Starting phenix.real_space_refine on Tue Jun 10 06:01:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jpo_36485/06_2025/8jpo_36485.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jpo_36485/06_2025/8jpo_36485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jpo_36485/06_2025/8jpo_36485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jpo_36485/06_2025/8jpo_36485.map" model { file = "/net/cci-nas-00/data/ceres_data/8jpo_36485/06_2025/8jpo_36485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jpo_36485/06_2025/8jpo_36485.cif" } resolution = 3.4 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= 0.004 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 70 5.16 5 Cl 4 4.86 5 C 7430 2.51 5 N 1922 2.21 5 O 2042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 11476 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 733, 5704 Classifications: {'peptide': 733} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 31, 'TRANS': 701} Chain breaks: 4 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 5704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 733, 5704 Classifications: {'peptide': 733} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 31, 'TRANS': 701} Chain breaks: 4 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CL': 2, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CL': 2, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 6.92, per 1000 atoms: 0.60 Number of scatterers: 11476 At special positions: 0 Unit cell: (92.9514, 96.301, 113.886, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 4 17.00 S 70 16.00 P 6 15.00 Mg 2 11.99 O 2042 8.00 N 1922 7.00 C 7430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 125 " distance=2.02 Simple disulfide: pdb=" SG CYS A 319 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A 399 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 125 " distance=2.02 Simple disulfide: pdb=" SG CYS B 319 " - pdb=" SG CYS B 326 " distance=2.03 Simple disulfide: pdb=" SG CYS B 399 " - pdb=" SG CYS B 430 " 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: 2.81 Conformation dependent library (CDL) restraints added in 1.4 seconds 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2696 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 8 sheets defined 65.4% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 58 through 68 Processing helix chain 'A' and resid 69 through 123 removed outlier: 3.554A pdb=" N LEU A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 151 removed outlier: 3.605A pdb=" N VAL A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 155 Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 161 through 166 removed outlier: 3.825A pdb=" N TYR A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 191 removed outlier: 3.618A pdb=" N GLY A 186 " --> pdb=" O CYS A 182 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 201 through 214 removed outlier: 4.341A pdb=" N HIS A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 233 removed outlier: 3.549A pdb=" N PHE A 232 " --> pdb=" O PHE A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 255 removed outlier: 4.087A pdb=" N ASP A 240 " --> pdb=" O ARG A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 266 Processing helix chain 'A' and resid 276 through 299 removed outlier: 3.681A pdb=" N PHE A 282 " --> pdb=" O TRP A 278 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN A 292 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 293 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY A 297 " --> pdb=" O PHE A 293 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN A 299 " --> pdb=" O ARG A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 366 removed outlier: 4.217A pdb=" N PHE A 336 " --> pdb=" O MET A 332 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 395 Processing helix chain 'A' and resid 437 through 443 Processing helix chain 'A' and resid 445 through 456 Processing helix chain 'A' and resid 461 through 480 Processing helix chain 'A' and resid 488 through 511 removed outlier: 3.760A pdb=" N CYS A 495 " --> pdb=" O PRO A 491 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 496 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 534 removed outlier: 3.816A pdb=" N ALA A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 550 through 552 No H-bonds generated for 'chain 'A' and resid 550 through 552' Processing helix chain 'A' and resid 553 through 569 removed outlier: 3.852A pdb=" N VAL A 563 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A 564 " --> pdb=" O THR A 560 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TRP A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 582 Processing helix chain 'A' and resid 593 through 598 Processing helix chain 'A' and resid 600 through 605 removed outlier: 3.793A pdb=" N ILE A 604 " --> pdb=" O ARG A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 628 Processing helix chain 'A' and resid 650 through 664 removed outlier: 3.605A pdb=" N ILE A 664 " --> pdb=" O LYS A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 677 Processing helix chain 'A' and resid 732 through 736 Processing helix chain 'A' and resid 747 through 756 Processing helix chain 'A' and resid 773 through 779 Processing helix chain 'A' and resid 819 through 830 Processing helix chain 'A' and resid 849 through 853 Processing helix chain 'A' and resid 854 through 869 Processing helix chain 'B' and resid 58 through 68 Processing helix chain 'B' and resid 69 through 123 removed outlier: 3.648A pdb=" N VAL B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER B 116 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 151 removed outlier: 3.600A pdb=" N VAL B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 155 Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' Processing helix chain 'B' and resid 161 through 166 removed outlier: 3.832A pdb=" N TYR B 165 " --> pdb=" O GLU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 191 removed outlier: 3.623A pdb=" N GLY B 186 " --> pdb=" O CYS B 182 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 199 through 214 removed outlier: 3.558A pdb=" N MET B 203 " --> pdb=" O LYS B 199 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE B 204 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N HIS B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 233 removed outlier: 3.527A pdb=" N PHE B 232 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 255 removed outlier: 4.067A pdb=" N ASP B 240 " --> pdb=" O ARG B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 266 Processing helix chain 'B' and resid 276 through 299 removed outlier: 3.668A pdb=" N PHE B 282 " --> pdb=" O TRP B 278 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN B 292 " --> pdb=" O THR B 288 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B 293 " --> pdb=" O PHE B 289 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 297 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN B 299 " --> pdb=" O ARG B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 366 removed outlier: 4.152A pdb=" N PHE B 336 " --> pdb=" O MET B 332 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG B 364 " --> pdb=" O LYS B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 395 removed outlier: 3.636A pdb=" N VAL B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 443 Processing helix chain 'B' and resid 445 through 456 removed outlier: 3.650A pdb=" N GLN B 456 " --> pdb=" O GLN B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 480 Processing helix chain 'B' and resid 488 through 511 removed outlier: 3.751A pdb=" N CYS B 495 " --> pdb=" O PRO B 491 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY B 496 " --> pdb=" O SER B 492 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 534 removed outlier: 3.904A pdb=" N ALA B 522 " --> pdb=" O SER B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 549 Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 553 through 569 removed outlier: 3.811A pdb=" N VAL B 563 " --> pdb=" O VAL B 559 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 564 " --> pdb=" O THR B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 582 Processing helix chain 'B' and resid 593 through 598 Processing helix chain 'B' and resid 600 through 605 removed outlier: 3.800A pdb=" N ILE B 604 " --> pdb=" O ARG B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 628 Processing helix chain 'B' and resid 650 through 664 removed outlier: 3.658A pdb=" N ILE B 664 " --> pdb=" O LYS B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 677 Processing helix chain 'B' and resid 732 through 736 Processing helix chain 'B' and resid 747 through 756 Processing helix chain 'B' and resid 773 through 779 Processing helix chain 'B' and resid 819 through 830 Processing helix chain 'B' and resid 854 through 869 Processing sheet with id=AA1, first strand: chain 'A' and resid 399 through 401 Processing sheet with id=AA2, first strand: chain 'A' and resid 616 through 617 Processing sheet with id=AA3, first strand: chain 'A' and resid 632 through 638 removed outlier: 6.546A pdb=" N THR A 637 " --> pdb=" O PHE A 741 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N PHE A 741 " --> pdb=" O THR A 637 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 835 through 838 removed outlier: 6.808A pdb=" N LEU A 835 " --> pdb=" O ILE A 847 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ILE A 847 " --> pdb=" O LEU A 835 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL A 837 " --> pdb=" O VAL A 845 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 399 through 401 Processing sheet with id=AA6, first strand: chain 'B' and resid 616 through 617 Processing sheet with id=AA7, first strand: chain 'B' and resid 632 through 638 removed outlier: 6.546A pdb=" N THR B 637 " --> pdb=" O PHE B 741 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE B 741 " --> pdb=" O THR B 637 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 835 through 838 removed outlier: 6.782A pdb=" N LEU B 835 " --> pdb=" O ILE B 847 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE B 847 " --> pdb=" O LEU B 835 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL B 837 " --> pdb=" O VAL B 845 " (cutoff:3.500A) 655 hydrogen bonds defined for protein. 1941 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: 3.36 Time building geometry restraints manager: 3.27 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: 3614 1.34 - 1.47: 2886 1.47 - 1.59: 5122 1.59 - 1.71: 2 1.71 - 1.83: 110 Bond restraints: 11734 Sorted by residual: bond pdb=" C HIS B 367 " pdb=" N PRO B 368 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.54e+00 bond pdb=" C HIS A 367 " pdb=" N PRO A 368 " ideal model delta sigma weight residual 1.334 1.370 -0.036 2.34e-02 1.83e+03 2.42e+00 bond pdb=" CA GLY B 397 " pdb=" C GLY B 397 " ideal model delta sigma weight residual 1.520 1.512 0.008 7.30e-03 1.88e+04 1.29e+00 bond pdb=" C VAL A 175 " pdb=" O VAL A 175 " ideal model delta sigma weight residual 1.236 1.223 0.013 1.19e-02 7.06e+03 1.16e+00 bond pdb=" CA GLY A 397 " pdb=" C GLY A 397 " ideal model delta sigma weight residual 1.520 1.512 0.008 7.30e-03 1.88e+04 1.13e+00 ... (remaining 11729 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 15186 1.28 - 2.56: 586 2.56 - 3.84: 117 3.84 - 5.12: 30 5.12 - 6.40: 9 Bond angle restraints: 15928 Sorted by residual: angle pdb=" N VAL A 162 " pdb=" CA VAL A 162 " pdb=" C VAL A 162 " ideal model delta sigma weight residual 112.96 107.99 4.97 1.00e+00 1.00e+00 2.47e+01 angle pdb=" N VAL B 162 " pdb=" CA VAL B 162 " pdb=" C VAL B 162 " ideal model delta sigma weight residual 112.96 108.09 4.87 1.00e+00 1.00e+00 2.37e+01 angle pdb=" C GLY A 158 " pdb=" N ILE A 159 " pdb=" CA ILE A 159 " ideal model delta sigma weight residual 120.24 122.96 -2.72 6.30e-01 2.52e+00 1.86e+01 angle pdb=" C GLY B 158 " pdb=" N ILE B 159 " pdb=" CA ILE B 159 " ideal model delta sigma weight residual 120.24 122.94 -2.70 6.30e-01 2.52e+00 1.83e+01 angle pdb=" C ILE A 159 " pdb=" CA ILE A 159 " pdb=" CB ILE A 159 " ideal model delta sigma weight residual 114.35 110.96 3.39 1.06e+00 8.90e-01 1.02e+01 ... (remaining 15923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.64: 6212 14.64 - 29.27: 527 29.27 - 43.91: 140 43.91 - 58.55: 46 58.55 - 73.19: 21 Dihedral angle restraints: 6946 sinusoidal: 2748 harmonic: 4198 Sorted by residual: dihedral pdb=" CB CYS A 120 " pdb=" SG CYS A 120 " pdb=" SG CYS A 125 " pdb=" CB CYS A 125 " ideal model delta sinusoidal sigma weight residual -86.00 -148.19 62.19 1 1.00e+01 1.00e-02 5.12e+01 dihedral pdb=" CB CYS B 120 " pdb=" SG CYS B 120 " pdb=" SG CYS B 125 " pdb=" CB CYS B 125 " ideal model delta sinusoidal sigma weight residual -86.00 -147.05 61.05 1 1.00e+01 1.00e-02 4.95e+01 dihedral pdb=" CA VAL A 171 " pdb=" C VAL A 171 " pdb=" N PRO A 172 " pdb=" CA PRO A 172 " ideal model delta harmonic sigma weight residual 180.00 -158.64 -21.36 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 6943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1173 0.032 - 0.064: 466 0.064 - 0.096: 132 0.096 - 0.128: 64 0.128 - 0.160: 7 Chirality restraints: 1842 Sorted by residual: chirality pdb=" CA VAL A 171 " pdb=" N VAL A 171 " pdb=" C VAL A 171 " pdb=" CB VAL A 171 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.44e-01 chirality pdb=" CA VAL B 171 " pdb=" N VAL B 171 " pdb=" C VAL B 171 " pdb=" CB VAL B 171 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.19e-01 chirality pdb=" CB VAL B 242 " pdb=" CA VAL B 242 " pdb=" CG1 VAL B 242 " pdb=" CG2 VAL B 242 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.86e-01 ... (remaining 1839 not shown) Planarity restraints: 1990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 769 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A 770 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 770 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 770 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 769 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO B 770 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 770 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 770 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 484 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO B 485 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 485 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 485 " 0.022 5.00e-02 4.00e+02 ... (remaining 1987 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2824 2.79 - 3.32: 11215 3.32 - 3.85: 18893 3.85 - 4.37: 22316 4.37 - 4.90: 39182 Nonbonded interactions: 94430 Sorted by model distance: nonbonded pdb=" O THR B 440 " pdb=" ND2 ASN B 444 " model vdw 2.267 3.120 nonbonded pdb=" O ASP A 603 " pdb=" NH1 ARG A 861 " model vdw 2.272 3.120 nonbonded pdb=" O ASP B 603 " pdb=" NH1 ARG B 861 " model vdw 2.284 3.120 nonbonded pdb=" O THR A 440 " pdb=" ND2 ASN A 444 " model vdw 2.302 3.120 nonbonded pdb=" O PRO B 431 " pdb=" OG1 THR B 434 " model vdw 2.308 3.040 ... (remaining 94425 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: 0.05 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 46 through 869 or resid 902 or resid 904)) selection = (chain 'B' and (resid 46 through 869 or resid 902 or resid 904)) } 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: 0.910 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: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 27.630 Find NCS groups from input model: 0.560 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 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 0.037 11740 Z= 0.166 Angle : 0.630 6.396 15940 Z= 0.373 Chirality : 0.041 0.160 1842 Planarity : 0.005 0.040 1990 Dihedral : 12.938 73.186 4232 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.44 (0.23), residues: 1446 helix: 1.12 (0.18), residues: 896 sheet: -2.55 (0.85), residues: 24 loop : -0.96 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 478 HIS 0.002 0.001 HIS A 851 PHE 0.014 0.001 PHE A 390 TYR 0.013 0.001 TYR A 781 ARG 0.005 0.000 ARG A 626 Details of bonding type rmsd hydrogen bonds : bond 0.17280 ( 655) hydrogen bonds : angle 6.01244 ( 1941) SS BOND : bond 0.00401 ( 6) SS BOND : angle 1.97106 ( 12) covalent geometry : bond 0.00375 (11734) covalent geometry : angle 0.62787 (15928) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.162 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.2342 time to fit residues: 39.8225 Evaluate side-chains 92 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 132 optimal weight: 0.0050 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 GLN B 764 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.114782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.089506 restraints weight = 13626.138| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.42 r_work: 0.2881 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.0865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11740 Z= 0.138 Angle : 0.553 8.196 15940 Z= 0.283 Chirality : 0.040 0.158 1842 Planarity : 0.005 0.038 1990 Dihedral : 7.754 59.708 1642 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.40 % Allowed : 5.92 % Favored : 93.68 % 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: 1.08 (0.23), residues: 1446 helix: 1.67 (0.18), residues: 902 sheet: -2.94 (0.80), residues: 24 loop : -0.80 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 278 HIS 0.003 0.001 HIS B 615 PHE 0.011 0.001 PHE A 351 TYR 0.026 0.001 TYR A 510 ARG 0.003 0.000 ARG A 861 Details of bonding type rmsd hydrogen bonds : bond 0.04572 ( 655) hydrogen bonds : angle 3.87028 ( 1941) SS BOND : bond 0.00163 ( 6) SS BOND : angle 1.01353 ( 12) covalent geometry : bond 0.00327 (11734) covalent geometry : angle 0.55294 (15928) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 2.619 Fit side-chains REVERT: B 75 ARG cc_start: 0.7394 (ttm170) cc_final: 0.6894 (ttt90) outliers start: 5 outliers final: 1 residues processed: 108 average time/residue: 0.2193 time to fit residues: 37.4616 Evaluate side-chains 90 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 84 optimal weight: 0.0020 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 20.0000 chunk 125 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 overall best weight: 2.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN B 515 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.109146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.083629 restraints weight = 14072.335| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.45 r_work: 0.2797 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 11740 Z= 0.231 Angle : 0.612 7.344 15940 Z= 0.314 Chirality : 0.044 0.158 1842 Planarity : 0.005 0.043 1990 Dihedral : 7.231 54.276 1642 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.88 % Allowed : 7.76 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.96 (0.23), residues: 1446 helix: 1.55 (0.18), residues: 912 sheet: -2.79 (0.83), residues: 24 loop : -0.84 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 303 HIS 0.004 0.001 HIS B 615 PHE 0.017 0.002 PHE B 351 TYR 0.019 0.002 TYR A 781 ARG 0.003 0.000 ARG B 103 Details of bonding type rmsd hydrogen bonds : bond 0.05135 ( 655) hydrogen bonds : angle 3.89556 ( 1941) SS BOND : bond 0.00201 ( 6) SS BOND : angle 1.04026 ( 12) covalent geometry : bond 0.00585 (11734) covalent geometry : angle 0.61109 (15928) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 1.268 Fit side-chains REVERT: A 120 CYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7541 (t) REVERT: B 120 CYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7559 (t) REVERT: B 332 MET cc_start: 0.8292 (mmt) cc_final: 0.7982 (ptm) outliers start: 11 outliers final: 8 residues processed: 103 average time/residue: 0.2621 time to fit residues: 42.0551 Evaluate side-chains 98 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 732 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 19 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 82 optimal weight: 2.9990 chunk 40 optimal weight: 0.1980 chunk 67 optimal weight: 0.0870 chunk 131 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 overall best weight: 2.0564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.111123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.085598 restraints weight = 13762.098| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.44 r_work: 0.2825 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11740 Z= 0.167 Angle : 0.541 6.632 15940 Z= 0.278 Chirality : 0.040 0.158 1842 Planarity : 0.005 0.041 1990 Dihedral : 6.960 55.235 1642 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.60 % Allowed : 7.92 % Favored : 90.48 % 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: 1.07 (0.23), residues: 1446 helix: 1.72 (0.18), residues: 906 sheet: -2.92 (0.84), residues: 24 loop : -0.93 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 278 HIS 0.003 0.001 HIS A 615 PHE 0.014 0.001 PHE B 101 TYR 0.017 0.001 TYR A 781 ARG 0.002 0.000 ARG B 103 Details of bonding type rmsd hydrogen bonds : bond 0.04439 ( 655) hydrogen bonds : angle 3.75917 ( 1941) SS BOND : bond 0.00144 ( 6) SS BOND : angle 0.97568 ( 12) covalent geometry : bond 0.00415 (11734) covalent geometry : angle 0.54074 (15928) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 1.283 Fit side-chains revert: symmetry clash REVERT: A 120 CYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7498 (t) REVERT: A 266 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8206 (pm20) REVERT: B 75 ARG cc_start: 0.7454 (ttm170) cc_final: 0.6970 (ttt90) REVERT: B 120 CYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7537 (t) REVERT: B 266 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8185 (pm20) REVERT: B 332 MET cc_start: 0.8303 (mmt) cc_final: 0.7994 (ptm) outliers start: 20 outliers final: 7 residues processed: 112 average time/residue: 0.2333 time to fit residues: 40.1148 Evaluate side-chains 103 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 732 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 62 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 141 optimal weight: 0.7980 chunk 134 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 HIS ** 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 = 0.3108 r_free = 0.3108 target = 0.110949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.085366 restraints weight = 13731.605| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.44 r_work: 0.2864 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11740 Z= 0.168 Angle : 0.550 8.184 15940 Z= 0.280 Chirality : 0.041 0.158 1842 Planarity : 0.005 0.040 1990 Dihedral : 6.793 56.458 1642 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.44 % Allowed : 9.28 % Favored : 89.28 % 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: 1.17 (0.23), residues: 1446 helix: 1.79 (0.18), residues: 904 sheet: None (None), residues: 0 loop : -0.98 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 278 HIS 0.003 0.001 HIS B 615 PHE 0.015 0.001 PHE A 101 TYR 0.017 0.001 TYR A 781 ARG 0.002 0.000 ARG B 103 Details of bonding type rmsd hydrogen bonds : bond 0.04426 ( 655) hydrogen bonds : angle 3.74053 ( 1941) SS BOND : bond 0.00155 ( 6) SS BOND : angle 1.01472 ( 12) covalent geometry : bond 0.00418 (11734) covalent geometry : angle 0.54998 (15928) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 2.250 Fit side-chains revert: symmetry clash REVERT: A 120 CYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7312 (t) REVERT: A 266 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8248 (pm20) REVERT: A 786 ASP cc_start: 0.8233 (t0) cc_final: 0.7922 (t0) REVERT: B 75 ARG cc_start: 0.7482 (ttm170) cc_final: 0.6966 (ttt90) REVERT: B 120 CYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7451 (t) REVERT: B 266 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8230 (pm20) REVERT: B 332 MET cc_start: 0.8401 (mmt) cc_final: 0.8033 (ptm) REVERT: B 786 ASP cc_start: 0.8193 (t0) cc_final: 0.7880 (t0) outliers start: 18 outliers final: 10 residues processed: 108 average time/residue: 0.2290 time to fit residues: 39.3372 Evaluate side-chains 106 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 761 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 130 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 0.3980 chunk 2 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.111393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.085712 restraints weight = 13878.461| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.45 r_work: 0.2853 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11740 Z= 0.153 Angle : 0.529 7.956 15940 Z= 0.270 Chirality : 0.040 0.158 1842 Planarity : 0.005 0.039 1990 Dihedral : 6.719 59.293 1642 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.36 % Allowed : 9.92 % Favored : 88.72 % 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: 1.23 (0.23), residues: 1446 helix: 1.86 (0.18), residues: 904 sheet: None (None), residues: 0 loop : -1.00 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 278 HIS 0.003 0.001 HIS B 615 PHE 0.014 0.001 PHE B 101 TYR 0.016 0.001 TYR A 781 ARG 0.002 0.000 ARG B 103 Details of bonding type rmsd hydrogen bonds : bond 0.04253 ( 655) hydrogen bonds : angle 3.71371 ( 1941) SS BOND : bond 0.00126 ( 6) SS BOND : angle 0.98819 ( 12) covalent geometry : bond 0.00377 (11734) covalent geometry : angle 0.52900 (15928) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 1.435 Fit side-chains revert: symmetry clash REVERT: A 120 CYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7409 (t) REVERT: A 266 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8190 (pm20) REVERT: A 786 ASP cc_start: 0.8244 (t0) cc_final: 0.7954 (t0) REVERT: B 75 ARG cc_start: 0.7424 (ttm170) cc_final: 0.6919 (ttt90) REVERT: B 120 CYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7579 (t) REVERT: B 266 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8160 (pm20) REVERT: B 332 MET cc_start: 0.8324 (mmt) cc_final: 0.8038 (ptm) REVERT: B 786 ASP cc_start: 0.8170 (t0) cc_final: 0.7913 (t0) outliers start: 17 outliers final: 9 residues processed: 110 average time/residue: 0.2012 time to fit residues: 34.7212 Evaluate side-chains 107 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 761 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 104 optimal weight: 0.5980 chunk 33 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 HIS ** 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 = 0.3162 r_free = 0.3162 target = 0.114847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.089430 restraints weight = 13726.376| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.43 r_work: 0.2887 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11740 Z= 0.100 Angle : 0.478 7.732 15940 Z= 0.243 Chirality : 0.037 0.157 1842 Planarity : 0.004 0.036 1990 Dihedral : 6.366 64.721 1642 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.52 % Allowed : 10.56 % Favored : 87.92 % 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: 1.45 (0.23), residues: 1446 helix: 2.11 (0.18), residues: 904 sheet: None (None), residues: 0 loop : -1.08 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 278 HIS 0.002 0.000 HIS B 515 PHE 0.012 0.001 PHE A 101 TYR 0.013 0.001 TYR A 781 ARG 0.002 0.000 ARG B 861 Details of bonding type rmsd hydrogen bonds : bond 0.03540 ( 655) hydrogen bonds : angle 3.57953 ( 1941) SS BOND : bond 0.00073 ( 6) SS BOND : angle 0.84682 ( 12) covalent geometry : bond 0.00221 (11734) covalent geometry : angle 0.47748 (15928) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 1.185 Fit side-chains revert: symmetry clash REVERT: A 120 CYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7551 (t) REVERT: A 360 LYS cc_start: 0.8933 (mttt) cc_final: 0.8646 (mtmm) REVERT: A 786 ASP cc_start: 0.8248 (t0) cc_final: 0.8036 (t0) REVERT: B 120 CYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7458 (t) REVERT: B 332 MET cc_start: 0.8279 (mmt) cc_final: 0.8010 (ptm) REVERT: B 786 ASP cc_start: 0.8180 (t0) cc_final: 0.7911 (t0) outliers start: 19 outliers final: 6 residues processed: 117 average time/residue: 0.1784 time to fit residues: 33.3893 Evaluate side-chains 106 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 761 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 91 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 HIS B 630 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.111664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.086091 restraints weight = 13851.584| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.44 r_work: 0.2830 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11740 Z= 0.157 Angle : 0.539 9.297 15940 Z= 0.271 Chirality : 0.040 0.178 1842 Planarity : 0.004 0.037 1990 Dihedral : 6.603 61.513 1642 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.20 % Allowed : 10.80 % Favored : 88.00 % 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: 1.33 (0.23), residues: 1446 helix: 2.01 (0.18), residues: 904 sheet: None (None), residues: 0 loop : -1.11 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 303 HIS 0.003 0.001 HIS B 615 PHE 0.013 0.001 PHE A 351 TYR 0.015 0.001 TYR A 781 ARG 0.002 0.000 ARG B 103 Details of bonding type rmsd hydrogen bonds : bond 0.04162 ( 655) hydrogen bonds : angle 3.64722 ( 1941) SS BOND : bond 0.00106 ( 6) SS BOND : angle 0.96711 ( 12) covalent geometry : bond 0.00388 (11734) covalent geometry : angle 0.53892 (15928) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 1.298 Fit side-chains REVERT: A 120 CYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7540 (t) REVERT: A 786 ASP cc_start: 0.8301 (t0) cc_final: 0.8071 (t0) REVERT: B 75 ARG cc_start: 0.7432 (ttm170) cc_final: 0.6879 (ttt90) REVERT: B 120 CYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7514 (t) REVERT: B 332 MET cc_start: 0.8368 (mmt) cc_final: 0.8028 (ptm) REVERT: B 786 ASP cc_start: 0.8221 (t0) cc_final: 0.7960 (t0) REVERT: B 850 ARG cc_start: 0.9283 (OUTLIER) cc_final: 0.8450 (ttm110) outliers start: 15 outliers final: 5 residues processed: 108 average time/residue: 0.1987 time to fit residues: 33.5253 Evaluate side-chains 101 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 850 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 5 optimal weight: 0.8980 chunk 137 optimal weight: 10.0000 chunk 47 optimal weight: 0.1980 chunk 68 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 HIS B 579 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.115575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.090144 restraints weight = 13661.232| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.43 r_work: 0.2891 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11740 Z= 0.101 Angle : 0.496 8.935 15940 Z= 0.247 Chirality : 0.038 0.165 1842 Planarity : 0.004 0.036 1990 Dihedral : 6.280 66.244 1642 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.80 % Allowed : 11.12 % Favored : 88.08 % 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: 1.52 (0.23), residues: 1446 helix: 2.18 (0.18), residues: 904 sheet: None (None), residues: 0 loop : -1.10 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 278 HIS 0.003 0.000 HIS B 515 PHE 0.011 0.001 PHE A 101 TYR 0.011 0.001 TYR A 781 ARG 0.002 0.000 ARG B 295 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 655) hydrogen bonds : angle 3.51030 ( 1941) SS BOND : bond 0.00058 ( 6) SS BOND : angle 0.82798 ( 12) covalent geometry : bond 0.00223 (11734) covalent geometry : angle 0.49599 (15928) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 1.220 Fit side-chains REVERT: A 120 CYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7552 (t) REVERT: A 360 LYS cc_start: 0.8936 (mttt) cc_final: 0.8647 (mtmm) REVERT: B 120 CYS cc_start: 0.7732 (OUTLIER) cc_final: 0.7502 (t) REVERT: B 332 MET cc_start: 0.8286 (mmt) cc_final: 0.8002 (ptm) outliers start: 10 outliers final: 6 residues processed: 107 average time/residue: 0.1834 time to fit residues: 31.5609 Evaluate side-chains 103 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 761 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.7203 > 50: distance: 53 - 55: 33.957 distance: 56 - 57: 56.108 distance: 56 - 59: 39.310 distance: 57 - 63: 38.952 distance: 64 - 65: 40.988 distance: 64 - 67: 18.161 distance: 65 - 66: 39.049 distance: 65 - 74: 40.139 distance: 67 - 68: 17.578 distance: 68 - 69: 56.496 distance: 68 - 70: 56.428 distance: 69 - 71: 40.673 distance: 70 - 72: 7.843 distance: 72 - 73: 32.429 distance: 74 - 75: 57.848 distance: 75 - 76: 38.828 distance: 75 - 78: 56.551 distance: 76 - 77: 66.282 distance: 76 - 81: 41.043 distance: 78 - 80: 56.451 distance: 81 - 82: 13.551 distance: 82 - 83: 42.077 distance: 82 - 85: 47.609 distance: 83 - 84: 39.051 distance: 83 - 86: 58.531 distance: 86 - 87: 43.197 distance: 87 - 88: 15.786 distance: 87 - 90: 69.399 distance: 88 - 89: 41.962 distance: 88 - 95: 42.233 distance: 91 - 92: 36.176 distance: 92 - 93: 39.779 distance: 95 - 96: 40.706 distance: 96 - 97: 18.940 distance: 97 - 98: 43.354 distance: 97 - 104: 45.693 distance: 100 - 101: 40.357 distance: 101 - 102: 40.230 distance: 101 - 103: 27.174 distance: 104 - 105: 56.575 distance: 105 - 106: 38.918 distance: 106 - 107: 40.826 distance: 106 - 108: 55.593 distance: 108 - 109: 39.241 distance: 108 - 114: 41.085 distance: 109 - 110: 40.089 distance: 109 - 112: 56.530 distance: 110 - 111: 55.594 distance: 110 - 115: 40.780 distance: 111 - 137: 33.318 distance: 115 - 116: 38.583 distance: 116 - 119: 40.141 distance: 117 - 118: 57.620 distance: 117 - 123: 38.708 distance: 118 - 143: 33.835 distance: 119 - 120: 40.049 distance: 120 - 121: 55.846 distance: 121 - 122: 56.775 distance: 124 - 125: 41.721 distance: 124 - 127: 40.181 distance: 125 - 126: 13.669 distance: 125 - 131: 29.694 distance: 126 - 147: 32.908 distance: 127 - 129: 40.571 distance: 128 - 130: 57.001