Starting phenix.real_space_refine on Wed Feb 4 18:20:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mbb_63772/02_2026/9mbb_63772_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mbb_63772/02_2026/9mbb_63772.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mbb_63772/02_2026/9mbb_63772_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mbb_63772/02_2026/9mbb_63772_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mbb_63772/02_2026/9mbb_63772.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mbb_63772/02_2026/9mbb_63772.map" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.023 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 80 5.16 5 C 7702 2.51 5 N 2008 2.21 5 O 2208 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11998 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 770, 5973 Classifications: {'peptide': 770} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 38, 'TRANS': 731} Chain breaks: 4 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 5973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 770, 5973 Classifications: {'peptide': 770} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 38, 'TRANS': 731} Chain breaks: 4 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 57 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'Z99': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'Z99': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.35, per 1000 atoms: 0.20 Number of scatterers: 11998 At special positions: 0 Unit cell: (127.5, 82.5, 192, 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 80 16.00 O 2208 8.00 N 2008 7.00 C 7702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 246 " - pdb=" SG CYS A 534 " distance=2.03 Simple disulfide: pdb=" SG CYS A 424 " - pdb=" SG CYS A 431 " distance=2.03 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 535 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 538 " distance=2.03 Simple disulfide: pdb=" SG CYS A 541 " - pdb=" SG CYS A 553 " distance=2.04 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 569 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 246 " - pdb=" SG CYS B 534 " distance=2.03 Simple disulfide: pdb=" SG CYS B 424 " - pdb=" SG CYS B 431 " distance=2.03 Simple disulfide: pdb=" SG CYS B 516 " - pdb=" SG CYS B 535 " distance=2.03 Simple disulfide: pdb=" SG CYS B 520 " - pdb=" SG CYS B 538 " distance=2.03 Simple disulfide: pdb=" SG CYS B 541 " - pdb=" SG CYS B 553 " distance=2.04 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 569 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 742 " 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=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 521.1 milliseconds 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2880 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 12 sheets defined 46.5% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 72 through 87 Processing helix chain 'A' and resid 108 through 120 removed outlier: 3.616A pdb=" N ALA A 112 " --> pdb=" O ARG A 108 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 168 Processing helix chain 'A' and resid 180 through 184 Processing helix chain 'A' and resid 198 through 201 Processing helix chain 'A' and resid 202 through 213 removed outlier: 3.541A pdb=" N MET A 206 " --> pdb=" O GLN A 202 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 240 removed outlier: 3.842A pdb=" N SER A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 283 through 294 removed outlier: 3.765A pdb=" N ILE A 287 " --> pdb=" O ASN A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 348 removed outlier: 3.653A pdb=" N ASP A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 368 removed outlier: 3.609A pdb=" N PHE A 367 " --> pdb=" O TRP A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 424 removed outlier: 3.704A pdb=" N VAL A 409 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 436 removed outlier: 4.506A pdb=" N THR A 436 " --> pdb=" O PRO A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 447 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 584 through 608 removed outlier: 3.562A pdb=" N THR A 599 " --> pdb=" O ILE A 595 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG A 607 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR A 608 " --> pdb=" O THR A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 619 removed outlier: 3.741A pdb=" N ARG A 619 " --> pdb=" O ARG A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 639 removed outlier: 3.927A pdb=" N TYR A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 675 removed outlier: 3.586A pdb=" N ARG A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 678 No H-bonds generated for 'chain 'A' and resid 676 through 678' Processing helix chain 'A' and resid 690 through 712 Processing helix chain 'A' and resid 745 through 753 Processing helix chain 'A' and resid 753 through 772 removed outlier: 4.300A pdb=" N GLY A 772 " --> pdb=" O ILE A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 796 removed outlier: 4.136A pdb=" N ILE A 783 " --> pdb=" O GLU A 779 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY A 784 " --> pdb=" O ALA A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 803 removed outlier: 3.726A pdb=" N ILE A 800 " --> pdb=" O ALA A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 806 No H-bonds generated for 'chain 'A' and resid 804 through 806' Processing helix chain 'A' and resid 809 through 830 Processing helix chain 'A' and resid 835 through 839 Processing helix chain 'B' and resid 72 through 87 Processing helix chain 'B' and resid 108 through 120 removed outlier: 3.616A pdb=" N ALA B 112 " --> pdb=" O ARG B 108 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 120 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 168 Processing helix chain 'B' and resid 180 through 184 Processing helix chain 'B' and resid 198 through 201 Processing helix chain 'B' and resid 202 through 213 removed outlier: 3.541A pdb=" N MET B 206 " --> pdb=" O GLN B 202 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 240 removed outlier: 3.841A pdb=" N SER B 230 " --> pdb=" O ASN B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 270 Processing helix chain 'B' and resid 283 through 294 removed outlier: 3.765A pdb=" N ILE B 287 " --> pdb=" O ASN B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 348 removed outlier: 3.653A pdb=" N ASP B 342 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 368 removed outlier: 3.610A pdb=" N PHE B 367 " --> pdb=" O TRP B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 424 removed outlier: 3.704A pdb=" N VAL B 409 " --> pdb=" O VAL B 405 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 436 removed outlier: 4.505A pdb=" N THR B 436 " --> pdb=" O PRO B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 447 Processing helix chain 'B' and resid 499 through 502 Processing helix chain 'B' and resid 584 through 608 removed outlier: 3.562A pdb=" N THR B 599 " --> pdb=" O ILE B 595 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG B 607 " --> pdb=" O VAL B 603 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR B 608 " --> pdb=" O THR B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 619 removed outlier: 3.742A pdb=" N ARG B 619 " --> pdb=" O ARG B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 639 removed outlier: 3.927A pdb=" N TYR B 623 " --> pdb=" O ARG B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 675 removed outlier: 3.586A pdb=" N ARG B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 678 No H-bonds generated for 'chain 'B' and resid 676 through 678' Processing helix chain 'B' and resid 690 through 712 Processing helix chain 'B' and resid 745 through 753 Processing helix chain 'B' and resid 753 through 772 removed outlier: 4.300A pdb=" N GLY B 772 " --> pdb=" O ILE B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 796 removed outlier: 4.136A pdb=" N ILE B 783 " --> pdb=" O GLU B 779 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY B 784 " --> pdb=" O ALA B 780 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 803 removed outlier: 3.726A pdb=" N ILE B 800 " --> pdb=" O ALA B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 806 No H-bonds generated for 'chain 'B' and resid 804 through 806' Processing helix chain 'B' and resid 809 through 830 Processing helix chain 'B' and resid 835 through 839 Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42 removed outlier: 3.604A pdb=" N ILE A 102 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE A 46 " --> pdb=" O GLY A 99 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ARG A 101 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU A 48 " --> pdb=" O ARG A 101 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU A 103 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY A 50 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE A 47 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N ILE A 151 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLY A 49 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N ILE A 174 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL A 150 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLN A 173 " --> pdb=" O SER A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 246 through 252 removed outlier: 7.526A pdb=" N VAL A 218 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N SER A 250 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THR A 220 " --> pdb=" O SER A 250 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LYS A 252 " --> pdb=" O THR A 220 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA A 222 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA A 277 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A 328 " --> pdb=" O TYR A 476 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR A 476 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A 489 " --> pdb=" O ILE A 473 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN A 475 " --> pdb=" O VAL A 487 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N VAL A 487 " --> pdb=" O GLN A 475 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N GLN A 477 " --> pdb=" O TYR A 485 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TYR A 485 " --> pdb=" O GLN A 477 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N THR A 479 " --> pdb=" O THR A 483 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N THR A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 451 through 452 removed outlier: 3.695A pdb=" N PHE A 451 " --> pdb=" O VAL A 459 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 524 through 528 Processing sheet with id=AA5, first strand: chain 'A' and resid 561 through 562 Processing sheet with id=AA6, first strand: chain 'A' and resid 722 through 723 Processing sheet with id=AA7, first strand: chain 'B' and resid 40 through 42 removed outlier: 3.605A pdb=" N ILE B 102 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE B 46 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ARG B 101 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU B 48 " --> pdb=" O ARG B 101 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU B 103 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY B 50 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE B 47 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N ILE B 151 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLY B 49 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N ILE B 174 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL B 150 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLN B 173 " --> pdb=" O SER B 193 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 246 through 252 removed outlier: 7.526A pdb=" N VAL B 218 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N SER B 250 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THR B 220 " --> pdb=" O SER B 250 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LYS B 252 " --> pdb=" O THR B 220 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA B 222 " --> pdb=" O LYS B 252 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ALA B 277 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA B 328 " --> pdb=" O TYR B 476 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR B 476 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY B 489 " --> pdb=" O ILE B 473 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN B 475 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N VAL B 487 " --> pdb=" O GLN B 475 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N GLN B 477 " --> pdb=" O TYR B 485 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TYR B 485 " --> pdb=" O GLN B 477 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR B 479 " --> pdb=" O THR B 483 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N THR B 483 " --> pdb=" O THR B 479 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 451 through 452 removed outlier: 3.695A pdb=" N PHE B 451 " --> pdb=" O VAL B 459 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 524 through 528 Processing sheet with id=AB2, first strand: chain 'B' and resid 561 through 562 Processing sheet with id=AB3, first strand: chain 'B' and resid 722 through 723 524 hydrogen bonds defined for protein. 1518 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3827 1.34 - 1.46: 2616 1.46 - 1.58: 5712 1.58 - 1.70: 1 1.70 - 1.82: 114 Bond restraints: 12270 Sorted by residual: bond pdb=" CAT Z99 A1001 " pdb=" OAP Z99 A1001 " ideal model delta sigma weight residual 1.364 1.437 -0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" CAS Z99 A1001 " pdb=" OAP Z99 A1001 " ideal model delta sigma weight residual 1.369 1.438 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" CAT Z99 B1001 " pdb=" OAP Z99 B1001 " ideal model delta sigma weight residual 1.364 1.430 -0.066 2.00e-02 2.50e+03 1.07e+01 bond pdb=" CAS Z99 B1001 " pdb=" OAP Z99 B1001 " ideal model delta sigma weight residual 1.369 1.428 -0.059 2.00e-02 2.50e+03 8.85e+00 bond pdb=" N LEU B 696 " pdb=" CA LEU B 696 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.20e-02 6.94e+03 7.47e+00 ... (remaining 12265 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 16249 2.19 - 4.39: 363 4.39 - 6.58: 48 6.58 - 8.77: 15 8.77 - 10.96: 3 Bond angle restraints: 16678 Sorted by residual: angle pdb=" CA GLU B 66 " pdb=" CB GLU B 66 " pdb=" CG GLU B 66 " ideal model delta sigma weight residual 114.10 122.10 -8.00 2.00e+00 2.50e-01 1.60e+01 angle pdb=" CA GLU A 66 " pdb=" CB GLU A 66 " pdb=" CG GLU A 66 " ideal model delta sigma weight residual 114.10 122.09 -7.99 2.00e+00 2.50e-01 1.60e+01 angle pdb=" CAO Z99 A1001 " pdb=" CAX Z99 A1001 " pdb=" CAQ Z99 A1001 " ideal model delta sigma weight residual 119.08 108.12 10.96 3.00e+00 1.11e-01 1.34e+01 angle pdb=" CAO Z99 B1001 " pdb=" CAZ Z99 B1001 " pdb=" CAY Z99 B1001 " ideal model delta sigma weight residual 121.02 110.28 10.74 3.00e+00 1.11e-01 1.28e+01 angle pdb=" CAO Z99 B1001 " pdb=" CAX Z99 B1001 " pdb=" CAQ Z99 B1001 " ideal model delta sigma weight residual 119.08 109.24 9.84 3.00e+00 1.11e-01 1.08e+01 ... (remaining 16673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 7258 35.87 - 71.74: 106 71.74 - 107.61: 5 107.61 - 143.48: 13 143.48 - 179.34: 8 Dihedral angle restraints: 7390 sinusoidal: 2920 harmonic: 4470 Sorted by residual: dihedral pdb=" CAN Z99 B1001 " pdb=" CAV Z99 B1001 " pdb=" CAW Z99 B1001 " pdb=" CAT Z99 B1001 " ideal model delta sinusoidal sigma weight residual 269.79 90.45 179.34 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CAL Z99 A1001 " pdb=" CAU Z99 A1001 " pdb=" CAW Z99 A1001 " pdb=" CAN Z99 A1001 " ideal model delta sinusoidal sigma weight residual 92.77 -85.19 177.96 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CAN Z99 A1001 " pdb=" CAU Z99 A1001 " pdb=" CAW Z99 A1001 " pdb=" CAS Z99 A1001 " ideal model delta sinusoidal sigma weight residual 87.26 -95.67 -177.07 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 7387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.119: 1906 1.119 - 2.239: 0 2.239 - 3.358: 0 3.358 - 4.478: 0 4.478 - 5.597: 2 Chirality restraints: 1908 Sorted by residual: chirality pdb=" CAW Z99 B1001 " pdb=" CAN Z99 B1001 " pdb=" CAU Z99 B1001 " pdb=" CAV Z99 B1001 " both_signs ideal model delta sigma weight residual False 2.61 -2.99 5.60 2.00e-01 2.50e+01 7.83e+02 chirality pdb=" CAW Z99 A1001 " pdb=" CAN Z99 A1001 " pdb=" CAU Z99 A1001 " pdb=" CAV Z99 A1001 " both_signs ideal model delta sigma weight residual False 2.61 -2.77 5.38 2.00e-01 2.50e+01 7.25e+02 chirality pdb=" CAX Z99 A1001 " pdb=" CAO Z99 A1001 " pdb=" CAQ Z99 A1001 " pdb=" CAZ Z99 A1001 " both_signs ideal model delta sigma weight residual True 2.43 2.79 -0.36 2.00e-01 2.50e+01 3.20e+00 ... (remaining 1905 not shown) Planarity restraints: 2112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 424 " 0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO B 425 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 425 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 425 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 424 " 0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO A 425 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 425 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 425 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 718 " 0.032 5.00e-02 4.00e+02 4.85e-02 3.77e+00 pdb=" N PRO B 719 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 719 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 719 " 0.027 5.00e-02 4.00e+02 ... (remaining 2109 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2001 2.76 - 3.30: 12347 3.30 - 3.83: 19717 3.83 - 4.37: 22445 4.37 - 4.90: 37560 Nonbonded interactions: 94070 Sorted by model distance: nonbonded pdb=" OE1 GLU A 322 " pdb=" OH TYR A 476 " model vdw 2.229 3.040 nonbonded pdb=" OE1 GLU B 322 " pdb=" OH TYR B 476 " model vdw 2.229 3.040 nonbonded pdb=" O SER B 745 " pdb=" OG SER B 748 " model vdw 2.232 3.040 nonbonded pdb=" O SER A 745 " pdb=" OG SER A 748 " model vdw 2.233 3.040 nonbonded pdb=" O VAL A 601 " pdb=" OG1 THR A 604 " model vdw 2.262 3.040 ... (remaining 94065 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.210 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 12284 Z= 0.200 Angle : 0.782 10.963 16706 Z= 0.404 Chirality : 0.185 5.597 1908 Planarity : 0.005 0.061 2112 Dihedral : 16.839 179.345 4468 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.21), residues: 1520 helix: 0.55 (0.20), residues: 640 sheet: -1.44 (0.44), residues: 144 loop : -2.00 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 41 TYR 0.022 0.002 TYR B 725 PHE 0.023 0.002 PHE B 345 TRP 0.015 0.001 TRP A 713 HIS 0.004 0.001 HIS A 580 Details of bonding type rmsd covalent geometry : bond 0.00416 (12270) covalent geometry : angle 0.78170 (16678) SS BOND : bond 0.00268 ( 14) SS BOND : angle 1.12356 ( 28) hydrogen bonds : bond 0.15627 ( 524) hydrogen bonds : angle 6.05633 ( 1518) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 364 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7297 (mp0) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1122 time to fit residues: 35.5136 Evaluate side-chains 107 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 GLN B 186 ASN ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.125524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.094024 restraints weight = 39111.053| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 3.78 r_work: 0.3523 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12284 Z= 0.204 Angle : 0.800 12.470 16706 Z= 0.398 Chirality : 0.049 0.377 1908 Planarity : 0.005 0.052 2112 Dihedral : 12.071 128.460 1714 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.50 % Favored : 92.37 % Rotamer: Outliers : 0.78 % Allowed : 11.09 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.22), residues: 1520 helix: 0.69 (0.20), residues: 640 sheet: -1.66 (0.43), residues: 156 loop : -1.59 (0.25), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 392 TYR 0.018 0.002 TYR B 427 PHE 0.027 0.002 PHE B 345 TRP 0.013 0.001 TRP A 504 HIS 0.004 0.001 HIS A 380 Details of bonding type rmsd covalent geometry : bond 0.00453 (12270) covalent geometry : angle 0.79888 (16678) SS BOND : bond 0.00381 ( 14) SS BOND : angle 1.10955 ( 28) hydrogen bonds : bond 0.05695 ( 524) hydrogen bonds : angle 5.17995 ( 1518) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8795 (ttm) REVERT: A 364 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7926 (pt0) REVERT: A 818 LEU cc_start: 0.9755 (pp) cc_final: 0.9428 (pp) REVERT: A 834 TYR cc_start: 0.8116 (p90) cc_final: 0.7735 (p90) REVERT: B 299 GLN cc_start: 0.6798 (pp30) cc_final: 0.6138 (pp30) REVERT: B 822 MET cc_start: 0.9367 (ttt) cc_final: 0.9107 (ptm) outliers start: 10 outliers final: 6 residues processed: 130 average time/residue: 0.0983 time to fit residues: 18.2885 Evaluate side-chains 96 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 801 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 109 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 chunk 2 optimal weight: 0.0670 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.123682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.092671 restraints weight = 40972.870| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 3.92 r_work: 0.3552 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12284 Z= 0.141 Angle : 0.684 12.389 16706 Z= 0.343 Chirality : 0.045 0.204 1908 Planarity : 0.005 0.050 2112 Dihedral : 9.530 139.027 1714 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.25 % Favored : 93.62 % Rotamer: Outliers : 1.63 % Allowed : 12.95 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.22), residues: 1520 helix: 0.62 (0.20), residues: 658 sheet: -1.33 (0.47), residues: 126 loop : -1.46 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 525 TYR 0.015 0.001 TYR A 217 PHE 0.019 0.001 PHE B 345 TRP 0.032 0.001 TRP B 713 HIS 0.002 0.001 HIS B 420 Details of bonding type rmsd covalent geometry : bond 0.00302 (12270) covalent geometry : angle 0.68327 (16678) SS BOND : bond 0.00374 ( 14) SS BOND : angle 0.87103 ( 28) hydrogen bonds : bond 0.04846 ( 524) hydrogen bonds : angle 4.84120 ( 1518) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8871 (ttm) REVERT: B 364 GLU cc_start: 0.8521 (mt-10) cc_final: 0.7888 (pt0) REVERT: B 577 LEU cc_start: 0.8690 (mm) cc_final: 0.7609 (pt) REVERT: B 797 PHE cc_start: 0.9076 (t80) cc_final: 0.8872 (t80) REVERT: B 822 MET cc_start: 0.9371 (ttt) cc_final: 0.9162 (ptm) outliers start: 21 outliers final: 7 residues processed: 118 average time/residue: 0.0901 time to fit residues: 15.8753 Evaluate side-chains 94 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 655 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 88 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 33 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 150 optimal weight: 0.0470 chunk 75 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 overall best weight: 1.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.121565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.089572 restraints weight = 40328.083| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 3.84 r_work: 0.3489 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12284 Z= 0.168 Angle : 0.679 11.597 16706 Z= 0.346 Chirality : 0.046 0.245 1908 Planarity : 0.005 0.049 2112 Dihedral : 8.920 136.922 1714 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.16 % Favored : 91.71 % Rotamer: Outliers : 2.09 % Allowed : 15.27 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.22), residues: 1520 helix: 0.69 (0.20), residues: 658 sheet: -1.11 (0.48), residues: 126 loop : -1.45 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 525 TYR 0.023 0.002 TYR A 663 PHE 0.023 0.002 PHE B 281 TRP 0.015 0.001 TRP B 504 HIS 0.003 0.001 HIS B 420 Details of bonding type rmsd covalent geometry : bond 0.00377 (12270) covalent geometry : angle 0.67937 (16678) SS BOND : bond 0.00306 ( 14) SS BOND : angle 0.74972 ( 28) hydrogen bonds : bond 0.04926 ( 524) hydrogen bonds : angle 4.82964 ( 1518) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8965 (ttm) REVERT: A 414 TYR cc_start: 0.8119 (m-80) cc_final: 0.7064 (m-10) REVERT: A 797 PHE cc_start: 0.8661 (t80) cc_final: 0.8389 (t80) REVERT: B 790 THR cc_start: 0.8903 (t) cc_final: 0.8689 (p) REVERT: B 797 PHE cc_start: 0.9059 (t80) cc_final: 0.8770 (t80) REVERT: B 834 TYR cc_start: 0.7949 (p90) cc_final: 0.7547 (p90) outliers start: 27 outliers final: 16 residues processed: 120 average time/residue: 0.0913 time to fit residues: 16.3176 Evaluate side-chains 101 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 801 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 80 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 144 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.119763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.088267 restraints weight = 39997.097| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 3.43 r_work: 0.3517 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12284 Z= 0.220 Angle : 0.724 14.540 16706 Z= 0.367 Chirality : 0.047 0.193 1908 Planarity : 0.005 0.046 2112 Dihedral : 8.957 138.508 1714 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.49 % Favored : 91.38 % Rotamer: Outliers : 2.40 % Allowed : 16.12 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.22), residues: 1520 helix: 0.48 (0.20), residues: 670 sheet: -1.04 (0.44), residues: 142 loop : -1.62 (0.25), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 566 TYR 0.018 0.002 TYR A 663 PHE 0.024 0.002 PHE B 345 TRP 0.041 0.002 TRP A 713 HIS 0.003 0.001 HIS A 537 Details of bonding type rmsd covalent geometry : bond 0.00496 (12270) covalent geometry : angle 0.72456 (16678) SS BOND : bond 0.00301 ( 14) SS BOND : angle 0.63418 ( 28) hydrogen bonds : bond 0.05286 ( 524) hydrogen bonds : angle 5.00326 ( 1518) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8502 (mp10) REVERT: A 280 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8869 (ttm) REVERT: A 389 ARG cc_start: 0.6527 (OUTLIER) cc_final: 0.5566 (mtm-85) REVERT: A 414 TYR cc_start: 0.8175 (m-80) cc_final: 0.7230 (m-10) REVERT: A 564 MET cc_start: 0.9232 (tpt) cc_final: 0.8923 (tmm) REVERT: A 661 PHE cc_start: 0.8898 (m-80) cc_final: 0.8394 (m-10) REVERT: A 663 TYR cc_start: 0.8700 (m-80) cc_final: 0.8473 (m-80) REVERT: A 797 PHE cc_start: 0.8739 (t80) cc_final: 0.8368 (t80) REVERT: B 427 TYR cc_start: 0.8084 (t80) cc_final: 0.7549 (t80) REVERT: B 564 MET cc_start: 0.9199 (tpt) cc_final: 0.8816 (tmm) REVERT: B 790 THR cc_start: 0.8964 (t) cc_final: 0.8744 (p) REVERT: B 797 PHE cc_start: 0.9055 (t80) cc_final: 0.8693 (t80) outliers start: 31 outliers final: 18 residues processed: 115 average time/residue: 0.0806 time to fit residues: 14.7275 Evaluate side-chains 103 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 783 ILE Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 801 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 107 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 146 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 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 = 0.4227 r_free = 0.4227 target = 0.119624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.088629 restraints weight = 40108.363| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 3.46 r_work: 0.3546 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12284 Z= 0.148 Angle : 0.679 13.521 16706 Z= 0.334 Chirality : 0.046 0.264 1908 Planarity : 0.004 0.046 2112 Dihedral : 8.605 139.330 1714 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.50 % Favored : 92.37 % Rotamer: Outliers : 2.09 % Allowed : 17.13 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.22), residues: 1520 helix: 0.66 (0.20), residues: 668 sheet: -0.87 (0.45), residues: 138 loop : -1.51 (0.25), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 525 TYR 0.019 0.001 TYR A 633 PHE 0.013 0.001 PHE B 281 TRP 0.015 0.001 TRP A 713 HIS 0.002 0.000 HIS A 580 Details of bonding type rmsd covalent geometry : bond 0.00337 (12270) covalent geometry : angle 0.67852 (16678) SS BOND : bond 0.00272 ( 14) SS BOND : angle 0.68998 ( 28) hydrogen bonds : bond 0.04650 ( 524) hydrogen bonds : angle 4.80504 ( 1518) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7353 (m-10) REVERT: A 414 TYR cc_start: 0.8141 (m-80) cc_final: 0.7203 (m-10) REVERT: A 659 MET cc_start: 0.7977 (ptm) cc_final: 0.7218 (ptm) REVERT: A 661 PHE cc_start: 0.8854 (m-80) cc_final: 0.8340 (m-10) REVERT: A 797 PHE cc_start: 0.8733 (t80) cc_final: 0.8277 (t80) REVERT: B 270 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7719 (tt) REVERT: B 427 TYR cc_start: 0.8157 (t80) cc_final: 0.7656 (t80) REVERT: B 564 MET cc_start: 0.9201 (tpt) cc_final: 0.8854 (tmm) REVERT: B 577 LEU cc_start: 0.8378 (mm) cc_final: 0.7544 (pt) REVERT: B 700 PHE cc_start: 0.6086 (m-10) cc_final: 0.5422 (m-80) REVERT: B 790 THR cc_start: 0.8938 (t) cc_final: 0.8731 (p) REVERT: B 797 PHE cc_start: 0.9018 (t80) cc_final: 0.8590 (t80) outliers start: 27 outliers final: 15 residues processed: 119 average time/residue: 0.0737 time to fit residues: 14.2984 Evaluate side-chains 103 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 712 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 60 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 141 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 0.0040 chunk 84 optimal weight: 0.0470 overall best weight: 1.8096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 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 = 0.4209 r_free = 0.4209 target = 0.119462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.087725 restraints weight = 39987.546| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 3.38 r_work: 0.3506 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12284 Z= 0.192 Angle : 0.718 15.494 16706 Z= 0.357 Chirality : 0.046 0.257 1908 Planarity : 0.005 0.058 2112 Dihedral : 8.706 140.111 1714 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.16 % Favored : 91.71 % Rotamer: Outliers : 1.63 % Allowed : 18.76 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.22), residues: 1520 helix: 0.61 (0.20), residues: 672 sheet: -1.12 (0.43), residues: 138 loop : -1.55 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 355 TYR 0.022 0.002 TYR B 834 PHE 0.015 0.001 PHE B 281 TRP 0.016 0.001 TRP B 504 HIS 0.002 0.001 HIS B 506 Details of bonding type rmsd covalent geometry : bond 0.00436 (12270) covalent geometry : angle 0.71800 (16678) SS BOND : bond 0.00267 ( 14) SS BOND : angle 0.60227 ( 28) hydrogen bonds : bond 0.05004 ( 524) hydrogen bonds : angle 4.90084 ( 1518) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ARG cc_start: 0.6234 (OUTLIER) cc_final: 0.5191 (mtm-85) REVERT: A 427 TYR cc_start: 0.8114 (t80) cc_final: 0.7527 (t80) REVERT: A 659 MET cc_start: 0.7620 (ptm) cc_final: 0.7320 (ptm) REVERT: A 740 LEU cc_start: 0.9150 (tt) cc_final: 0.8844 (pt) REVERT: A 822 MET cc_start: 0.9291 (ptt) cc_final: 0.9058 (ptm) REVERT: B 281 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7873 (m-10) REVERT: B 389 ARG cc_start: 0.6753 (OUTLIER) cc_final: 0.5186 (mtm-85) REVERT: B 427 TYR cc_start: 0.8234 (t80) cc_final: 0.7669 (t80) REVERT: B 564 MET cc_start: 0.9259 (tpt) cc_final: 0.8919 (tmm) REVERT: B 577 LEU cc_start: 0.8694 (mm) cc_final: 0.7670 (pt) REVERT: B 659 MET cc_start: 0.8778 (mmp) cc_final: 0.8569 (ptp) REVERT: B 661 PHE cc_start: 0.8832 (m-80) cc_final: 0.8355 (m-80) REVERT: B 700 PHE cc_start: 0.6119 (m-10) cc_final: 0.5474 (m-80) REVERT: B 740 LEU cc_start: 0.9190 (tt) cc_final: 0.8773 (pt) REVERT: B 790 THR cc_start: 0.8965 (t) cc_final: 0.8752 (p) REVERT: B 797 PHE cc_start: 0.9070 (t80) cc_final: 0.8614 (t80) REVERT: B 811 MET cc_start: 0.8840 (pmm) cc_final: 0.8462 (pmm) REVERT: B 835 MET cc_start: 0.8137 (ppp) cc_final: 0.7861 (ppp) outliers start: 21 outliers final: 16 residues processed: 110 average time/residue: 0.0840 time to fit residues: 14.5501 Evaluate side-chains 107 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 801 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 46 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 113 optimal weight: 0.0570 chunk 124 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 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 = 0.4214 r_free = 0.4214 target = 0.119019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.088071 restraints weight = 40249.521| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 3.36 r_work: 0.3499 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.5361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12284 Z= 0.163 Angle : 0.710 16.068 16706 Z= 0.351 Chirality : 0.047 0.289 1908 Planarity : 0.004 0.053 2112 Dihedral : 8.592 140.880 1714 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.37 % Favored : 92.50 % Rotamer: Outliers : 1.55 % Allowed : 18.99 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.22), residues: 1520 helix: 0.78 (0.20), residues: 658 sheet: -1.30 (0.41), residues: 150 loop : -1.38 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 433 TYR 0.021 0.001 TYR A 834 PHE 0.018 0.001 PHE A 797 TRP 0.013 0.001 TRP A 504 HIS 0.002 0.001 HIS B 506 Details of bonding type rmsd covalent geometry : bond 0.00372 (12270) covalent geometry : angle 0.71048 (16678) SS BOND : bond 0.00248 ( 14) SS BOND : angle 0.62496 ( 28) hydrogen bonds : bond 0.04686 ( 524) hydrogen bonds : angle 4.81264 ( 1518) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 TYR cc_start: 0.8129 (m-80) cc_final: 0.7195 (m-10) REVERT: A 740 LEU cc_start: 0.9263 (tt) cc_final: 0.8874 (pt) REVERT: A 797 PHE cc_start: 0.8679 (t80) cc_final: 0.8198 (t80) REVERT: A 835 MET cc_start: 0.8346 (ppp) cc_final: 0.8126 (ppp) REVERT: B 389 ARG cc_start: 0.6635 (OUTLIER) cc_final: 0.4891 (mtm-85) REVERT: B 414 TYR cc_start: 0.8110 (m-80) cc_final: 0.7217 (m-10) REVERT: B 427 TYR cc_start: 0.8237 (t80) cc_final: 0.7821 (t80) REVERT: B 508 GLU cc_start: 0.5340 (OUTLIER) cc_final: 0.5041 (pm20) REVERT: B 564 MET cc_start: 0.9366 (tpt) cc_final: 0.8969 (tmm) REVERT: B 577 LEU cc_start: 0.8798 (mm) cc_final: 0.7867 (pt) REVERT: B 659 MET cc_start: 0.8746 (mmp) cc_final: 0.8515 (ptm) REVERT: B 661 PHE cc_start: 0.8840 (m-80) cc_final: 0.8370 (m-10) REVERT: B 700 PHE cc_start: 0.6116 (m-10) cc_final: 0.5483 (m-80) REVERT: B 740 LEU cc_start: 0.9114 (tt) cc_final: 0.8638 (pt) REVERT: B 797 PHE cc_start: 0.9076 (t80) cc_final: 0.8572 (t80) outliers start: 20 outliers final: 13 residues processed: 113 average time/residue: 0.0761 time to fit residues: 13.8872 Evaluate side-chains 101 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 508 GLU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 712 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 0.3980 chunk 17 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 55 optimal weight: 0.0170 chunk 6 optimal weight: 0.0970 chunk 63 optimal weight: 10.0000 chunk 111 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 overall best weight: 0.8218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 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 = 0.4228 r_free = 0.4228 target = 0.119927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.088965 restraints weight = 39976.932| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 3.44 r_work: 0.3520 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.5458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12284 Z= 0.138 Angle : 0.715 17.671 16706 Z= 0.349 Chirality : 0.047 0.291 1908 Planarity : 0.004 0.051 2112 Dihedral : 8.487 141.442 1714 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.63 % Favored : 92.24 % Rotamer: Outliers : 1.40 % Allowed : 19.84 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.22), residues: 1520 helix: 0.86 (0.20), residues: 660 sheet: -0.94 (0.44), residues: 138 loop : -1.43 (0.25), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 672 TYR 0.020 0.001 TYR B 834 PHE 0.016 0.001 PHE A 281 TRP 0.012 0.001 TRP A 713 HIS 0.002 0.000 HIS A 580 Details of bonding type rmsd covalent geometry : bond 0.00314 (12270) covalent geometry : angle 0.71530 (16678) SS BOND : bond 0.00266 ( 14) SS BOND : angle 0.64989 ( 28) hydrogen bonds : bond 0.04410 ( 524) hydrogen bonds : angle 4.68734 ( 1518) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 TYR cc_start: 0.8102 (m-80) cc_final: 0.7635 (m-10) REVERT: A 564 MET cc_start: 0.9332 (tpt) cc_final: 0.9020 (tmm) REVERT: A 577 LEU cc_start: 0.8550 (mm) cc_final: 0.7698 (pt) REVERT: A 740 LEU cc_start: 0.9326 (tt) cc_final: 0.8971 (pt) REVERT: A 797 PHE cc_start: 0.8642 (t80) cc_final: 0.8126 (t80) REVERT: A 835 MET cc_start: 0.8225 (ppp) cc_final: 0.7961 (ppp) REVERT: B 270 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7705 (tt) REVERT: B 414 TYR cc_start: 0.8094 (m-80) cc_final: 0.7640 (m-10) REVERT: B 427 TYR cc_start: 0.8232 (t80) cc_final: 0.7840 (t80) REVERT: B 508 GLU cc_start: 0.5428 (OUTLIER) cc_final: 0.5200 (pm20) REVERT: B 564 MET cc_start: 0.9361 (tpt) cc_final: 0.8970 (tmm) REVERT: B 577 LEU cc_start: 0.8878 (mm) cc_final: 0.8001 (pt) REVERT: B 659 MET cc_start: 0.8843 (mmp) cc_final: 0.8602 (ptm) REVERT: B 661 PHE cc_start: 0.8691 (m-80) cc_final: 0.8274 (m-10) REVERT: B 740 LEU cc_start: 0.9248 (tt) cc_final: 0.8863 (pt) REVERT: B 797 PHE cc_start: 0.9080 (t80) cc_final: 0.8587 (t80) outliers start: 18 outliers final: 13 residues processed: 107 average time/residue: 0.0713 time to fit residues: 12.5185 Evaluate side-chains 101 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 508 GLU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 712 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 105 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 39 optimal weight: 0.0670 chunk 86 optimal weight: 4.9990 chunk 140 optimal weight: 9.9990 chunk 151 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 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 = 0.4234 r_free = 0.4234 target = 0.119696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.088977 restraints weight = 40718.542| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 3.46 r_work: 0.3555 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.5607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12284 Z= 0.134 Angle : 0.717 16.794 16706 Z= 0.349 Chirality : 0.047 0.330 1908 Planarity : 0.004 0.049 2112 Dihedral : 8.420 141.750 1714 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.30 % Favored : 92.57 % Rotamer: Outliers : 1.32 % Allowed : 20.16 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.22), residues: 1520 helix: 0.80 (0.20), residues: 664 sheet: -0.98 (0.42), residues: 150 loop : -1.40 (0.25), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 288 TYR 0.019 0.001 TYR B 834 PHE 0.016 0.001 PHE B 281 TRP 0.013 0.001 TRP A 504 HIS 0.002 0.000 HIS A 580 Details of bonding type rmsd covalent geometry : bond 0.00304 (12270) covalent geometry : angle 0.71663 (16678) SS BOND : bond 0.00278 ( 14) SS BOND : angle 0.66666 ( 28) hydrogen bonds : bond 0.04291 ( 524) hydrogen bonds : angle 4.69496 ( 1518) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 TYR cc_start: 0.8093 (m-80) cc_final: 0.7644 (m-10) REVERT: A 564 MET cc_start: 0.9293 (tpt) cc_final: 0.8967 (tmm) REVERT: A 577 LEU cc_start: 0.8409 (mm) cc_final: 0.7600 (pt) REVERT: A 740 LEU cc_start: 0.9251 (tt) cc_final: 0.8889 (pt) REVERT: A 797 PHE cc_start: 0.8669 (t80) cc_final: 0.8098 (t80) REVERT: B 270 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7684 (tt) REVERT: B 389 ARG cc_start: 0.6430 (OUTLIER) cc_final: 0.4575 (mtm-85) REVERT: B 414 TYR cc_start: 0.8075 (m-80) cc_final: 0.7208 (m-10) REVERT: B 427 TYR cc_start: 0.8216 (t80) cc_final: 0.7820 (t80) REVERT: B 430 LEU cc_start: 0.8102 (mt) cc_final: 0.7864 (pt) REVERT: B 564 MET cc_start: 0.9354 (tpt) cc_final: 0.8956 (tmm) REVERT: B 577 LEU cc_start: 0.8763 (mm) cc_final: 0.7831 (pt) REVERT: B 661 PHE cc_start: 0.8472 (m-80) cc_final: 0.8066 (m-10) REVERT: B 740 LEU cc_start: 0.9170 (tt) cc_final: 0.8784 (pt) REVERT: B 797 PHE cc_start: 0.9089 (t80) cc_final: 0.8593 (t80) outliers start: 17 outliers final: 11 residues processed: 111 average time/residue: 0.0906 time to fit residues: 15.4366 Evaluate side-chains 105 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 712 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 118 optimal weight: 0.4980 chunk 138 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 59 optimal weight: 0.3980 chunk 29 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 0.0470 chunk 50 optimal weight: 0.6980 chunk 147 optimal weight: 30.0000 chunk 68 optimal weight: 0.9990 overall best weight: 0.5280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 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 = 0.4241 r_free = 0.4241 target = 0.120003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.089511 restraints weight = 40507.466| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 3.45 r_work: 0.3564 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.5745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12284 Z= 0.129 Angle : 0.724 17.077 16706 Z= 0.352 Chirality : 0.047 0.327 1908 Planarity : 0.004 0.049 2112 Dihedral : 8.345 142.003 1714 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.24 % Favored : 92.63 % Rotamer: Outliers : 1.01 % Allowed : 20.47 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.22), residues: 1520 helix: 0.79 (0.20), residues: 676 sheet: -0.84 (0.43), residues: 150 loop : -1.44 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 540 TYR 0.019 0.001 TYR B 834 PHE 0.031 0.001 PHE B 281 TRP 0.012 0.001 TRP A 713 HIS 0.002 0.000 HIS A 580 Details of bonding type rmsd covalent geometry : bond 0.00292 (12270) covalent geometry : angle 0.72392 (16678) SS BOND : bond 0.00308 ( 14) SS BOND : angle 0.63565 ( 28) hydrogen bonds : bond 0.04162 ( 524) hydrogen bonds : angle 4.65251 ( 1518) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2969.92 seconds wall clock time: 51 minutes 30.93 seconds (3090.93 seconds total)