Starting phenix.real_space_refine on Fri Mar 6 19:54:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7o1v_12697/03_2026/7o1v_12697.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o1v_12697/03_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_12697/03_2026/7o1v_12697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o1v_12697/03_2026/7o1v_12697.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7o1v_12697/03_2026/7o1v_12697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o1v_12697/03_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-5986/lib/python3.9/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: 4.45, per 1000 atoms: 0.21 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: 1.82 Conformation dependent library (CDL) restraints added in 665.2 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: 0.43 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: 2.87 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 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 - 21.96: 8640 21.96 - 43.91: 1146 43.91 - 65.87: 406 65.87 - 87.83: 53 87.83 - 109.79: 19 Dihedral angle restraints: 10264 sinusoidal: 4953 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 10261 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.020 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 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 : 21.507 109.785 6882 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 covalent geometry : bond 0.02488 (22111) covalent geometry : angle 2.76916 (31358) hydrogen bonds : bond 0.14622 ( 780) hydrogen bonds : angle 6.14354 ( 2268) metal coordination : bond 0.01695 ( 12) metal coordination : angle 20.68809 ( 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 : 0.393 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: 0.1262 time to fit residues: 75.3861 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 : 0.564 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3257 r_free = 0.3257 target = 0.109725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.091699 restraints weight = 41864.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.094495 restraints weight = 21066.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.096372 restraints weight = 13463.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.097450 restraints weight = 10058.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.098342 restraints weight = 8384.748| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22123 Z= 0.160 Angle : 0.925 65.348 31394 Z= 0.306 Chirality : 0.044 0.187 2654 Planarity : 0.004 0.067 4080 Dihedral : 20.462 89.053 3749 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.77 % Favored : 96.17 % Rotamer: Outliers : 0.20 % Allowed : 6.13 % Favored : 93.68 % 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: -0.63 (0.19), residues: 1858 helix: 0.63 (0.16), residues: 1014 sheet: -1.43 (0.59), residues: 82 loop : -1.75 (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 0.025 0.002 PHE A 84 TRP 0.026 0.001 TRP B 190 HIS 0.006 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00352 (22111) covalent geometry : angle 0.68859 (31358) hydrogen bonds : bond 0.05027 ( 780) hydrogen bonds : angle 4.59536 ( 2268) metal coordination : bond 0.01104 ( 12) metal coordination : angle 18.24373 ( 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 372 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 369 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7095 (tp30) cc_final: 0.6789 (tp30) REVERT: A 197 MET cc_start: 0.8428 (mmm) cc_final: 0.8095 (tmm) REVERT: A 244 LEU cc_start: 0.8753 (tt) cc_final: 0.8334 (mt) REVERT: A 300 ILE cc_start: 0.9171 (tp) cc_final: 0.8956 (tp) REVERT: A 342 GLU cc_start: 0.8214 (mp0) cc_final: 0.7996 (mp0) REVERT: A 352 LEU cc_start: 0.8823 (tt) cc_final: 0.8519 (tt) REVERT: A 434 ASP cc_start: 0.8648 (p0) cc_final: 0.7998 (p0) REVERT: A 603 SER cc_start: 0.8823 (m) cc_final: 0.8614 (m) REVERT: A 719 SER cc_start: 0.8951 (t) cc_final: 0.8604 (m) REVERT: A 744 LEU cc_start: 0.8771 (mp) cc_final: 0.8564 (mp) REVERT: B 290 MET cc_start: 0.7625 (mmp) cc_final: 0.7385 (ttp) REVERT: B 326 ASN cc_start: 0.7954 (m-40) cc_final: 0.7433 (t0) REVERT: B 348 GLN cc_start: 0.8771 (tt0) cc_final: 0.8550 (tt0) REVERT: C 39 ILE cc_start: 0.8736 (tt) cc_final: 0.8467 (tt) REVERT: D 49 ILE cc_start: 0.8447 (mt) cc_final: 0.8169 (tp) REVERT: D 55 ASN cc_start: 0.8527 (m-40) cc_final: 0.8283 (m-40) REVERT: D 122 ILE cc_start: 0.6664 (mm) cc_final: 0.6315 (tp) REVERT: E 7 ASP cc_start: 0.5758 (m-30) cc_final: 0.5164 (t70) REVERT: E 8 LYS cc_start: 0.7625 (ttmm) cc_final: 0.7053 (ttmt) REVERT: E 43 ARG cc_start: 0.8379 (mtm180) cc_final: 0.8174 (mtm180) REVERT: E 58 THR cc_start: 0.7830 (m) cc_final: 0.7624 (m) REVERT: K 38 TYR cc_start: 0.5231 (t80) cc_final: 0.4789 (t80) REVERT: K 70 MET cc_start: 0.7138 (ttt) cc_final: 0.6702 (ttp) outliers start: 3 outliers final: 2 residues processed: 369 average time/residue: 0.1402 time to fit residues: 84.0722 Evaluate side-chains 298 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 296 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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: 4.9990 chunk 101 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 47 optimal weight: 9.9990 chunk 166 optimal weight: 0.9990 chunk 177 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 HIS ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 HIS A 543 HIS ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 HIS ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS B 582 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.089474 restraints weight = 42416.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.092260 restraints weight = 21299.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.094119 restraints weight = 13621.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.095143 restraints weight = 10178.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.095966 restraints weight = 8600.108| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22123 Z= 0.154 Angle : 0.872 66.361 31394 Z= 0.292 Chirality : 0.043 0.192 2654 Planarity : 0.004 0.061 4080 Dihedral : 19.327 84.711 3749 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.10 % Favored : 95.85 % Rotamer: Outliers : 0.07 % Allowed : 4.93 % Favored : 95.01 % 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: -0.30 (0.19), residues: 1858 helix: 0.86 (0.16), residues: 1024 sheet: -1.56 (0.58), residues: 84 loop : -1.54 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 560 TYR 0.021 0.002 TYR B 291 PHE 0.033 0.002 PHE A 609 TRP 0.017 0.001 TRP B 591 HIS 0.015 0.001 HIS A 608 Details of bonding type rmsd covalent geometry : bond 0.00342 (22111) covalent geometry : angle 0.64372 (31358) hydrogen bonds : bond 0.04955 ( 780) hydrogen bonds : angle 4.48740 ( 2268) metal coordination : bond 0.01049 ( 12) metal coordination : angle 17.40347 ( 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 367 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 366 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7244 (tp30) cc_final: 0.6896 (tp30) REVERT: A 168 MET cc_start: 0.8450 (ppp) cc_final: 0.8190 (ppp) REVERT: A 241 GLU cc_start: 0.7709 (pp20) cc_final: 0.7447 (pp20) REVERT: A 244 LEU cc_start: 0.8733 (tt) cc_final: 0.8404 (mt) REVERT: A 292 ASP cc_start: 0.8164 (m-30) cc_final: 0.7946 (m-30) REVERT: A 310 MET cc_start: 0.8903 (tpp) cc_final: 0.7969 (mmm) REVERT: A 344 LEU cc_start: 0.9173 (tt) cc_final: 0.8972 (tt) REVERT: A 478 LEU cc_start: 0.9103 (mp) cc_final: 0.8816 (mp) REVERT: A 532 PHE cc_start: 0.9405 (t80) cc_final: 0.8478 (t80) REVERT: A 560 ARG cc_start: 0.7354 (ptt-90) cc_final: 0.7101 (ptt-90) REVERT: A 598 MET cc_start: 0.8673 (tmm) cc_final: 0.8327 (tmm) REVERT: A 603 SER cc_start: 0.8623 (m) cc_final: 0.8399 (m) REVERT: A 684 MET cc_start: 0.8949 (tpp) cc_final: 0.8402 (tpp) REVERT: A 719 SER cc_start: 0.8953 (t) cc_final: 0.8682 (m) REVERT: B 37 MET cc_start: 0.7590 (tpt) cc_final: 0.7351 (tpt) REVERT: B 326 ASN cc_start: 0.7914 (m-40) cc_final: 0.7466 (t0) REVERT: B 348 GLN cc_start: 0.8919 (tt0) cc_final: 0.8693 (tt0) REVERT: B 582 ASN cc_start: 0.8166 (OUTLIER) cc_final: 0.7923 (t0) REVERT: C 47 ASP cc_start: 0.7959 (m-30) cc_final: 0.7611 (m-30) REVERT: C 75 ARG cc_start: 0.8028 (tpt-90) cc_final: 0.7776 (tpt170) REVERT: D 1 MET cc_start: 0.4380 (tpp) cc_final: 0.3955 (tpt) REVERT: D 49 ILE cc_start: 0.8570 (mt) cc_final: 0.8232 (tp) REVERT: D 55 ASN cc_start: 0.8476 (m-40) cc_final: 0.8201 (m-40) REVERT: D 72 LEU cc_start: 0.8542 (mp) cc_final: 0.8263 (mp) REVERT: D 122 ILE cc_start: 0.6794 (mm) cc_final: 0.6482 (tp) REVERT: E 3 LEU cc_start: 0.6823 (mt) cc_final: 0.6602 (mt) REVERT: E 7 ASP cc_start: 0.5907 (m-30) cc_final: 0.5308 (t0) REVERT: E 8 LYS cc_start: 0.7585 (ttmm) cc_final: 0.6617 (ttmt) REVERT: E 15 GLU cc_start: 0.6952 (mp0) cc_final: 0.6675 (mp0) REVERT: K 38 TYR cc_start: 0.5094 (t80) cc_final: 0.4704 (t80) REVERT: K 58 LYS cc_start: 0.4713 (ptpp) cc_final: 0.4136 (mtmm) REVERT: M 5 ASP cc_start: 0.7621 (p0) cc_final: 0.7201 (p0) outliers start: 1 outliers final: 0 residues processed: 367 average time/residue: 0.1450 time to fit residues: 85.1754 Evaluate side-chains 293 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 292 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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: 9.9990 chunk 153 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 168 optimal weight: 9.9990 chunk 177 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 136 optimal weight: 0.2980 chunk 71 optimal weight: 2.9990 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN A 457 HIS ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 HIS B 177 HIS ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS ** B 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.103517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.085893 restraints weight = 43247.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.088582 restraints weight = 21502.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.090360 restraints weight = 13722.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.091533 restraints weight = 10282.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.092172 restraints weight = 8509.700| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 22123 Z= 0.220 Angle : 0.961 75.618 31394 Z= 0.326 Chirality : 0.047 0.230 2654 Planarity : 0.005 0.055 4080 Dihedral : 19.318 88.934 3749 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.64 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % 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: -0.28 (0.20), residues: 1858 helix: 0.83 (0.16), residues: 1019 sheet: -1.30 (0.58), residues: 90 loop : -1.47 (0.23), residues: 749 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 0.025 0.002 PHE A 84 TRP 0.042 0.002 TRP A 693 HIS 0.011 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00488 (22111) covalent geometry : angle 0.71751 (31358) hydrogen bonds : bond 0.05565 ( 780) hydrogen bonds : angle 4.61034 ( 2268) metal coordination : bond 0.01534 ( 12) metal coordination : angle 18.90257 ( 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 : 0.602 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.8393 (mmm) cc_final: 0.7958 (tmm) REVERT: A 241 GLU cc_start: 0.7917 (pp20) cc_final: 0.7613 (pp20) REVERT: A 244 LEU cc_start: 0.8748 (tt) cc_final: 0.8430 (mt) REVERT: A 352 LEU cc_start: 0.8904 (tt) cc_final: 0.8661 (tt) REVERT: A 434 ASP cc_start: 0.8741 (p0) cc_final: 0.8012 (p0) REVERT: A 584 GLN cc_start: 0.8707 (mt0) cc_final: 0.8165 (mp10) REVERT: A 598 MET cc_start: 0.8978 (tmm) cc_final: 0.8521 (tmm) REVERT: A 603 SER cc_start: 0.8867 (m) cc_final: 0.8646 (m) REVERT: A 613 MET cc_start: 0.8829 (mtp) cc_final: 0.8493 (mtp) REVERT: B 37 MET cc_start: 0.7747 (tpt) cc_final: 0.7284 (tpt) REVERT: B 262 HIS cc_start: 0.8313 (t70) cc_final: 0.7570 (t70) REVERT: B 673 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8427 (tm-30) REVERT: C 47 ASP cc_start: 0.8399 (m-30) cc_final: 0.8030 (m-30) REVERT: C 75 ARG cc_start: 0.7966 (tpt-90) cc_final: 0.7695 (tpt-90) REVERT: C 77 MET cc_start: 0.7926 (tpp) cc_final: 0.7706 (tpp) REVERT: D 1 MET cc_start: 0.4039 (tpp) cc_final: 0.3593 (tpt) REVERT: D 55 ASN cc_start: 0.8413 (m-40) cc_final: 0.8210 (m-40) REVERT: D 57 LEU cc_start: 0.7817 (tt) cc_final: 0.7458 (tt) REVERT: D 72 LEU cc_start: 0.8688 (mp) cc_final: 0.8427 (mp) REVERT: D 122 ILE cc_start: 0.6895 (mm) cc_final: 0.6666 (tp) REVERT: E 3 LEU cc_start: 0.6913 (mt) cc_final: 0.6608 (mt) REVERT: E 5 ARG cc_start: 0.6591 (mtt180) cc_final: 0.5791 (mmp80) REVERT: E 7 ASP cc_start: 0.6158 (m-30) cc_final: 0.5327 (t0) REVERT: E 8 LYS cc_start: 0.7660 (ttmm) cc_final: 0.6599 (mttm) REVERT: E 15 GLU cc_start: 0.7273 (mp0) cc_final: 0.7017 (mp0) REVERT: E 52 SER cc_start: 0.8669 (m) cc_final: 0.8469 (m) REVERT: E 58 THR cc_start: 0.7779 (m) cc_final: 0.7522 (m) REVERT: K 38 TYR cc_start: 0.5208 (t80) cc_final: 0.4721 (t80) REVERT: M 5 ASP cc_start: 0.7716 (p0) cc_final: 0.7220 (m-30) outliers start: 0 outliers final: 0 residues processed: 365 average time/residue: 0.1426 time to fit residues: 83.7801 Evaluate side-chains 286 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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: 9.9990 chunk 86 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 139 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 chunk 1 optimal weight: 0.0770 chunk 26 optimal weight: 9.9990 overall best weight: 1.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 GLN ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 ASN D 55 ASN ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 74 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.108518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.090380 restraints weight = 42684.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.093196 restraints weight = 21206.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.094919 restraints weight = 13532.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.096229 restraints weight = 10299.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.096999 restraints weight = 8507.741| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 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 = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22123 Z= 0.133 Angle : 0.868 67.380 31394 Z= 0.281 Chirality : 0.042 0.252 2654 Planarity : 0.004 0.050 4080 Dihedral : 18.566 86.334 3749 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.88 % Favored : 96.06 % Rotamer: Outliers : 0.07 % Allowed : 3.00 % Favored : 96.94 % 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: 0.02 (0.20), residues: 1858 helix: 1.08 (0.16), residues: 1027 sheet: -1.33 (0.58), residues: 89 loop : -1.33 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 112 TYR 0.021 0.001 TYR B 574 PHE 0.032 0.002 PHE B 429 TRP 0.025 0.001 TRP A 645 HIS 0.006 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00296 (22111) covalent geometry : angle 0.61879 (31358) hydrogen bonds : bond 0.04648 ( 780) hydrogen bonds : angle 4.31049 ( 2268) metal coordination : bond 0.01342 ( 12) metal coordination : angle 17.99636 ( 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 381 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 380 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8435 (ppp) cc_final: 0.8181 (ppp) REVERT: A 197 MET cc_start: 0.8409 (mmm) cc_final: 0.7780 (tmm) REVERT: A 221 MET cc_start: 0.9110 (mmm) cc_final: 0.8901 (mmm) REVERT: A 242 PHE cc_start: 0.7093 (m-80) cc_final: 0.6620 (m-80) REVERT: A 244 LEU cc_start: 0.8724 (tt) cc_final: 0.8401 (mt) REVERT: A 323 GLU cc_start: 0.8726 (tp30) cc_final: 0.8472 (tm-30) REVERT: A 352 LEU cc_start: 0.8793 (tt) cc_final: 0.8430 (tt) REVERT: A 560 ARG cc_start: 0.7319 (ptt-90) cc_final: 0.7063 (ptt-90) REVERT: A 584 GLN cc_start: 0.8619 (mt0) cc_final: 0.8143 (mp10) REVERT: A 598 MET cc_start: 0.8879 (tmm) cc_final: 0.8455 (tmm) REVERT: A 603 SER cc_start: 0.8665 (m) cc_final: 0.8381 (m) REVERT: A 613 MET cc_start: 0.8809 (mtp) cc_final: 0.8410 (mtp) REVERT: A 684 MET cc_start: 0.9122 (tpp) cc_final: 0.8383 (tpp) REVERT: B 142 LEU cc_start: 0.9392 (mp) cc_final: 0.9011 (tp) REVERT: B 262 HIS cc_start: 0.8174 (t70) cc_final: 0.7657 (t70) REVERT: B 582 ASN cc_start: 0.8052 (OUTLIER) cc_final: 0.7636 (t0) REVERT: C 47 ASP cc_start: 0.8306 (m-30) cc_final: 0.7952 (m-30) REVERT: C 75 ARG cc_start: 0.7894 (tpt-90) cc_final: 0.7601 (tpt-90) REVERT: D 49 ILE cc_start: 0.8601 (mt) cc_final: 0.8198 (tp) REVERT: D 57 LEU cc_start: 0.7782 (tt) cc_final: 0.7295 (tt) REVERT: D 72 LEU cc_start: 0.8645 (mp) cc_final: 0.8399 (mp) REVERT: D 122 ILE cc_start: 0.7081 (mm) cc_final: 0.6876 (tp) REVERT: E 3 LEU cc_start: 0.6819 (mt) cc_final: 0.6513 (mt) REVERT: E 5 ARG cc_start: 0.6841 (mtt180) cc_final: 0.5966 (mmp80) REVERT: E 7 ASP cc_start: 0.6159 (m-30) cc_final: 0.5470 (t0) REVERT: E 8 LYS cc_start: 0.7624 (ttmm) cc_final: 0.6521 (mttm) REVERT: E 14 THR cc_start: 0.8011 (m) cc_final: 0.7785 (m) REVERT: E 15 GLU cc_start: 0.7309 (mp0) cc_final: 0.6916 (mp0) REVERT: E 52 SER cc_start: 0.8651 (m) cc_final: 0.8434 (m) REVERT: E 58 THR cc_start: 0.7716 (m) cc_final: 0.7510 (m) REVERT: K 38 TYR cc_start: 0.5179 (t80) cc_final: 0.4752 (t80) REVERT: M 5 ASP cc_start: 0.7711 (p0) cc_final: 0.7192 (m-30) outliers start: 1 outliers final: 0 residues processed: 381 average time/residue: 0.1434 time to fit residues: 88.2383 Evaluate side-chains 290 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 289 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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: 9.9990 chunk 79 optimal weight: 9.9990 chunk 151 optimal weight: 8.9990 chunk 172 optimal weight: 30.0000 chunk 93 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 HIS A 722 GLN B 73 ASN B 158 GLN B 176 ASN ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS ** B 401 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.099733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.082431 restraints weight = 43762.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.085025 restraints weight = 21936.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.086660 restraints weight = 14062.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.087841 restraints weight = 10618.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.088477 restraints weight = 8813.578| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2898 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2898 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 22123 Z= 0.320 Angle : 1.099 81.761 31394 Z= 0.381 Chirality : 0.052 0.326 2654 Planarity : 0.005 0.062 4080 Dihedral : 19.223 88.821 3749 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.88 % Favored : 94.07 % Rotamer: Outliers : 0.07 % Allowed : 3.20 % Favored : 96.74 % 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: -0.34 (0.19), residues: 1858 helix: 0.77 (0.16), residues: 1007 sheet: -1.32 (0.58), residues: 89 loop : -1.42 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 13 TYR 0.026 0.002 TYR B 574 PHE 0.028 0.003 PHE A 84 TRP 0.026 0.002 TRP A 693 HIS 0.010 0.002 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00709 (22111) covalent geometry : angle 0.84367 (31358) hydrogen bonds : bond 0.06395 ( 780) hydrogen bonds : angle 4.97718 ( 2268) metal coordination : bond 0.01624 ( 12) metal coordination : angle 20.83759 ( 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 343 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 342 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8446 (mmm) cc_final: 0.7865 (tmm) REVERT: A 244 LEU cc_start: 0.8726 (tt) cc_final: 0.8458 (mt) REVERT: A 310 MET cc_start: 0.8876 (mmm) cc_final: 0.8553 (tpp) REVERT: A 352 LEU cc_start: 0.8903 (tt) cc_final: 0.8605 (tt) REVERT: A 434 ASP cc_start: 0.8818 (p0) cc_final: 0.8099 (p0) REVERT: A 613 MET cc_start: 0.8760 (mtp) cc_final: 0.8343 (mtp) REVERT: A 684 MET cc_start: 0.9183 (tpp) cc_final: 0.8597 (tpp) REVERT: B 262 HIS cc_start: 0.8474 (t70) cc_final: 0.7977 (t70) REVERT: B 372 HIS cc_start: 0.8647 (t70) cc_final: 0.8253 (t70) REVERT: C 46 GLU cc_start: 0.8508 (pp20) cc_final: 0.8080 (pp20) REVERT: D 57 LEU cc_start: 0.7739 (tt) cc_final: 0.7196 (tt) REVERT: D 72 LEU cc_start: 0.8769 (mp) cc_final: 0.8445 (mp) REVERT: E 8 LYS cc_start: 0.7802 (ttmm) cc_final: 0.7397 (mttm) REVERT: E 18 TRP cc_start: 0.8222 (m-10) cc_final: 0.7776 (m-10) REVERT: E 52 SER cc_start: 0.8825 (m) cc_final: 0.8590 (m) REVERT: K 38 TYR cc_start: 0.5314 (t80) cc_final: 0.4735 (t80) REVERT: M 5 ASP cc_start: 0.8019 (p0) cc_final: 0.7376 (m-30) outliers start: 1 outliers final: 0 residues processed: 342 average time/residue: 0.1421 time to fit residues: 77.7268 Evaluate side-chains 275 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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: 8.9990 chunk 158 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 119 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 63 optimal weight: 0.1980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 ASN ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 ASN C 3 HIS D 109 ASN K 74 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.105735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.088215 restraints weight = 42450.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.091015 restraints weight = 20943.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.092860 restraints weight = 13206.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.093897 restraints weight = 9794.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.094799 restraints weight = 8200.225| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 22123 Z= 0.144 Angle : 0.892 61.822 31394 Z= 0.298 Chirality : 0.044 0.245 2654 Planarity : 0.004 0.054 4080 Dihedral : 18.327 89.338 3749 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.10 % Favored : 95.85 % Rotamer: Outliers : 0.07 % Allowed : 1.80 % Favored : 98.14 % 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: 0.04 (0.20), residues: 1858 helix: 1.05 (0.16), residues: 1015 sheet: -1.37 (0.58), residues: 89 loop : -1.20 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 539 TYR 0.020 0.001 TYR B 714 PHE 0.022 0.002 PHE K 39 TRP 0.029 0.001 TRP A 693 HIS 0.006 0.001 HIS K 74 Details of bonding type rmsd covalent geometry : bond 0.00324 (22111) covalent geometry : angle 0.65570 (31358) hydrogen bonds : bond 0.04924 ( 780) hydrogen bonds : angle 4.48837 ( 2268) metal coordination : bond 0.01150 ( 12) metal coordination : angle 17.85074 ( 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 364 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 363 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7323 (tp30) cc_final: 0.6558 (mm-30) REVERT: A 197 MET cc_start: 0.8296 (mmm) cc_final: 0.7708 (tmm) REVERT: A 244 LEU cc_start: 0.8648 (tt) cc_final: 0.8384 (mt) REVERT: A 352 LEU cc_start: 0.8798 (tt) cc_final: 0.8414 (tt) REVERT: A 598 MET cc_start: 0.8994 (tmm) cc_final: 0.8633 (tmm) REVERT: A 613 MET cc_start: 0.8769 (mtp) cc_final: 0.8388 (mtp) REVERT: B 262 HIS cc_start: 0.8197 (t70) cc_final: 0.7849 (t70) REVERT: B 348 GLN cc_start: 0.8879 (tt0) cc_final: 0.8564 (tt0) REVERT: C 47 ASP cc_start: 0.8671 (m-30) cc_final: 0.8204 (m-30) REVERT: D 28 TYR cc_start: 0.8077 (m-80) cc_final: 0.7800 (m-10) REVERT: D 72 LEU cc_start: 0.8745 (mp) cc_final: 0.8455 (mp) REVERT: D 97 LEU cc_start: 0.8253 (mm) cc_final: 0.8043 (mm) REVERT: E 8 LYS cc_start: 0.7779 (ttmm) cc_final: 0.7370 (mttm) REVERT: E 14 THR cc_start: 0.8200 (m) cc_final: 0.7978 (m) REVERT: E 15 GLU cc_start: 0.7101 (mp0) cc_final: 0.6817 (mp0) REVERT: E 18 TRP cc_start: 0.8297 (m-10) cc_final: 0.7742 (m-10) REVERT: E 52 SER cc_start: 0.8720 (m) cc_final: 0.8440 (m) REVERT: K 38 TYR cc_start: 0.5270 (t80) cc_final: 0.4721 (t80) REVERT: M 5 ASP cc_start: 0.7852 (p0) cc_final: 0.7296 (m-30) outliers start: 1 outliers final: 1 residues processed: 364 average time/residue: 0.1401 time to fit residues: 81.8726 Evaluate side-chains 286 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 285 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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: 0.7980 chunk 38 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 122 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 169 optimal weight: 20.0000 chunk 117 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN K 74 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.105863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.088203 restraints weight = 42386.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.091010 restraints weight = 21210.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.092849 restraints weight = 13440.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.093906 restraints weight = 10005.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.094793 restraints weight = 8352.433| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22123 Z= 0.156 Angle : 0.911 65.553 31394 Z= 0.302 Chirality : 0.044 0.227 2654 Planarity : 0.004 0.053 4080 Dihedral : 18.067 88.859 3749 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.64 % Favored : 95.31 % Rotamer: Outliers : 0.07 % Allowed : 1.46 % Favored : 98.47 % 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: 0.10 (0.20), residues: 1858 helix: 1.12 (0.16), residues: 1010 sheet: -1.35 (0.58), residues: 89 loop : -1.18 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 539 TYR 0.018 0.001 TYR B 574 PHE 0.026 0.002 PHE A 685 TRP 0.030 0.001 TRP A 693 HIS 0.015 0.001 HIS D 98 Details of bonding type rmsd covalent geometry : bond 0.00351 (22111) covalent geometry : angle 0.66054 (31358) hydrogen bonds : bond 0.04927 ( 780) hydrogen bonds : angle 4.42416 ( 2268) metal coordination : bond 0.01456 ( 12) metal coordination : angle 18.53311 ( 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 364 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 363 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7286 (tp30) cc_final: 0.6558 (mm-30) REVERT: A 197 MET cc_start: 0.8276 (mmm) cc_final: 0.7736 (tmm) REVERT: A 244 LEU cc_start: 0.8672 (tt) cc_final: 0.8349 (mt) REVERT: A 352 LEU cc_start: 0.8792 (tt) cc_final: 0.8427 (tt) REVERT: A 434 ASP cc_start: 0.8737 (p0) cc_final: 0.8023 (p0) REVERT: A 584 GLN cc_start: 0.8764 (mt0) cc_final: 0.8316 (mp10) REVERT: A 613 MET cc_start: 0.8770 (mtp) cc_final: 0.8405 (mtp) REVERT: B 37 MET cc_start: 0.7553 (tpt) cc_final: 0.7280 (tpt) REVERT: B 290 MET cc_start: 0.8509 (mmm) cc_final: 0.7035 (ttt) REVERT: B 348 GLN cc_start: 0.8722 (tt0) cc_final: 0.8364 (tt0) REVERT: B 533 LYS cc_start: 0.8969 (ttpp) cc_final: 0.8629 (tmmt) REVERT: C 47 ASP cc_start: 0.8657 (m-30) cc_final: 0.8045 (m-30) REVERT: D 28 TYR cc_start: 0.8098 (m-80) cc_final: 0.7845 (m-10) REVERT: D 72 LEU cc_start: 0.8624 (mp) cc_final: 0.8315 (mp) REVERT: D 97 LEU cc_start: 0.8052 (mm) cc_final: 0.7845 (mm) REVERT: E 5 ARG cc_start: 0.6989 (mtt180) cc_final: 0.5797 (mmp80) REVERT: E 8 LYS cc_start: 0.7748 (ttmm) cc_final: 0.7330 (mttm) REVERT: E 18 TRP cc_start: 0.8322 (m-10) cc_final: 0.7692 (m-10) REVERT: E 52 SER cc_start: 0.8646 (m) cc_final: 0.8372 (m) REVERT: E 58 THR cc_start: 0.7870 (m) cc_final: 0.7548 (m) REVERT: K 38 TYR cc_start: 0.5285 (t80) cc_final: 0.4764 (t80) REVERT: K 43 LYS cc_start: 0.7119 (ptpp) cc_final: 0.6414 (ptmt) REVERT: M 5 ASP cc_start: 0.7858 (p0) cc_final: 0.7278 (m-30) outliers start: 1 outliers final: 0 residues processed: 364 average time/residue: 0.1396 time to fit residues: 81.7990 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 : 0.649 ------------------------------------------------------------------------------- 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: 0.7980 chunk 91 optimal weight: 10.0000 chunk 160 optimal weight: 8.9990 chunk 114 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.104891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.087421 restraints weight = 42274.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.090202 restraints weight = 20904.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.092035 restraints weight = 13175.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.093121 restraints weight = 9733.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.093906 restraints weight = 8065.916| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22123 Z= 0.155 Angle : 0.899 65.600 31394 Z= 0.299 Chirality : 0.044 0.243 2654 Planarity : 0.004 0.052 4080 Dihedral : 17.847 87.755 3749 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.99 % Favored : 95.96 % Rotamer: Outliers : 0.07 % Allowed : 0.53 % Favored : 99.40 % 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: 0.13 (0.20), residues: 1858 helix: 1.13 (0.16), residues: 1013 sheet: -1.31 (0.58), residues: 89 loop : -1.16 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 539 TYR 0.022 0.001 TYR B 125 PHE 0.020 0.002 PHE B 647 TRP 0.038 0.001 TRP A 693 HIS 0.014 0.001 HIS D 98 Details of bonding type rmsd covalent geometry : bond 0.00348 (22111) covalent geometry : angle 0.65361 (31358) hydrogen bonds : bond 0.04868 ( 780) hydrogen bonds : angle 4.44905 ( 2268) metal coordination : bond 0.01408 ( 12) metal coordination : angle 18.23311 ( 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 361 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 360 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7298 (tp30) cc_final: 0.6509 (mm-30) REVERT: A 197 MET cc_start: 0.8327 (mmm) cc_final: 0.7777 (tmm) REVERT: A 244 LEU cc_start: 0.8684 (tt) cc_final: 0.8329 (mt) REVERT: A 310 MET cc_start: 0.8709 (mmm) cc_final: 0.8312 (mmm) REVERT: A 352 LEU cc_start: 0.8804 (tt) cc_final: 0.8455 (tt) REVERT: A 584 GLN cc_start: 0.8771 (mt0) cc_final: 0.8303 (mp10) REVERT: A 613 MET cc_start: 0.8722 (mtp) cc_final: 0.8374 (mtp) REVERT: B 262 HIS cc_start: 0.8377 (t-90) cc_final: 0.7873 (t70) REVERT: B 290 MET cc_start: 0.8432 (mmm) cc_final: 0.6842 (ttt) REVERT: B 348 GLN cc_start: 0.8695 (tt0) cc_final: 0.8342 (tt0) REVERT: B 542 LYS cc_start: 0.7885 (mmmm) cc_final: 0.7494 (mttt) REVERT: B 659 MET cc_start: 0.7975 (ttp) cc_final: 0.7458 (ttp) REVERT: C 47 ASP cc_start: 0.8630 (m-30) cc_final: 0.7935 (m-30) REVERT: C 68 TYR cc_start: 0.8653 (m-80) cc_final: 0.8383 (m-80) REVERT: D 28 TYR cc_start: 0.8120 (m-80) cc_final: 0.7827 (m-10) REVERT: D 57 LEU cc_start: 0.7483 (tt) cc_final: 0.7199 (tt) REVERT: D 72 LEU cc_start: 0.8510 (mp) cc_final: 0.8210 (mp) REVERT: D 97 LEU cc_start: 0.8128 (mm) cc_final: 0.7876 (mm) REVERT: E 5 ARG cc_start: 0.6901 (mtt180) cc_final: 0.5797 (mmp80) REVERT: E 8 LYS cc_start: 0.7748 (ttmm) cc_final: 0.7318 (mttm) REVERT: E 18 TRP cc_start: 0.8291 (m-10) cc_final: 0.7691 (m-10) REVERT: E 52 SER cc_start: 0.8648 (m) cc_final: 0.8310 (m) REVERT: E 58 THR cc_start: 0.7841 (m) cc_final: 0.7552 (m) REVERT: K 38 TYR cc_start: 0.5308 (t80) cc_final: 0.4782 (t80) REVERT: K 43 LYS cc_start: 0.7174 (ptpp) cc_final: 0.6207 (ptmt) REVERT: K 46 LYS cc_start: 0.7724 (pttt) cc_final: 0.7006 (mptt) REVERT: K 48 LYS cc_start: 0.3391 (tptp) cc_final: 0.3038 (tptp) REVERT: M 5 ASP cc_start: 0.7885 (p0) cc_final: 0.7284 (m-30) outliers start: 1 outliers final: 0 residues processed: 361 average time/residue: 0.1453 time to fit residues: 84.9333 Evaluate side-chains 287 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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: 2.9990 chunk 83 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 99 optimal weight: 8.9990 chunk 175 optimal weight: 7.9990 chunk 164 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 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 = 0.3089 r_free = 0.3089 target = 0.098428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.080566 restraints weight = 43897.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.083223 restraints weight = 21503.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.084980 restraints weight = 13632.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.086246 restraints weight = 10140.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.086889 restraints weight = 8331.912| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 22123 Z= 0.288 Angle : 1.053 72.535 31394 Z= 0.374 Chirality : 0.051 0.305 2654 Planarity : 0.005 0.055 4080 Dihedral : 18.606 85.820 3749 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.20 % Favored : 93.75 % Rotamer: Outliers : 0.07 % Allowed : 0.53 % Favored : 99.40 % 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: -0.30 (0.20), residues: 1858 helix: 0.74 (0.16), residues: 1016 sheet: -1.51 (0.56), residues: 89 loop : -1.29 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 560 TYR 0.031 0.002 TYR A 692 PHE 0.024 0.002 PHE B 647 TRP 0.073 0.002 TRP A 693 HIS 0.013 0.002 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00638 (22111) covalent geometry : angle 0.81703 (31358) hydrogen bonds : bond 0.06160 ( 780) hydrogen bonds : angle 4.91451 ( 2268) metal coordination : bond 0.01555 ( 12) metal coordination : angle 19.63733 ( 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 350 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 349 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.8459 (mmm) cc_final: 0.7737 (tmm) REVERT: A 244 LEU cc_start: 0.8693 (tt) cc_final: 0.8392 (mt) REVERT: A 352 LEU cc_start: 0.8870 (tt) cc_final: 0.8544 (tt) REVERT: A 434 ASP cc_start: 0.8801 (p0) cc_final: 0.8049 (p0) REVERT: A 584 GLN cc_start: 0.8908 (mt0) cc_final: 0.8467 (mt0) REVERT: A 613 MET cc_start: 0.8772 (mtp) cc_final: 0.8572 (mtp) REVERT: B 262 HIS cc_start: 0.8527 (t-90) cc_final: 0.8113 (t70) REVERT: B 295 TRP cc_start: 0.8553 (m-90) cc_final: 0.8331 (m-90) REVERT: B 348 GLN cc_start: 0.8816 (tt0) cc_final: 0.8476 (tt0) REVERT: B 372 HIS cc_start: 0.8665 (t70) cc_final: 0.8075 (t70) REVERT: B 542 LYS cc_start: 0.7887 (mmmm) cc_final: 0.7423 (mttt) REVERT: C 47 ASP cc_start: 0.8845 (m-30) cc_final: 0.8391 (m-30) REVERT: D 57 LEU cc_start: 0.7623 (tt) cc_final: 0.7298 (tt) REVERT: D 72 LEU cc_start: 0.8393 (mp) cc_final: 0.8141 (mp) REVERT: D 97 LEU cc_start: 0.8270 (mm) cc_final: 0.8057 (mm) REVERT: E 8 LYS cc_start: 0.7905 (ttmm) cc_final: 0.7518 (mttm) REVERT: E 18 TRP cc_start: 0.8294 (m-10) cc_final: 0.7858 (m-10) REVERT: E 52 SER cc_start: 0.8855 (m) cc_final: 0.8552 (m) REVERT: K 38 TYR cc_start: 0.5368 (t80) cc_final: 0.4707 (t80) REVERT: K 48 LYS cc_start: 0.3386 (tptp) cc_final: 0.3025 (tptp) REVERT: M 5 ASP cc_start: 0.8009 (p0) cc_final: 0.7418 (m-30) outliers start: 1 outliers final: 0 residues processed: 350 average time/residue: 0.1408 time to fit residues: 79.5232 Evaluate side-chains 281 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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: 3.9990 chunk 118 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 158 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 708 ASN B 176 ASN ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 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** 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 = 0.3210 r_free = 0.3210 target = 0.106582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.089004 restraints weight = 42005.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.091825 restraints weight = 21003.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.093642 restraints weight = 13288.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.094934 restraints weight = 9903.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.095593 restraints weight = 8076.105| |-----------------------------------------------------------------------------| 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 = 0.48 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 = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 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 : 0.003 0.041 22123 Z= 0.133 Angle : 0.901 63.746 31394 Z= 0.303 Chirality : 0.044 0.254 2654 Planarity : 0.004 0.052 4080 Dihedral : 17.850 88.769 3749 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.99 % Favored : 95.96 % 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: 0.10 (0.20), residues: 1858 helix: 1.10 (0.16), residues: 1007 sheet: -1.25 (0.58), residues: 85 loop : -1.17 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 560 TYR 0.018 0.001 TYR B 574 PHE 0.020 0.002 PHE B 257 TRP 0.016 0.001 TRP B 654 HIS 0.007 0.001 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00297 (22111) covalent geometry : angle 0.66429 (31358) hydrogen bonds : bond 0.04787 ( 780) hydrogen bonds : angle 4.44825 ( 2268) metal coordination : bond 0.01247 ( 12) metal coordination : angle 17.97640 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3556.29 seconds wall clock time: 62 minutes 36.29 seconds (3756.29 seconds total)