Starting phenix.real_space_refine on Tue Jul 29 08:12:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mtr_23995/07_2025/7mtr_23995.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mtr_23995/07_2025/7mtr_23995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mtr_23995/07_2025/7mtr_23995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mtr_23995/07_2025/7mtr_23995.map" model { file = "/net/cci-nas-00/data/ceres_data/7mtr_23995/07_2025/7mtr_23995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mtr_23995/07_2025/7mtr_23995.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 6961 2.51 5 N 1912 2.21 5 O 1994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10933 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 5404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 5404 Classifications: {'peptide': 760} Incomplete info: {'truncation_to_alanine': 153} Link IDs: {'PTRANS': 37, 'TRANS': 722} Chain breaks: 4 Unresolved non-hydrogen bonds: 537 Unresolved non-hydrogen angles: 673 Unresolved non-hydrogen dihedrals: 429 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 5, 'ASP:plan': 2, 'PHE:plan': 7, 'GLU:plan': 16, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 272 Chain: "A" Number of atoms: 5451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 5451 Classifications: {'peptide': 764} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'PTRANS': 37, 'TRANS': 726} Chain breaks: 3 Unresolved non-hydrogen bonds: 525 Unresolved non-hydrogen angles: 661 Unresolved non-hydrogen dihedrals: 417 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 9, 'GLU:plan': 16, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 291 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'NAG': 1, 'ZQY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.86, per 1000 atoms: 1.08 Number of scatterers: 10933 At special positions: 0 Unit cell: (106.727, 91.9762, 186.555, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1994 8.00 N 1912 7.00 C 6961 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 518 " distance=2.04 Simple disulfide: pdb=" SG CYS B 400 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 500 " - pdb=" SG CYS B 519 " distance=2.04 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 525 " - pdb=" SG CYS B 537 " distance=2.04 Simple disulfide: pdb=" SG CYS B 540 " - pdb=" SG CYS B 553 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 362 " distance=2.03 Simple disulfide: pdb=" SG CYS A 400 " - pdb=" SG CYS A 407 " distance=2.04 Simple disulfide: pdb=" SG CYS A 500 " - pdb=" SG CYS A 519 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 537 " distance=2.03 Simple disulfide: pdb=" SG CYS A 540 " - pdb=" SG CYS A 553 " distance=2.03 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=1, symmetry=0 Links applied NAG-ASN " NAG A 902 " - " ASN A 203 " " NAG B 902 " - " ASN B 203 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.96 Conformation dependent library (CDL) restraints added in 2.1 seconds 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2850 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 16 sheets defined 49.3% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.73 Creating SS restraints... Processing helix chain 'B' and resid 58 through 73 Processing helix chain 'B' and resid 94 through 107 removed outlier: 4.767A pdb=" N ASP B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N PHE B 105 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 156 removed outlier: 3.544A pdb=" N LEU B 154 " --> pdb=" O GLN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 174 Processing helix chain 'B' and resid 190 through 202 removed outlier: 3.548A pdb=" N ARG B 200 " --> pdb=" O ALA B 196 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE B 202 " --> pdb=" O ILE B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 231 Processing helix chain 'B' and resid 246 through 260 removed outlier: 4.462A pdb=" N LYS B 260 " --> pdb=" O ALA B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 285 Processing helix chain 'B' and resid 307 through 312 Processing helix chain 'B' and resid 324 through 333 removed outlier: 4.098A pdb=" N ALA B 328 " --> pdb=" O ILE B 324 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 354 Processing helix chain 'B' and resid 377 through 400 removed outlier: 3.639A pdb=" N VAL B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 422 Processing helix chain 'B' and resid 423 through 426 removed outlier: 3.653A pdb=" N VAL B 426 " --> pdb=" O VAL B 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 423 through 426' Processing helix chain 'B' and resid 565 through 592 Proline residue: B 571 - end of helix Processing helix chain 'B' and resid 595 through 602 removed outlier: 3.983A pdb=" N SER B 601 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY B 602 " --> pdb=" O VAL B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 624 removed outlier: 4.191A pdb=" N ILE B 624 " --> pdb=" O THR B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 659 removed outlier: 4.955A pdb=" N GLY B 640 " --> pdb=" O ARG B 636 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 659 " --> pdb=" O ASN B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 701 Processing helix chain 'B' and resid 725 through 727 No H-bonds generated for 'chain 'B' and resid 725 through 727' Processing helix chain 'B' and resid 728 through 749 removed outlier: 3.560A pdb=" N LEU B 732 " --> pdb=" O MET B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 783 Proline residue: B 778 - end of helix Processing helix chain 'B' and resid 786 through 819 removed outlier: 3.550A pdb=" N VAL B 805 " --> pdb=" O SER B 801 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B 811 " --> pdb=" O GLY B 807 " (cutoff:3.500A) Proline residue: B 812 - end of helix Processing helix chain 'A' and resid 58 through 74 Processing helix chain 'A' and resid 94 through 102 Processing helix chain 'A' and resid 102 through 107 removed outlier: 3.986A pdb=" N VAL A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 156 Processing helix chain 'A' and resid 170 through 174 Processing helix chain 'A' and resid 188 through 202 removed outlier: 3.910A pdb=" N ALA A 192 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS A 193 " --> pdb=" O PHE A 189 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 202 " --> pdb=" O ILE A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 230 Processing helix chain 'A' and resid 246 through 259 Processing helix chain 'A' and resid 271 through 286 Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 324 through 332 removed outlier: 3.850A pdb=" N ALA A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 354 Processing helix chain 'A' and resid 377 through 400 removed outlier: 3.747A pdb=" N CYS A 400 " --> pdb=" O HIS A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 411 removed outlier: 3.580A pdb=" N ARG A 411 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 423 Processing helix chain 'A' and resid 485 through 489 removed outlier: 3.505A pdb=" N ALA A 488 " --> pdb=" O ILE A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 592 Proline residue: A 571 - end of helix Processing helix chain 'A' and resid 595 through 601 removed outlier: 3.842A pdb=" N SER A 601 " --> pdb=" O VAL A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 625 removed outlier: 4.510A pdb=" N THR A 620 " --> pdb=" O CYS A 616 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE A 621 " --> pdb=" O TYR A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 660 removed outlier: 4.347A pdb=" N LEU A 639 " --> pdb=" O ARG A 635 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLY A 640 " --> pdb=" O ARG A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 701 removed outlier: 3.841A pdb=" N GLN A 690 " --> pdb=" O LEU A 686 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 693 " --> pdb=" O GLY A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 749 removed outlier: 4.665A pdb=" N LEU A 738 " --> pdb=" O TYR A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 775 Processing helix chain 'A' and resid 775 through 783 removed outlier: 4.279A pdb=" N ILE A 779 " --> pdb=" O ALA A 775 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR A 781 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 783 " --> pdb=" O ILE A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 791 Processing helix chain 'A' and resid 793 through 820 removed outlier: 3.628A pdb=" N LEU A 800 " --> pdb=" O VAL A 796 " (cutoff:3.500A) Proline residue: A 812 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.737A pdb=" N LEU B 32 " --> pdb=" O GLY B 85 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N HIS B 87 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU B 34 " --> pdb=" O HIS B 87 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU B 89 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLY B 36 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY B 138 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL B 139 " --> pdb=" O ILE B 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 41 through 43 Processing sheet with id=AA3, first strand: chain 'B' and resid 234 through 241 removed outlier: 7.085A pdb=" N VAL B 207 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER B 238 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR B 209 " --> pdb=" O SER B 238 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LYS B 240 " --> pdb=" O THR B 209 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ALA B 211 " --> pdb=" O LYS B 240 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N TYR B 206 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N VAL B 267 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER B 208 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N PHE B 269 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL B 210 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N TRP B 291 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N ILE B 317 " --> pdb=" O TRP B 291 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ALA B 293 " --> pdb=" O ILE B 317 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N LEU B 319 " --> pdb=" O ALA B 293 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY B 472 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR B 457 " --> pdb=" O LYS B 470 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LYS B 470 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU B 459 " --> pdb=" O TYR B 468 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N TYR B 468 " --> pdb=" O LEU B 459 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 428 through 429 removed outlier: 3.881A pdb=" N PHE B 428 " --> pdb=" O VAL B 441 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 508 through 511 Processing sheet with id=AA6, first strand: chain 'B' and resid 529 through 531 Processing sheet with id=AA7, first strand: chain 'B' and resid 544 through 546 Processing sheet with id=AA8, first strand: chain 'B' and resid 705 through 708 removed outlier: 3.750A pdb=" N THR B 718 " --> pdb=" O GLU B 708 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.628A pdb=" N LEU A 32 " --> pdb=" O GLY A 85 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N HIS A 87 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU A 34 " --> pdb=" O HIS A 87 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU A 89 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY A 36 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL A 33 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ILE A 140 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY A 35 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N ILE A 163 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A 139 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 41 through 43 Processing sheet with id=AB2, first strand: chain 'A' and resid 234 through 241 removed outlier: 8.183A pdb=" N VAL A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N SER A 238 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N THR A 209 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LYS A 240 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA A 211 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL A 265 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TRP A 291 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ILE A 317 " --> pdb=" O TRP A 291 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ALA A 293 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N LEU A 319 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR A 453 " --> pdb=" O TYR A 473 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N TYR A 473 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ILE A 455 " --> pdb=" O VAL A 471 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 428 through 429 removed outlier: 3.974A pdb=" N PHE A 428 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 508 through 512 removed outlier: 3.611A pdb=" N SER A 511 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 521 " --> pdb=" O SER A 511 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 529 through 533 removed outlier: 3.687A pdb=" N LEU A 532 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 544 through 546 Processing sheet with id=AB7, first strand: chain 'A' and resid 705 through 707 574 hydrogen bonds defined for protein. 1689 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: 4.37 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1811 1.31 - 1.44: 3117 1.44 - 1.57: 6186 1.57 - 1.70: 0 1.70 - 1.83: 84 Bond restraints: 11198 Sorted by residual: bond pdb=" C1 ZQY A 903 " pdb=" C2 ZQY A 903 " ideal model delta sigma weight residual 1.390 1.528 -0.138 2.00e-02 2.50e+03 4.75e+01 bond pdb=" C5 ZQY A 903 " pdb=" C6 ZQY A 903 " ideal model delta sigma weight residual 1.392 1.519 -0.127 2.00e-02 2.50e+03 4.06e+01 bond pdb=" C3 ZQY A 903 " pdb=" C4 ZQY A 903 " ideal model delta sigma weight residual 1.394 1.520 -0.126 2.00e-02 2.50e+03 3.94e+01 bond pdb=" C9 ZQY A 903 " pdb=" N1 ZQY A 903 " ideal model delta sigma weight residual 1.337 1.446 -0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" N LYS A 748 " pdb=" CA LYS A 748 " ideal model delta sigma weight residual 1.456 1.522 -0.066 1.33e-02 5.65e+03 2.50e+01 ... (remaining 11193 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 14508 1.88 - 3.75: 637 3.75 - 5.63: 128 5.63 - 7.50: 35 7.50 - 9.38: 12 Bond angle restraints: 15320 Sorted by residual: angle pdb=" N ARG A 750 " pdb=" CA ARG A 750 " pdb=" C ARG A 750 " ideal model delta sigma weight residual 112.38 104.26 8.12 1.22e+00 6.72e-01 4.43e+01 angle pdb=" N CYS B 752 " pdb=" CA CYS B 752 " pdb=" C CYS B 752 " ideal model delta sigma weight residual 109.48 118.32 -8.84 1.44e+00 4.82e-01 3.77e+01 angle pdb=" C TRP A 773 " pdb=" N LEU A 774 " pdb=" CA LEU A 774 " ideal model delta sigma weight residual 120.60 111.22 9.38 1.60e+00 3.91e-01 3.43e+01 angle pdb=" N LYS A 751 " pdb=" CA LYS A 751 " pdb=" C LYS A 751 " ideal model delta sigma weight residual 110.53 118.02 -7.49 1.29e+00 6.01e-01 3.37e+01 angle pdb=" N LYS A 760 " pdb=" CA LYS A 760 " pdb=" C LYS A 760 " ideal model delta sigma weight residual 112.54 105.55 6.99 1.22e+00 6.72e-01 3.28e+01 ... (remaining 15315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 5970 17.10 - 34.21: 454 34.21 - 51.31: 121 51.31 - 68.41: 27 68.41 - 85.51: 11 Dihedral angle restraints: 6583 sinusoidal: 2170 harmonic: 4413 Sorted by residual: dihedral pdb=" CB CYS A 540 " pdb=" SG CYS A 540 " pdb=" SG CYS A 553 " pdb=" CB CYS A 553 " ideal model delta sinusoidal sigma weight residual 93.00 178.51 -85.51 1 1.00e+01 1.00e-02 8.85e+01 dihedral pdb=" CB CYS A 234 " pdb=" SG CYS A 234 " pdb=" SG CYS A 518 " pdb=" CB CYS A 518 " ideal model delta sinusoidal sigma weight residual -86.00 -147.09 61.09 1 1.00e+01 1.00e-02 4.96e+01 dihedral pdb=" CA ILE B 140 " pdb=" C ILE B 140 " pdb=" N GLY B 141 " pdb=" CA GLY B 141 " ideal model delta harmonic sigma weight residual 180.00 -154.25 -25.75 0 5.00e+00 4.00e-02 2.65e+01 ... (remaining 6580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1431 0.066 - 0.133: 267 0.133 - 0.199: 36 0.199 - 0.265: 7 0.265 - 0.332: 3 Chirality restraints: 1744 Sorted by residual: chirality pdb=" CA ALA A 775 " pdb=" N ALA A 775 " pdb=" C ALA A 775 " pdb=" CB ALA A 775 " both_signs ideal model delta sigma weight residual False 2.48 2.15 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA LYS A 748 " pdb=" N LYS A 748 " pdb=" C LYS A 748 " pdb=" CB LYS A 748 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA LYS B 420 " pdb=" N LYS B 420 " pdb=" C LYS B 420 " pdb=" CB LYS B 420 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 1741 not shown) Planarity restraints: 2008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 260 " 0.081 5.00e-02 4.00e+02 1.25e-01 2.50e+01 pdb=" N PRO A 261 " -0.216 5.00e-02 4.00e+02 pdb=" CA PRO A 261 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO A 261 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 772 " 0.024 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C ILE A 772 " -0.085 2.00e-02 2.50e+03 pdb=" O ILE A 772 " 0.032 2.00e-02 2.50e+03 pdb=" N TRP A 773 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 676 " -0.024 2.00e-02 2.50e+03 4.83e-02 2.33e+01 pdb=" C PRO A 676 " 0.084 2.00e-02 2.50e+03 pdb=" O PRO A 676 " -0.031 2.00e-02 2.50e+03 pdb=" N ALA A 677 " -0.028 2.00e-02 2.50e+03 ... (remaining 2005 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2072 2.77 - 3.30: 10098 3.30 - 3.83: 16992 3.83 - 4.37: 18518 4.37 - 4.90: 33353 Nonbonded interactions: 81033 Sorted by model distance: nonbonded pdb=" O ASP A 421 " pdb=" ND2 ASN A 425 " model vdw 2.236 3.120 nonbonded pdb=" O VAL B 207 " pdb=" N ALA B 236 " model vdw 2.237 3.120 nonbonded pdb=" OD1 ASN B 203 " pdb=" N2 NAG B 902 " model vdw 2.251 3.120 nonbonded pdb=" O GLU B 29 " pdb=" NH1 ARG B 83 " model vdw 2.276 3.120 nonbonded pdb=" NH2 ARG A 467 " pdb=" OE1 GLN A 469 " model vdw 2.285 3.120 ... (remaining 81028 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB )) or resid 30 through 204 or (resid 205 and (name N or n \ ame CA or name C or name O or name CB )) or resid 206 through 242 or (resid 243 \ through 244 and (name N or name CA or name C or name O or name CB )) or resid 24 \ 5 through 258 or (resid 259 and (name N or name CA or name C or name O or name C \ B or name CG )) or (resid 260 and (name N or name CA or name C or name O or name \ CB )) or resid 261 through 263 or (resid 264 and (name N or name CA or name C o \ r name O or name CB )) or resid 265 through 358 or resid 361 through 404 or (res \ id 405 and (name N or name CA or name C or name O or name CB )) or resid 406 thr \ ough 407 or (resid 408 through 409 and (name N or name CA or name C or name O or \ name CB )) or resid 410 or (resid 411 and (name N or name CA or name C or name \ O or name CB )) or resid 412 through 419 or (resid 420 and (name N or name CA or \ name C or name O or name CB )) or resid 421 through 462 or resid 465 through 47 \ 5 or (resid 476 and (name N or name CA or name C or name O or name CB )) or resi \ d 477 through 498 or (resid 499 and (name N or name CA or name C or name O or na \ me CB )) or resid 500 or (resid 501 through 502 and (name N or name CA or name C \ or name O or name CB )) or resid 503 through 504 or (resid 505 through 506 and \ (name N or name CA or name C or name O or name CB )) or resid 507 through 512 or \ (resid 513 and (name N or name CA or name C or name O or name CB )) or resid 51 \ 4 through 557 or (resid 558 through 559 and (name N or name CA or name C or name \ O or name CB )) or resid 560 through 589 or (resid 590 through 591 and (name N \ or name CA or name C or name O or name CB )) or resid 592 through 594 or (resid \ 595 and (name N or name CA or name C or name O or name CB )) or resid 596 throug \ h 600 or (resid 601 and (name N or name CA or name C or name O or name CB )) or \ (resid 602 through 605 and (name N or name CA or name C or name O or name CB )) \ or resid 606 through 607 or (resid 608 through 610 and (name N or name CA or nam \ e C or name O or name CB )) or resid 611 through 618 or (resid 619 and (name N o \ r name CA or name C or name O or name CB )) or resid 620 through 621 or (resid 6 \ 22 and (name N or name CA or name C or name O or name CB )) or resid 623 or (res \ id 624 through 626 and (name N or name CA or name C or name O or name CB )) or r \ esid 627 through 631 or (resid 632 through 637 and (name N or name CA or name C \ or name O or name CB )) or resid 638 through 650 or (resid 651 and (name N or na \ me CA or name C or name O or name CB )) or resid 652 through 659 or (resid 673 t \ hrough 675 and (name N or name CA or name C or name O or name CB )) or resid 676 \ through 677 or (resid 678 through 679 and (name N or name CA or name C or name \ O or name CB )) or resid 680 through 681 or (resid 682 through 688 and (name N o \ r name CA or name C or name O or name CB )) or (resid 689 through 696 and (name \ N or name CA or name C or name O or name CB )) or resid 697 through 698 or (resi \ d 699 through 702 and (name N or name CA or name C or name O or name CB )) or re \ sid 703 through 704 or (resid 705 and (name N or name CA or name C or name O or \ name CB )) or (resid 706 through 710 and (name N or name CA or name C or name O \ or name CB )) or resid 711 through 712 or (resid 713 through 723 and (name N or \ name CA or name C or name O or name CB )) or resid 724 through 730 or (resid 731 \ through 734 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 35 through 738 or (resid 739 through 741 and (name N or name CA or name C or nam \ e O or name CB )) or resid 742 through 743 or (resid 744 through 746 and (name N \ or name CA or name C or name O or name CB )) or resid 747 through 759 or (resid \ 760 through 762 and (name N or name CA or name C or name O or name CB )) or res \ id 763 or (resid 764 through 768 and (name N or name CA or name C or name O or n \ ame CB )) or resid 769 or (resid 770 through 771 and (name N or name CA or name \ C or name O or name CB )) or resid 772 through 773 or (resid 774 through 775 and \ (name N or name CA or name C or name O or name CB )) or resid 776 or (resid 777 \ and (name N or name CA or name C or name O or name CB )) or resid 778 through 7 \ 79 or (resid 780 through 781 and (name N or name CA or name C or name O or name \ CB )) or resid 782 through 788 or (resid 789 and (name N or name CA or name C or \ name O or name CB )) or resid 790 through 799 or (resid 800 through 801 and (na \ me N or name CA or name C or name O or name CB )) or resid 802 through 807 or (r \ esid 808 through 811 and (name N or name CA or name C or name O or name CB )) or \ resid 812 or (resid 813 through 820 and (name N or name CA or name C or name O \ or name CB )) or resid 821 through 822)) selection = (chain 'B' and (resid 23 through 221 or (resid 222 through 223 and (name N or na \ me CA or name C or name O or name CB )) or resid 224 or (resid 225 and (name N o \ r name CA or name C or name O or name CB )) or resid 226 through 239 or (resid 2 \ 40 and (name N or name CA or name C or name O or name CB )) or resid 241 through \ 353 or (resid 354 and (name N or name CA or name C or name O or name CB )) or r \ esid 355 through 435 or (resid 436 and (name N or name CA or name C or name O or \ name CB )) or resid 437 through 444 or (resid 445 and (name N or name CA or nam \ e C or name O or name CB )) or resid 446 through 447 or (resid 448 and (name N o \ r name CA or name C or name O or name CB )) or resid 449 through 510 or (resid 5 \ 11 and (name N or name CA or name C or name O or name CB )) or resid 512 through \ 522 or (resid 523 and (name N or name CA or name C or name O or name CB )) or r \ esid 524 through 525 or (resid 526 and (name N or name CA or name C or name O or \ name CB )) or resid 527 through 530 or (resid 531 and (name N or name CA or nam \ e C or name O or name CB )) or resid 532 through 564 or (resid 565 through 566 a \ nd (name N or name CA or name C or name O or name CB )) or resid 567 through 568 \ or (resid 569 and (name N or name CA or name C or name O or name CB )) or resid \ 570 through 571 or (resid 572 through 575 and (name N or name CA or name C or n \ ame O or name CB )) or resid 576 or (resid 577 and (name N or name CA or name C \ or name O or name CB )) or (resid 578 through 583 and (name N or name CA or name \ C or name O or name CB )) or resid 584 or (resid 585 through 586 and (name N or \ name CA or name C or name O or name CB )) or resid 587 through 590 or (resid 59 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 592 or (resi \ d 593 through 595 and (name N or name CA or name C or name O or name CB )) or re \ sid 596 through 608 or (resid 609 through 610 and (name N or name CA or name C o \ r name O or name CB )) or resid 611 through 613 or (resid 614 through 615 and (n \ ame N or name CA or name C or name O or name CB )) or resid 616 through 617 or ( \ resid 618 through 619 and (name N or name CA or name C or name O or name CB )) o \ r resid 620 or (resid 621 through 622 and (name N or name CA or name C or name O \ or name CB )) or resid 623 through 628 or (resid 629 through 630 and (name N or \ name CA or name C or name O or name CB )) or resid 631 through 632 or (resid 63 \ 3 through 637 and (name N or name CA or name C or name O or name CB )) or resid \ 638 or (resid 639 and (name N or name CA or name C or name O or name CB )) or re \ sid 640 through 649 or (resid 650 through 651 and (name N or name CA or name C o \ r name O or name CB )) or resid 652 through 683 or (resid 684 through 688 and (n \ ame N or name CA or name C or name O or name CB )) or resid 689 or (resid 690 th \ rough 696 and (name N or name CA or name C or name O or name CB )) or resid 697 \ through 700 or (resid 701 through 702 and (name N or name CA or name C or name O \ or name CB )) or resid 703 through 726 or (resid 727 and (name N or name CA or \ name C or name O or name CB )) or resid 728 through 733 or (resid 734 and (name \ N or name CA or name C or name O or name CB )) or resid 735 or (resid 736 throug \ h 741 and (name N or name CA or name C or name O or name CB )) or resid 742 thro \ ugh 748 or (resid 749 through 752 and (name N or name CA or name C or name O or \ name CB )) or resid 753 through 760 or (resid 761 through 762 and (name N or nam \ e CA or name C or name O or name CB )) or resid 763 through 782 or (resid 783 th \ rough 785 and (name N or name CA or name C or name O or name CB )) or resid 786 \ through 790 or (resid 791 through 796 and (name N or name CA or name C or name O \ or name CB )) or resid 797 or (resid 798 through 801 and (name N or name CA or \ name C or name O or name CB )) or (resid 802 through 804 and (name N or name CA \ or name C or name O or name CB )) or resid 805 or (resid 806 and (name N or name \ CA or name C or name O or name CB )) or (resid 807 through 811 and (name N or n \ ame CA or name C or name O or name CB )) or resid 812 through 814 or (resid 815 \ through 820 and (name N or name CA or name C or name O or name CB )) or resid 82 \ 1 through 822)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 745.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.010 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 38.590 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 789.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 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 : 0.007 0.438 11214 Z= 0.522 Angle : 0.938 9.375 15352 Z= 0.567 Chirality : 0.054 0.332 1744 Planarity : 0.009 0.125 2006 Dihedral : 14.012 85.411 3694 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.25 % Allowed : 9.38 % Favored : 89.38 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.21), residues: 1506 helix: 1.04 (0.20), residues: 694 sheet: -0.05 (0.39), residues: 172 loop : -1.45 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 520 HIS 0.009 0.001 HIS B 56 PHE 0.029 0.002 PHE B 810 TYR 0.018 0.002 TYR B 216 ARG 0.004 0.001 ARG B 433 Details of bonding type rmsd link_NAG-ASN : bond 0.01410 ( 2) link_NAG-ASN : angle 4.32049 ( 6) hydrogen bonds : bond 0.15610 ( 574) hydrogen bonds : angle 5.95769 ( 1689) SS BOND : bond 0.00515 ( 13) SS BOND : angle 1.98285 ( 26) covalent geometry : bond 0.00581 (11198) covalent geometry : angle 0.93156 (15320) Misc. bond : bond 0.43813 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: A 171 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7884 (mtmt) REVERT: A 728 MET cc_start: 0.4844 (mmp) cc_final: 0.4588 (mmp) REVERT: A 780 PHE cc_start: 0.7328 (OUTLIER) cc_final: 0.6597 (t80) outliers start: 12 outliers final: 5 residues processed: 199 average time/residue: 0.3844 time to fit residues: 103.2810 Evaluate side-chains 183 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 177 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 697 TRP Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 760 LYS Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 780 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 138 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN A 438 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.144287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.117352 restraints weight = 17621.473| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.35 r_work: 0.3438 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 11214 Z= 0.241 Angle : 0.654 9.769 15352 Z= 0.348 Chirality : 0.046 0.165 1744 Planarity : 0.006 0.077 2006 Dihedral : 7.105 81.394 1701 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.77 % Allowed : 10.62 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.21), residues: 1506 helix: 1.42 (0.20), residues: 714 sheet: 0.06 (0.39), residues: 169 loop : -1.36 (0.22), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 291 HIS 0.007 0.002 HIS B 97 PHE 0.038 0.003 PHE B 67 TYR 0.022 0.002 TYR B 216 ARG 0.008 0.001 ARG A 713 Details of bonding type rmsd link_NAG-ASN : bond 0.00952 ( 2) link_NAG-ASN : angle 5.73916 ( 6) hydrogen bonds : bond 0.06589 ( 574) hydrogen bonds : angle 4.61553 ( 1689) SS BOND : bond 0.00332 ( 13) SS BOND : angle 1.15206 ( 26) covalent geometry : bond 0.00570 (11198) covalent geometry : angle 0.64314 (15320) Misc. bond : bond 0.00061 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 191 time to evaluate : 1.249 Fit side-chains REVERT: B 55 GLU cc_start: 0.7077 (tm-30) cc_final: 0.6819 (tm-30) REVERT: B 427 LYS cc_start: 0.8816 (tttm) cc_final: 0.8599 (tttm) REVERT: A 171 LYS cc_start: 0.8757 (mtpt) cc_final: 0.8540 (mtpt) REVERT: A 760 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7272 (pptt) outliers start: 17 outliers final: 8 residues processed: 202 average time/residue: 0.2884 time to fit residues: 77.4530 Evaluate side-chains 191 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 182 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 697 TRP Chi-restraints excluded: chain A residue 760 LYS Chi-restraints excluded: chain A residue 776 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 77 optimal weight: 0.0670 chunk 35 optimal weight: 1.9990 chunk 41 optimal weight: 0.0870 chunk 146 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 overall best weight: 0.5696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 GLN B 232 ASN B 332 GLN A 425 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.144339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.116881 restraints weight = 17837.274| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.41 r_work: 0.3430 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11214 Z= 0.169 Angle : 0.562 9.735 15352 Z= 0.296 Chirality : 0.043 0.166 1744 Planarity : 0.005 0.064 2006 Dihedral : 6.435 78.888 1695 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.81 % Allowed : 12.19 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.22), residues: 1506 helix: 1.64 (0.20), residues: 713 sheet: -0.01 (0.39), residues: 171 loop : -1.21 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 291 HIS 0.004 0.001 HIS B 97 PHE 0.027 0.002 PHE B 67 TYR 0.015 0.002 TYR B 216 ARG 0.006 0.001 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.01054 ( 2) link_NAG-ASN : angle 5.47732 ( 6) hydrogen bonds : bond 0.05495 ( 574) hydrogen bonds : angle 4.33603 ( 1689) SS BOND : bond 0.00343 ( 13) SS BOND : angle 0.83016 ( 26) covalent geometry : bond 0.00396 (11198) covalent geometry : angle 0.55103 (15320) Misc. bond : bond 0.00087 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 1.090 Fit side-chains REVERT: A 399 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7975 (mp) REVERT: A 760 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7350 (pptt) outliers start: 27 outliers final: 18 residues processed: 205 average time/residue: 0.2761 time to fit residues: 75.9987 Evaluate side-chains 197 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 553 CYS Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain B residue 747 PHE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 697 TRP Chi-restraints excluded: chain A residue 760 LYS Chi-restraints excluded: chain A residue 776 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 57 optimal weight: 2.9990 chunk 108 optimal weight: 0.1980 chunk 112 optimal weight: 0.2980 chunk 141 optimal weight: 0.4980 chunk 79 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.144184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.117303 restraints weight = 17629.063| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.33 r_work: 0.3443 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11214 Z= 0.136 Angle : 0.526 9.958 15352 Z= 0.274 Chirality : 0.041 0.165 1744 Planarity : 0.005 0.070 2006 Dihedral : 6.194 76.639 1695 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.12 % Allowed : 12.81 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.22), residues: 1506 helix: 1.80 (0.20), residues: 711 sheet: -0.08 (0.39), residues: 172 loop : -1.04 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 349 HIS 0.003 0.001 HIS B 97 PHE 0.022 0.001 PHE B 67 TYR 0.012 0.001 TYR B 216 ARG 0.007 0.000 ARG A 713 Details of bonding type rmsd link_NAG-ASN : bond 0.01087 ( 2) link_NAG-ASN : angle 5.49676 ( 6) hydrogen bonds : bond 0.04878 ( 574) hydrogen bonds : angle 4.16509 ( 1689) SS BOND : bond 0.00164 ( 13) SS BOND : angle 0.67484 ( 26) covalent geometry : bond 0.00309 (11198) covalent geometry : angle 0.51441 (15320) Misc. bond : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 1.157 Fit side-chains REVERT: A 295 ASP cc_start: 0.8005 (t0) cc_final: 0.7747 (t0) REVERT: A 399 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7930 (mp) REVERT: A 760 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7349 (pptt) outliers start: 30 outliers final: 23 residues processed: 206 average time/residue: 0.2818 time to fit residues: 77.7754 Evaluate side-chains 207 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 553 CYS Chi-restraints excluded: chain B residue 607 TYR Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 747 PHE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 697 TRP Chi-restraints excluded: chain A residue 760 LYS Chi-restraints excluded: chain A residue 776 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 71 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 150 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 141 optimal weight: 0.0040 chunk 101 optimal weight: 0.0470 chunk 125 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 98 optimal weight: 0.3980 overall best weight: 0.4092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.144566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.117662 restraints weight = 17641.033| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.33 r_work: 0.3438 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11214 Z= 0.132 Angle : 0.518 9.979 15352 Z= 0.269 Chirality : 0.042 0.160 1744 Planarity : 0.005 0.065 2006 Dihedral : 5.981 75.376 1695 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.81 % Allowed : 14.58 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.22), residues: 1506 helix: 1.87 (0.20), residues: 705 sheet: -0.07 (0.39), residues: 177 loop : -0.96 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 349 HIS 0.003 0.001 HIS B 97 PHE 0.022 0.001 PHE B 67 TYR 0.012 0.001 TYR B 216 ARG 0.005 0.000 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.01070 ( 2) link_NAG-ASN : angle 5.46786 ( 6) hydrogen bonds : bond 0.04710 ( 574) hydrogen bonds : angle 4.09436 ( 1689) SS BOND : bond 0.00202 ( 13) SS BOND : angle 0.60007 ( 26) covalent geometry : bond 0.00304 (11198) covalent geometry : angle 0.50665 (15320) Misc. bond : bond 0.00033 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 184 time to evaluate : 1.150 Fit side-chains REVERT: B 109 SER cc_start: 0.7491 (OUTLIER) cc_final: 0.7173 (t) REVERT: B 427 LYS cc_start: 0.8607 (tttm) cc_final: 0.8338 (tttm) REVERT: B 440 GLU cc_start: 0.7830 (tt0) cc_final: 0.7381 (tt0) REVERT: A 140 ILE cc_start: 0.8163 (mt) cc_final: 0.7841 (mt) REVERT: A 295 ASP cc_start: 0.7981 (t0) cc_final: 0.7713 (t0) REVERT: A 335 ASP cc_start: 0.8229 (p0) cc_final: 0.7991 (p0) REVERT: A 399 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7869 (mp) REVERT: A 760 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7347 (pptt) outliers start: 27 outliers final: 21 residues processed: 202 average time/residue: 0.2859 time to fit residues: 77.1984 Evaluate side-chains 201 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 553 CYS Chi-restraints excluded: chain B residue 607 TYR Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 747 PHE Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 697 TRP Chi-restraints excluded: chain A residue 760 LYS Chi-restraints excluded: chain A residue 776 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 145 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 151 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 79 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.142802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.115642 restraints weight = 17657.982| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.38 r_work: 0.3408 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11214 Z= 0.179 Angle : 0.554 10.030 15352 Z= 0.291 Chirality : 0.043 0.204 1744 Planarity : 0.005 0.080 2006 Dihedral : 6.021 75.814 1695 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.54 % Allowed : 15.21 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.22), residues: 1506 helix: 1.74 (0.20), residues: 706 sheet: -0.04 (0.39), residues: 178 loop : -1.01 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 291 HIS 0.005 0.001 HIS B 97 PHE 0.029 0.002 PHE B 67 TYR 0.015 0.002 TYR B 216 ARG 0.008 0.001 ARG A 713 Details of bonding type rmsd link_NAG-ASN : bond 0.01015 ( 2) link_NAG-ASN : angle 5.50872 ( 6) hydrogen bonds : bond 0.05432 ( 574) hydrogen bonds : angle 4.20986 ( 1689) SS BOND : bond 0.00270 ( 13) SS BOND : angle 0.60795 ( 26) covalent geometry : bond 0.00425 (11198) covalent geometry : angle 0.54268 (15320) Misc. bond : bond 0.00041 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 25 VAL cc_start: 0.8771 (t) cc_final: 0.8496 (m) REVERT: B 109 SER cc_start: 0.7517 (OUTLIER) cc_final: 0.7232 (t) REVERT: A 140 ILE cc_start: 0.8208 (mt) cc_final: 0.7926 (mt) REVERT: A 335 ASP cc_start: 0.8219 (p0) cc_final: 0.7973 (p0) REVERT: A 399 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7931 (mp) REVERT: A 442 ARG cc_start: 0.8273 (mtm-85) cc_final: 0.8046 (mtm110) outliers start: 34 outliers final: 28 residues processed: 200 average time/residue: 0.2783 time to fit residues: 74.6936 Evaluate side-chains 203 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 607 TYR Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 747 PHE Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 697 TRP Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 760 LYS Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 808 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 11 optimal weight: 0.2980 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.142417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.116095 restraints weight = 18030.384| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.24 r_work: 0.3418 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11214 Z= 0.184 Angle : 0.560 10.021 15352 Z= 0.293 Chirality : 0.043 0.220 1744 Planarity : 0.005 0.076 2006 Dihedral : 5.992 77.753 1695 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.44 % Allowed : 16.15 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.22), residues: 1506 helix: 1.69 (0.20), residues: 703 sheet: -0.07 (0.39), residues: 178 loop : -1.06 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 349 HIS 0.005 0.001 HIS B 97 PHE 0.028 0.002 PHE B 67 TYR 0.014 0.002 TYR B 466 ARG 0.009 0.001 ARG A 713 Details of bonding type rmsd link_NAG-ASN : bond 0.01005 ( 2) link_NAG-ASN : angle 5.47326 ( 6) hydrogen bonds : bond 0.05410 ( 574) hydrogen bonds : angle 4.23882 ( 1689) SS BOND : bond 0.00246 ( 13) SS BOND : angle 0.57586 ( 26) covalent geometry : bond 0.00439 (11198) covalent geometry : angle 0.54917 (15320) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 182 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 25 VAL cc_start: 0.8779 (t) cc_final: 0.8507 (m) REVERT: B 109 SER cc_start: 0.7534 (OUTLIER) cc_final: 0.7281 (t) REVERT: B 351 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8211 (tt0) REVERT: A 140 ILE cc_start: 0.8194 (mt) cc_final: 0.7927 (mt) REVERT: A 321 SER cc_start: 0.8343 (p) cc_final: 0.8042 (m) REVERT: A 335 ASP cc_start: 0.8177 (p0) cc_final: 0.7938 (p0) REVERT: A 399 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7905 (mp) REVERT: A 442 ARG cc_start: 0.8247 (mtm-85) cc_final: 0.8000 (mtm110) outliers start: 33 outliers final: 27 residues processed: 203 average time/residue: 0.2717 time to fit residues: 74.4772 Evaluate side-chains 206 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 176 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 607 TYR Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 747 PHE Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 697 TRP Chi-restraints excluded: chain A residue 760 LYS Chi-restraints excluded: chain A residue 776 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 140 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 21 optimal weight: 0.0060 chunk 17 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 29 optimal weight: 0.1980 chunk 32 optimal weight: 0.5980 chunk 138 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.143563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.117292 restraints weight = 17563.828| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.20 r_work: 0.3440 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11214 Z= 0.134 Angle : 0.541 10.122 15352 Z= 0.278 Chirality : 0.042 0.226 1744 Planarity : 0.005 0.083 2006 Dihedral : 5.855 76.788 1695 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.23 % Allowed : 16.35 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.22), residues: 1506 helix: 1.78 (0.20), residues: 704 sheet: -0.08 (0.39), residues: 178 loop : -1.02 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 349 HIS 0.003 0.001 HIS B 97 PHE 0.021 0.001 PHE B 67 TYR 0.012 0.001 TYR B 165 ARG 0.006 0.000 ARG A 397 Details of bonding type rmsd link_NAG-ASN : bond 0.01120 ( 2) link_NAG-ASN : angle 5.42267 ( 6) hydrogen bonds : bond 0.04902 ( 574) hydrogen bonds : angle 4.13869 ( 1689) SS BOND : bond 0.00180 ( 13) SS BOND : angle 1.01142 ( 26) covalent geometry : bond 0.00307 (11198) covalent geometry : angle 0.52869 (15320) Misc. bond : bond 0.00054 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 25 VAL cc_start: 0.8738 (t) cc_final: 0.8486 (m) REVERT: B 109 SER cc_start: 0.7483 (OUTLIER) cc_final: 0.7244 (t) REVERT: B 351 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8138 (tt0) REVERT: B 427 LYS cc_start: 0.8553 (tttm) cc_final: 0.8257 (tttm) REVERT: A 140 ILE cc_start: 0.8134 (mt) cc_final: 0.7857 (mt) REVERT: A 321 SER cc_start: 0.8347 (p) cc_final: 0.8034 (m) REVERT: A 335 ASP cc_start: 0.8122 (p0) cc_final: 0.7855 (p0) REVERT: A 399 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7872 (mp) outliers start: 31 outliers final: 28 residues processed: 196 average time/residue: 0.4021 time to fit residues: 107.5317 Evaluate side-chains 205 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 607 TYR Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 747 PHE Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 697 TRP Chi-restraints excluded: chain A residue 760 LYS Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 776 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 100 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 148 optimal weight: 0.2980 chunk 136 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 390 HIS ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.141863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.115796 restraints weight = 17601.163| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.16 r_work: 0.3411 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 11214 Z= 0.200 Angle : 0.582 10.003 15352 Z= 0.303 Chirality : 0.044 0.227 1744 Planarity : 0.005 0.085 2006 Dihedral : 5.966 76.859 1695 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.02 % Allowed : 16.77 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.22), residues: 1506 helix: 1.63 (0.20), residues: 703 sheet: -0.01 (0.39), residues: 178 loop : -1.11 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 349 HIS 0.005 0.001 HIS B 97 PHE 0.030 0.002 PHE B 67 TYR 0.016 0.002 TYR B 216 ARG 0.011 0.001 ARG A 713 Details of bonding type rmsd link_NAG-ASN : bond 0.01008 ( 2) link_NAG-ASN : angle 5.45027 ( 6) hydrogen bonds : bond 0.05688 ( 574) hydrogen bonds : angle 4.27785 ( 1689) SS BOND : bond 0.00332 ( 13) SS BOND : angle 0.77079 ( 26) covalent geometry : bond 0.00477 (11198) covalent geometry : angle 0.57188 (15320) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 183 time to evaluate : 4.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 25 VAL cc_start: 0.8726 (t) cc_final: 0.8466 (m) REVERT: B 349 TRP cc_start: 0.7984 (t-100) cc_final: 0.7694 (t-100) REVERT: B 351 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8210 (tt0) REVERT: B 427 LYS cc_start: 0.8555 (tttm) cc_final: 0.8257 (tttm) REVERT: A 140 ILE cc_start: 0.8207 (mt) cc_final: 0.7953 (mt) REVERT: A 321 SER cc_start: 0.8331 (p) cc_final: 0.8040 (m) REVERT: A 335 ASP cc_start: 0.8094 (p0) cc_final: 0.7863 (p0) REVERT: A 442 ARG cc_start: 0.8287 (mtm-85) cc_final: 0.8039 (mtm110) outliers start: 29 outliers final: 27 residues processed: 201 average time/residue: 0.5242 time to fit residues: 145.7482 Evaluate side-chains 209 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 607 TYR Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 747 PHE Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 697 TRP Chi-restraints excluded: chain A residue 760 LYS Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 776 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 142 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 112 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.141308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.115388 restraints weight = 17480.465| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.14 r_work: 0.3405 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 11214 Z= 0.210 Angle : 0.592 9.983 15352 Z= 0.308 Chirality : 0.044 0.241 1744 Planarity : 0.005 0.079 2006 Dihedral : 6.041 77.177 1695 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.12 % Allowed : 17.08 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.22), residues: 1506 helix: 1.57 (0.20), residues: 697 sheet: -0.07 (0.39), residues: 178 loop : -1.14 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 349 HIS 0.004 0.001 HIS B 97 PHE 0.030 0.002 PHE B 67 TYR 0.016 0.002 TYR B 466 ARG 0.013 0.001 ARG A 713 Details of bonding type rmsd link_NAG-ASN : bond 0.00966 ( 2) link_NAG-ASN : angle 5.47757 ( 6) hydrogen bonds : bond 0.05775 ( 574) hydrogen bonds : angle 4.33169 ( 1689) SS BOND : bond 0.00298 ( 13) SS BOND : angle 0.70069 ( 26) covalent geometry : bond 0.00503 (11198) covalent geometry : angle 0.58165 (15320) Misc. bond : bond 0.00033 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 1.182 Fit side-chains revert: symmetry clash REVERT: B 25 VAL cc_start: 0.8722 (t) cc_final: 0.8456 (m) REVERT: B 351 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8220 (tt0) REVERT: B 427 LYS cc_start: 0.8555 (tttm) cc_final: 0.8325 (tttm) REVERT: A 140 ILE cc_start: 0.8205 (mt) cc_final: 0.7955 (mt) REVERT: A 321 SER cc_start: 0.8304 (p) cc_final: 0.8043 (m) REVERT: A 335 ASP cc_start: 0.8100 (p0) cc_final: 0.7877 (p0) outliers start: 30 outliers final: 28 residues processed: 197 average time/residue: 0.3083 time to fit residues: 85.3739 Evaluate side-chains 205 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 607 TYR Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 747 PHE Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 697 TRP Chi-restraints excluded: chain A residue 760 LYS Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 776 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 chunk 150 optimal weight: 0.7980 chunk 75 optimal weight: 0.1980 chunk 112 optimal weight: 0.0470 chunk 36 optimal weight: 0.9980 chunk 118 optimal weight: 0.2980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.143045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.117054 restraints weight = 17460.812| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.15 r_work: 0.3431 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11214 Z= 0.140 Angle : 0.542 10.057 15352 Z= 0.280 Chirality : 0.042 0.217 1744 Planarity : 0.005 0.075 2006 Dihedral : 5.855 76.810 1695 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.81 % Allowed : 17.40 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.22), residues: 1506 helix: 1.75 (0.20), residues: 697 sheet: -0.07 (0.39), residues: 178 loop : -1.06 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 349 HIS 0.003 0.001 HIS B 97 PHE 0.022 0.001 PHE B 67 TYR 0.013 0.001 TYR B 165 ARG 0.013 0.000 ARG A 713 Details of bonding type rmsd link_NAG-ASN : bond 0.01073 ( 2) link_NAG-ASN : angle 5.39705 ( 6) hydrogen bonds : bond 0.04890 ( 574) hydrogen bonds : angle 4.15754 ( 1689) SS BOND : bond 0.00173 ( 13) SS BOND : angle 0.59891 ( 26) covalent geometry : bond 0.00323 (11198) covalent geometry : angle 0.53114 (15320) Misc. bond : bond 0.00019 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7971.68 seconds wall clock time: 143 minutes 43.95 seconds (8623.95 seconds total)