p0) cc_final: 0.7702 (p0) REVERT: A 584 GLN cc_start: 0.8849 (mt0) cc_final: 0.8369 (mp10) REVERT: A 613 MET cc_start: 0.8858 (mtp) cc_final: 0.8322 (mtm) REVERT: B 262 HIS cc_start: 0.8255 (t-170) cc_final: 0.7640 (t70) REVERT: B 290 MET cc_start: 0.8700 (tpt) cc_final: 0.7118 (tpp) REVERT: B 381 MET cc_start: 0.8718 (ptm) cc_final: 0.8271 (tmm) REVERT: C 41 SER cc_start: 0.8794 (p) cc_final: 0.8437 (m) REVERT: C 47 ASP cc_start: 0.8829 (m-30) cc_final: 0.8283 (m-30) REVERT: D 28 TYR cc_start: 0.8141 (m-80) cc_final: 0.7849 (m-10) REVERT: D 72 LEU cc_start: 0.8663 (mp) cc_final: 0.8393 (mp) REVERT: E 8 LYS cc_start: 0.7885 (ttmm) cc_final: 0.7476 (mttm) REVERT: E 18 TRP cc_start: 0.8264 (m-10) cc_final: 0.7705 (m-10) REVERT: E 52 SER cc_start: 0.8759 (m) cc_final: 0.8479 (m) REVERT: E 58 THR cc_start: 0.7833 (m) cc_final: 0.7598 (m) REVERT: K 38 TYR cc_start: 0.5278 (t80) cc_final: 0.4675 (t80) REVERT: M 5 ASP cc_start: 0.5881 (t70) cc_final: 0.5539 (t70) outliers start: 1 outliers final: 1 residues processed: 347 average time/residue: 0.1389 time to fit residues: 77.8660 Evaluate side-chains 281 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 280 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 53 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 99 optimal weight: 0.0470 chunk 175 optimal weight: 0.9990 chunk 164 optimal weight: 0.2980 chunk 46 optimal weight: 0.0870 overall best weight: 1.4860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 708 ASN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 HIS ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN K 74 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.106689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.089083 restraints weight = 42397.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.091927 restraints weight = 20934.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.093736 restraints weight = 13168.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.095037 restraints weight = 9767.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.095678 restraints weight = 7986.579| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22123 Z= 0.129 Angle : 0.891 64.499 31394 Z= 0.297 Chirality : 0.043 0.247 2654 Planarity : 0.004 0.052 4080 Dihedral : 17.857 85.193 3544 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.77 % Favored : 96.17 % Rotamer: Outliers : 0.07 % Allowed : 0.13 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: 0.05 (0.20), residues: 1858 helix: 1.06 (0.16), residues: 1013 sheet: -1.43 (0.55), residues: 95 loop : -1.17 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 539 TYR 0.015 0.001 TYR B 125 PHE 0.036 0.002 PHE A 92 TRP 0.018 0.001 TRP B 645 HIS 0.009 0.001 HIS B 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (22111) covalent geometry : angle 0.65115 / 0.29 (31358) hydrogen bonds : bond 0.04766 / 3.18 ( 780) hydrogen bonds : angle 4.44887 / 3.22 ( 2268) metal coordination : bond 0.01262 / 0.49 ( 12) metal coordination : angle 17.97876 / 12.15 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 360 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7127 (tp30) cc_final: 0.6244 (mm-30) REVERT: A 117 VAL cc_start: 0.9312 (t) cc_final: 0.9096 (p) REVERT: A 197 MET cc_start: 0.8256 (mmm) cc_final: 0.7888 (tmm) REVERT: A 221 MET cc_start: 0.8987 (mmm) cc_final: 0.8747 (mmm) REVERT: A 241 GLU cc_start: 0.8003 (pp20) cc_final: 0.7555 (pp20) REVERT: A 244 LEU cc_start: 0.8688 (tt) cc_final: 0.8296 (mt) REVERT: A 310 MET cc_start: 0.8258 (tpt) cc_final: 0.7913 (tpt) REVERT: A 352 LEU cc_start: 0.8693 (tt) cc_final: 0.8329 (tt) REVERT: A 429 MET cc_start: 0.8262 (mmp) cc_final: 0.7924 (mmp) REVERT: A 461 MET cc_start: 0.7980 (mmm) cc_final: 0.7637 (mmm) REVERT: A 584 GLN cc_start: 0.8662 (mt0) cc_final: 0.8266 (mp10) REVERT: A 598 MET cc_start: 0.8719 (tmm) cc_final: 0.8395 (tmm) REVERT: A 613 MET cc_start: 0.8807 (mtp) cc_final: 0.8075 (mtm) REVERT: A 684 MET cc_start: 0.8993 (tpp) cc_final: 0.8314 (tpp) REVERT: A 698 GLU cc_start: 0.8347 (tm-30) cc_final: 0.8138 (tm-30) REVERT: A 719 SER cc_start: 0.8804 (t) cc_final: 0.8553 (m) REVERT: B 201 GLU cc_start: 0.5582 (mm-30) cc_final: 0.5259 (mm-30) REVERT: B 262 HIS cc_start: 0.8057 (t-170) cc_final: 0.7449 (t70) REVERT: B 290 MET cc_start: 0.8374 (tpt) cc_final: 0.7845 (tpp) REVERT: B 348 GLN cc_start: 0.8758 (tt0) cc_final: 0.8538 (tt0) REVERT: B 381 MET cc_start: 0.8589 (ptm) cc_final: 0.8148 (tmm) REVERT: B 542 LYS cc_start: 0.7825 (mmmm) cc_final: 0.7416 (mttt) REVERT: B 557 ASP cc_start: 0.7761 (t0) cc_final: 0.7230 (t0) REVERT: B 659 MET cc_start: 0.8116 (ttp) cc_final: 0.7769 (ttp) REVERT: C 41 SER cc_start: 0.8797 (p) cc_final: 0.8393 (m) REVERT: D 28 TYR cc_start: 0.8062 (m-80) cc_final: 0.7843 (m-10) REVERT: D 57 LEU cc_start: 0.7582 (tt) cc_final: 0.7293 (tt) REVERT: D 72 LEU cc_start: 0.8664 (mp) cc_final: 0.8385 (mp) REVERT: D 97 LEU cc_start: 0.8210 (mm) cc_final: 0.7853 (mp) REVERT: E 8 LYS cc_start: 0.7795 (ttmm) cc_final: 0.7303 (mttm) REVERT: E 18 TRP cc_start: 0.8365 (m-10) cc_final: 0.7727 (m-10) REVERT: E 52 SER cc_start: 0.8636 (m) cc_final: 0.8327 (m) REVERT: E 58 THR cc_start: 0.7731 (m) cc_final: 0.7517 (m) REVERT: K 38 TYR cc_start: 0.5211 (t80) cc_final: 0.4727 (t80) REVERT: M 5 ASP cc_start: 0.5732 (t70) cc_final: 0.5410 (t70) outliers start: 1 outliers final: 0 residues processed: 360 average time/residue: 0.1293 time to fit residues: 75.2686 Evaluate side-chains 289 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 37 optimal weight: 6.9990 chunk 118 optimal weight: 0.0470 chunk 106 optimal weight: 3.9990 chunk 73 optimal weight: 0.0060 chunk 39 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 overall best weight: 1.4100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN A 421 ASN A 458 ASN ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 ASN E 60 ASN K 74 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.107111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.089431 restraints weight = 42118.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.092277 restraints weight = 20986.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.094147 restraints weight = 13259.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.095288 restraints weight = 9846.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.096197 restraints weight = 8131.710| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22123 Z= 0.125 Angle : 0.864 63.021 31394 Z= 0.288 Chirality : 0.042 0.235 2654 Planarity : 0.004 0.050 4080 Dihedral : 17.508 83.513 3544 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.15 % Favored : 95.80 % Rotamer: Outliers : 0.13 % Allowed : 0.27 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: 0.15 (0.20), residues: 1858 helix: 1.15 (0.16), residues: 1021 sheet: -1.19 (0.58), residues: 85 loop : -1.19 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 539 TYR 0.025 0.001 TYR B 632 PHE 0.027 0.002 PHE A 84 TRP 0.015 0.001 TRP B 645 HIS 0.014 0.001 HIS A 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (22111) covalent geometry : angle 0.62989 / 0.28 (31358) hydrogen bonds : bond 0.04505 / 3.01 ( 780) hydrogen bonds : angle 4.34325 / 3.15 ( 2268) metal coordination : bond 0.01255 / 0.47 ( 12) metal coordination : angle 17.49591 / 11.91 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3392.73 seconds wall clock time: 59 minutes 29.33 seconds (3569.33 seconds total)