Starting phenix.real_space_refine on Tue Feb 3 23:44:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rps_54170/02_2026/9rps_54170.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rps_54170/02_2026/9rps_54170.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rps_54170/02_2026/9rps_54170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rps_54170/02_2026/9rps_54170.map" model { file = "/net/cci-nas-00/data/ceres_data/9rps_54170/02_2026/9rps_54170.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rps_54170/02_2026/9rps_54170.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 31 5.16 5 C 4855 2.51 5 N 1329 2.21 5 O 1490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s 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: 7705 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 738, 5987 Classifications: {'peptide': 738} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 708} Chain breaks: 3 Chain: "B" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1187 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 8, 'TRANS': 142} Chain: "D" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 392 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 83 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 3, 'TRANS': 7} Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PXS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.41, per 1000 atoms: 0.18 Number of scatterers: 7705 At special positions: 0 Unit cell: (106.56, 78.44, 103.6, 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 31 16.00 O 1490 8.00 N 1329 7.00 C 4855 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 724 " distance=2.03 Simple disulfide: pdb=" SG CYS A 173 " - pdb=" SG CYS A 725 " distance=2.03 Simple disulfide: pdb=" SG CYS D 30 " - pdb=" SG CYS D 38 " 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 261.3 milliseconds 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1770 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 5 sheets defined 12.8% alpha, 40.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 26 through 34 removed outlier: 4.447A pdb=" N GLY A 34 " --> pdb=" O GLN A 30 " (cutoff:3.500A) 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 295 through 302 removed outlier: 3.668A pdb=" N ASP A 300 " --> pdb=" O LYS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 463 through 469 removed outlier: 3.830A pdb=" N ARG A 469 " --> pdb=" O TRP A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 542 removed outlier: 3.639A pdb=" N PHE A 541 " --> pdb=" O SER A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 660 through 668 Processing helix chain 'A' and resid 669 through 674 removed outlier: 3.514A pdb=" N SER A 673 " --> pdb=" O LYS A 670 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 674 " --> pdb=" O TYR A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 774 removed outlier: 3.802A pdb=" N ARG A 774 " --> pdb=" O GLN A 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 Processing helix chain 'B' and resid 45 through 59 Processing helix chain 'B' and resid 132 through 158 removed outlier: 3.704A pdb=" N ASP B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 169 removed outlier: 3.514A pdb=" N ILE B 162 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 70 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 68 through 70 current: chain 'A' and resid 81 through 83 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 81 through 83 current: chain 'A' and resid 103 through 113 removed outlier: 6.702A pdb=" N VAL A 104 " --> pdb=" O ASN A 127 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ASN A 127 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA A 106 " --> pdb=" O TRP A 125 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N TRP A 125 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLY A 108 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LYS A 123 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL A 117 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N MET A 142 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU A 119 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYR A 140 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N GLY A 121 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N GLY A 138 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LYS A 123 " --> pdb=" O TRP A 136 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP A 132 " --> pdb=" O ASN A 127 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASN A 134 " --> pdb=" O LYS A 155 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LYS A 155 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TRP A 136 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU A 153 " --> pdb=" O TRP A 136 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 151 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA A 151 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLY A 168 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 153 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER A 185 " --> pdb=" O ASN A 167 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLY A 184 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA A 201 " --> pdb=" O GLY A 184 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU A 186 " --> pdb=" O TRP A 199 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP A 190 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 195 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 236 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 242 through 244 current: chain 'A' and resid 255 through 264 removed outlier: 3.587A pdb=" N MET A 264 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN A 269 " --> pdb=" O MET A 264 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N THR A 356 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 9.716A pdb=" N VAL A 334 " --> pdb=" O TYR A 354 " (cutoff:3.500A) removed outlier: 12.111A pdb=" N TYR A 354 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A 368 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N LYS A 375 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLU A 391 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N PHE A 377 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N SER A 389 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ALA A 390 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL A 418 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 427 " --> pdb=" O PHE A 417 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 426 through 432 current: chain 'A' and resid 445 through 461 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 477 through 491 current: chain 'A' and resid 505 through 508 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 505 through 508 current: chain 'A' and resid 555 through 567 removed outlier: 7.591A pdb=" N ASN A 556 " --> pdb=" O TYR A 584 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N TYR A 584 " --> pdb=" O ASN A 556 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL A 558 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ILE A 582 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR A 560 " --> pdb=" O GLY A 580 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY A 580 " --> pdb=" O THR A 560 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL A 562 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER A 578 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER A 564 " --> pdb=" O ASN A 576 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN A 576 " --> pdb=" O SER A 564 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE A 566 " --> pdb=" O ARG A 574 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL A 607 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N TYR A 584 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER A 605 " --> pdb=" O TYR A 584 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR A 612 " --> pdb=" O GLY A 624 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASP A 629 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N VAL A 635 " --> pdb=" O ASP A 629 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL A 700 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU A 717 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA A 702 " --> pdb=" O SER A 715 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER A 715 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TYR A 704 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 13.208A pdb=" N LYS A 711 " --> pdb=" O GLY A 738 " (cutoff:3.500A) removed outlier: 13.170A pdb=" N GLY A 738 " --> pdb=" O LYS A 711 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N ALA A 713 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 736 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY A 731 " --> pdb=" O GLY A 753 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL A 747 " --> pdb=" O ASN A 737 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N TRP A 739 " --> pdb=" O HIS A 745 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N HIS A 745 " --> pdb=" O TRP A 739 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 745 through 758 current: chain 'D' and resid 37 through 42 Processing sheet with id=AA4, first strand: chain 'B' and resid 61 through 63 removed outlier: 6.949A pdb=" N MET B 36 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N LEU B 75 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE B 37 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU B 77 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ASP B 39 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 9.292A pdb=" N LYS B 79 " --> pdb=" O ASP B 39 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ASN B 105 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL B 80 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR B 103 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE B 82 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE B 101 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS B 84 " --> pdb=" O GLN B 99 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLN B 99 " --> pdb=" O LYS B 84 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N THR B 86 " --> pdb=" O GLU B 97 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N GLU B 97 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N SER B 88 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N THR B 95 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP B 114 " --> pdb=" O ILE B 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 55 through 57 274 hydrogen bonds defined for protein. 777 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: 1.12 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1300 1.31 - 1.44: 2261 1.44 - 1.57: 4272 1.57 - 1.70: 0 1.70 - 1.83: 54 Bond restraints: 7887 Sorted by residual: bond pdb=" C16 PXS C 101 " pdb=" O17 PXS C 101 " ideal model delta sigma weight residual 1.330 1.401 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C22 PXS C 101 " pdb=" O21 PXS C 101 " ideal model delta sigma weight residual 1.331 1.395 -0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C CYS C 20A" pdb=" O CYS C 20A" ideal model delta sigma weight residual 1.231 1.181 0.050 2.00e-02 2.50e+03 6.37e+00 bond pdb=" C1 PLM A 801 " pdb=" O2 PLM A 801 " ideal model delta sigma weight residual 1.249 1.202 0.047 2.00e-02 2.50e+03 5.60e+00 bond pdb=" C19 PXS C 101 " pdb=" O21 PXS C 101 " ideal model delta sigma weight residual 1.438 1.391 0.047 2.00e-02 2.50e+03 5.53e+00 ... (remaining 7882 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 10553 1.73 - 3.47: 114 3.47 - 5.20: 23 5.20 - 6.94: 1 6.94 - 8.67: 2 Bond angle restraints: 10693 Sorted by residual: angle pdb=" C23 PXS C 101 " pdb=" C22 PXS C 101 " pdb=" O21 PXS C 101 " ideal model delta sigma weight residual 111.52 120.19 -8.67 3.00e+00 1.11e-01 8.36e+00 angle pdb=" C15 PXS C 101 " pdb=" C16 PXS C 101 " pdb=" O17 PXS C 101 " ideal model delta sigma weight residual 111.74 120.12 -8.38 3.00e+00 1.11e-01 7.80e+00 angle pdb=" C GLY A 158 " pdb=" N GLU A 159 " pdb=" CA GLU A 159 " ideal model delta sigma weight residual 121.54 126.02 -4.48 1.91e+00 2.74e-01 5.51e+00 angle pdb=" N PRO D 26 " pdb=" CA PRO D 26 " pdb=" C PRO D 26 " ideal model delta sigma weight residual 110.40 113.87 -3.47 1.61e+00 3.86e-01 4.65e+00 angle pdb=" C VAL A 208 " pdb=" N PRO A 209 " pdb=" CA PRO A 209 " ideal model delta sigma weight residual 119.84 122.40 -2.56 1.25e+00 6.40e-01 4.18e+00 ... (remaining 10688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 4334 16.69 - 33.38: 281 33.38 - 50.07: 52 50.07 - 66.76: 24 66.76 - 83.44: 5 Dihedral angle restraints: 4696 sinusoidal: 1918 harmonic: 2778 Sorted by residual: dihedral pdb=" CA ARG A 145 " pdb=" C ARG A 145 " pdb=" N GLN A 146 " pdb=" CA GLN A 146 " ideal model delta harmonic sigma weight residual -180.00 -158.66 -21.34 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA TYR A 678 " pdb=" C TYR A 678 " pdb=" N LYS A 679 " pdb=" CA LYS A 679 " ideal model delta harmonic sigma weight residual -180.00 -162.79 -17.21 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA PHE A 343 " pdb=" C PHE A 343 " pdb=" N ASP A 344 " pdb=" CA ASP A 344 " ideal model delta harmonic sigma weight residual 180.00 163.49 16.51 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 4693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 624 0.029 - 0.058: 306 0.058 - 0.087: 91 0.087 - 0.116: 80 0.116 - 0.146: 15 Chirality restraints: 1116 Sorted by residual: chirality pdb=" CA ILE A 118 " pdb=" N ILE A 118 " pdb=" C ILE A 118 " pdb=" CB ILE A 118 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CA ILE A 525 " pdb=" N ILE A 525 " pdb=" C ILE A 525 " pdb=" CB ILE A 525 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA VAL A 652 " pdb=" N VAL A 652 " pdb=" C VAL A 652 " pdb=" CB VAL A 652 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 1113 not shown) Planarity restraints: 1404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 391 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.72e+00 pdb=" N PRO A 392 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 392 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 392 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 404 " 0.026 5.00e-02 4.00e+02 3.87e-02 2.40e+00 pdb=" N PRO A 405 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 405 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 405 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 252 " -0.023 5.00e-02 4.00e+02 3.47e-02 1.92e+00 pdb=" N PRO A 253 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " -0.020 5.00e-02 4.00e+02 ... (remaining 1401 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.04: 4358 3.04 - 3.51: 6979 3.51 - 3.97: 11726 3.97 - 4.44: 14419 4.44 - 4.90: 24644 Nonbonded interactions: 62126 Sorted by model distance: nonbonded pdb=" N VAL A 52 " pdb=" N THR A 53 " model vdw 2.580 2.560 nonbonded pdb=" N THR B 27 " pdb=" OG1 THR B 27 " model vdw 2.596 2.496 nonbonded pdb=" N VAL A 403 " pdb=" N GLY A 404 " model vdw 2.608 2.560 nonbonded pdb=" O THR A 590 " pdb=" OG1 THR A 590 " model vdw 2.615 3.040 nonbonded pdb=" CA GLY A 227 " pdb=" O2 PLM A 801 " model vdw 2.618 2.752 ... (remaining 62121 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 3.730 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.590 Find NCS groups from input model: 0.020 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 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 0.071 7893 Z= 0.198 Angle : 0.529 8.673 10699 Z= 0.272 Chirality : 0.045 0.146 1116 Planarity : 0.004 0.041 1404 Dihedral : 12.302 83.444 2917 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.22 % Favored : 94.68 % Rotamer: Outliers : 1.45 % Allowed : 6.67 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.48 (0.27), residues: 939 helix: -2.36 (0.40), residues: 95 sheet: -0.47 (0.25), residues: 441 loop : -1.07 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 225 TYR 0.014 0.001 TYR A 678 PHE 0.008 0.001 PHE A 241 TRP 0.006 0.001 TRP A 136 HIS 0.004 0.001 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 7887) covalent geometry : angle 0.52864 (10693) SS BOND : bond 0.00235 ( 3) SS BOND : angle 0.65441 ( 6) hydrogen bonds : bond 0.24718 ( 274) hydrogen bonds : angle 9.80455 ( 777) Misc. bond : bond 0.04629 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.8190 (t0) cc_final: 0.7722 (m-40) REVERT: A 600 ASP cc_start: 0.7679 (t0) cc_final: 0.7452 (t0) REVERT: A 691 ARG cc_start: 0.7543 (pmt170) cc_final: 0.7299 (tpp-160) outliers start: 12 outliers final: 5 residues processed: 133 average time/residue: 0.0885 time to fit residues: 15.5502 Evaluate side-chains 104 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 27 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 146 GLN A 383 GLN A 576 ASN A 653 GLN B 131 GLN B 138 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.108869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.080515 restraints weight = 12106.201| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.27 r_work: 0.2968 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7893 Z= 0.111 Angle : 0.483 5.755 10699 Z= 0.261 Chirality : 0.044 0.164 1116 Planarity : 0.004 0.044 1404 Dihedral : 7.893 68.303 1126 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.33 % Allowed : 11.15 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.84 (0.28), residues: 939 helix: -0.11 (0.51), residues: 95 sheet: -0.21 (0.26), residues: 428 loop : -0.92 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 469 TYR 0.011 0.001 TYR A 244 PHE 0.008 0.001 PHE A 541 TRP 0.006 0.001 TRP A 608 HIS 0.002 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 7887) covalent geometry : angle 0.48257 (10693) SS BOND : bond 0.00438 ( 3) SS BOND : angle 0.85333 ( 6) hydrogen bonds : bond 0.03884 ( 274) hydrogen bonds : angle 5.94510 ( 777) Misc. bond : bond 0.00058 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 55 ASN cc_start: 0.8148 (t0) cc_final: 0.7572 (m-40) REVERT: A 299 GLU cc_start: 0.8564 (tp30) cc_final: 0.8320 (tm-30) REVERT: A 301 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7964 (pt0) REVERT: A 543 ASP cc_start: 0.8674 (p0) cc_final: 0.8437 (p0) REVERT: A 600 ASP cc_start: 0.8037 (t0) cc_final: 0.7685 (t0) REVERT: A 691 ARG cc_start: 0.7509 (pmt170) cc_final: 0.6956 (tpp-160) REVERT: D 56 ARG cc_start: 0.8843 (mtt180) cc_final: 0.8388 (mtt90) outliers start: 11 outliers final: 8 residues processed: 121 average time/residue: 0.0857 time to fit residues: 13.8278 Evaluate side-chains 106 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 167 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 71 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.105961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.077861 restraints weight = 12086.205| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.17 r_work: 0.2937 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7893 Z= 0.181 Angle : 0.499 5.088 10699 Z= 0.268 Chirality : 0.045 0.150 1116 Planarity : 0.004 0.040 1404 Dihedral : 7.662 56.969 1124 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.94 % Allowed : 11.52 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.75 (0.28), residues: 939 helix: 0.89 (0.55), residues: 94 sheet: -0.24 (0.26), residues: 412 loop : -0.98 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 469 TYR 0.014 0.001 TYR A 244 PHE 0.009 0.001 PHE A 241 TRP 0.006 0.001 TRP A 136 HIS 0.003 0.001 HIS A 745 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 7887) covalent geometry : angle 0.49853 (10693) SS BOND : bond 0.00144 ( 3) SS BOND : angle 0.84962 ( 6) hydrogen bonds : bond 0.04120 ( 274) hydrogen bonds : angle 5.52568 ( 777) Misc. bond : bond 0.00102 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 55 ASN cc_start: 0.8146 (t0) cc_final: 0.7630 (m-40) REVERT: A 82 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8222 (tt) REVERT: A 299 GLU cc_start: 0.8682 (tp30) cc_final: 0.8432 (mm-30) REVERT: A 301 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8085 (pt0) REVERT: A 600 ASP cc_start: 0.7961 (t0) cc_final: 0.7603 (t0) REVERT: A 691 ARG cc_start: 0.7653 (pmt170) cc_final: 0.7148 (tpp-160) outliers start: 16 outliers final: 11 residues processed: 109 average time/residue: 0.0928 time to fit residues: 13.2814 Evaluate side-chains 106 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain D residue 53 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 83 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.106682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.078750 restraints weight = 12200.339| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.14 r_work: 0.2949 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7893 Z= 0.134 Angle : 0.462 5.079 10699 Z= 0.249 Chirality : 0.044 0.150 1116 Planarity : 0.004 0.042 1404 Dihedral : 7.439 58.843 1124 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.94 % Allowed : 11.52 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.59 (0.28), residues: 939 helix: 1.25 (0.56), residues: 95 sheet: -0.14 (0.26), residues: 408 loop : -0.94 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 225 TYR 0.011 0.001 TYR A 244 PHE 0.007 0.001 PHE A 241 TRP 0.006 0.001 TRP A 136 HIS 0.003 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 7887) covalent geometry : angle 0.46214 (10693) SS BOND : bond 0.00112 ( 3) SS BOND : angle 0.54562 ( 6) hydrogen bonds : bond 0.03458 ( 274) hydrogen bonds : angle 5.21161 ( 777) Misc. bond : bond 0.00084 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 55 ASN cc_start: 0.8149 (t0) cc_final: 0.7621 (m-40) REVERT: A 77 GLN cc_start: 0.7062 (tp40) cc_final: 0.6845 (tp-100) REVERT: A 82 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8165 (tt) REVERT: A 202 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7386 (mtm180) REVERT: A 691 ARG cc_start: 0.7654 (pmt170) cc_final: 0.7095 (tpp-160) REVERT: D 70 TYR cc_start: 0.8890 (m-80) cc_final: 0.8652 (m-80) outliers start: 16 outliers final: 11 residues processed: 109 average time/residue: 0.0870 time to fit residues: 12.6065 Evaluate side-chains 110 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 167 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 88 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.106454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.078373 restraints weight = 12133.817| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.16 r_work: 0.2939 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7893 Z= 0.149 Angle : 0.465 5.055 10699 Z= 0.250 Chirality : 0.044 0.143 1116 Planarity : 0.004 0.041 1404 Dihedral : 7.427 57.548 1124 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.42 % Allowed : 12.12 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 (0.28), residues: 939 helix: 1.44 (0.56), residues: 94 sheet: -0.13 (0.26), residues: 410 loop : -0.94 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 225 TYR 0.011 0.001 TYR A 244 PHE 0.008 0.001 PHE A 241 TRP 0.005 0.001 TRP A 180 HIS 0.002 0.001 HIS A 745 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 7887) covalent geometry : angle 0.46451 (10693) SS BOND : bond 0.00107 ( 3) SS BOND : angle 0.55210 ( 6) hydrogen bonds : bond 0.03474 ( 274) hydrogen bonds : angle 5.12355 ( 777) Misc. bond : bond 0.00094 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 55 ASN cc_start: 0.8171 (t0) cc_final: 0.7656 (m-40) REVERT: A 77 GLN cc_start: 0.6961 (tp40) cc_final: 0.6741 (tp-100) REVERT: A 82 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8201 (tt) REVERT: A 202 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7413 (mtm180) REVERT: A 691 ARG cc_start: 0.7665 (pmt170) cc_final: 0.7151 (tpp-160) REVERT: D 70 TYR cc_start: 0.8934 (m-80) cc_final: 0.8668 (m-80) outliers start: 20 outliers final: 15 residues processed: 115 average time/residue: 0.0825 time to fit residues: 12.6699 Evaluate side-chains 114 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 167 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 1 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 0.0970 chunk 5 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.104174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.075964 restraints weight = 12288.121| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.16 r_work: 0.2899 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 7893 Z= 0.250 Angle : 0.534 4.949 10699 Z= 0.287 Chirality : 0.046 0.153 1116 Planarity : 0.004 0.042 1404 Dihedral : 7.670 57.418 1124 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.67 % Allowed : 12.00 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.69 (0.28), residues: 939 helix: 1.23 (0.56), residues: 95 sheet: -0.24 (0.26), residues: 411 loop : -0.98 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 225 TYR 0.017 0.001 TYR A 244 PHE 0.012 0.002 PHE B 126 TRP 0.006 0.001 TRP A 180 HIS 0.003 0.001 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00596 ( 7887) covalent geometry : angle 0.53357 (10693) SS BOND : bond 0.00171 ( 3) SS BOND : angle 0.72188 ( 6) hydrogen bonds : bond 0.04068 ( 274) hydrogen bonds : angle 5.34186 ( 777) Misc. bond : bond 0.00137 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 55 ASN cc_start: 0.8240 (t0) cc_final: 0.7675 (m-40) REVERT: A 82 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8275 (tt) REVERT: A 202 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7550 (mtm180) REVERT: A 691 ARG cc_start: 0.7672 (pmt170) cc_final: 0.7160 (tpp-160) REVERT: D 70 TYR cc_start: 0.8936 (m-80) cc_final: 0.8658 (m-80) outliers start: 22 outliers final: 16 residues processed: 109 average time/residue: 0.1060 time to fit residues: 15.1450 Evaluate side-chains 112 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain D residue 53 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.104854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.076738 restraints weight = 12193.562| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.15 r_work: 0.2914 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7893 Z= 0.201 Angle : 0.508 7.206 10699 Z= 0.272 Chirality : 0.045 0.144 1116 Planarity : 0.004 0.041 1404 Dihedral : 7.639 58.346 1124 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.42 % Allowed : 12.48 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.28), residues: 939 helix: 1.37 (0.56), residues: 95 sheet: -0.19 (0.26), residues: 409 loop : -1.02 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 225 TYR 0.013 0.001 TYR A 112 PHE 0.009 0.001 PHE B 126 TRP 0.006 0.001 TRP A 180 HIS 0.003 0.001 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 7887) covalent geometry : angle 0.50819 (10693) SS BOND : bond 0.00152 ( 3) SS BOND : angle 0.61893 ( 6) hydrogen bonds : bond 0.03766 ( 274) hydrogen bonds : angle 5.22106 ( 777) Misc. bond : bond 0.00117 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8275 (tt) REVERT: A 202 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7552 (mtm180) REVERT: A 301 GLU cc_start: 0.8430 (mm-30) cc_final: 0.7888 (mt-10) REVERT: A 691 ARG cc_start: 0.7666 (pmt170) cc_final: 0.7164 (tpp-160) REVERT: D 70 TYR cc_start: 0.8956 (m-80) cc_final: 0.8655 (m-80) outliers start: 20 outliers final: 16 residues processed: 110 average time/residue: 0.1023 time to fit residues: 14.6813 Evaluate side-chains 110 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain D residue 53 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 59 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 90 optimal weight: 0.0770 chunk 80 optimal weight: 0.8980 chunk 64 optimal weight: 0.0070 chunk 53 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 0.0970 chunk 84 optimal weight: 2.9990 overall best weight: 0.3554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.108393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.080500 restraints weight = 12017.297| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.12 r_work: 0.2978 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 7893 Z= 0.081 Angle : 0.443 7.125 10699 Z= 0.237 Chirality : 0.043 0.140 1116 Planarity : 0.004 0.042 1404 Dihedral : 7.304 58.231 1124 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.94 % Allowed : 12.97 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.36 (0.28), residues: 939 helix: 1.91 (0.57), residues: 94 sheet: -0.00 (0.26), residues: 408 loop : -0.89 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 163 TYR 0.015 0.001 TYR A 112 PHE 0.007 0.001 PHE A 575 TRP 0.007 0.001 TRP A 125 HIS 0.004 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00180 ( 7887) covalent geometry : angle 0.44282 (10693) SS BOND : bond 0.00065 ( 3) SS BOND : angle 0.36740 ( 6) hydrogen bonds : bond 0.02853 ( 274) hydrogen bonds : angle 4.80198 ( 777) Misc. bond : bond 0.00062 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 202 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7461 (mtm180) REVERT: A 301 GLU cc_start: 0.8443 (mm-30) cc_final: 0.7869 (mt-10) REVERT: A 691 ARG cc_start: 0.7632 (pmt170) cc_final: 0.7085 (tpp-160) REVERT: D 70 TYR cc_start: 0.8963 (m-80) cc_final: 0.8681 (m-80) outliers start: 16 outliers final: 10 residues processed: 111 average time/residue: 0.0880 time to fit residues: 13.1794 Evaluate side-chains 103 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 167 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 24 optimal weight: 4.9990 chunk 47 optimal weight: 0.0670 chunk 41 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 16 optimal weight: 0.0980 chunk 74 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 2 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.108949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.081069 restraints weight = 12043.601| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.12 r_work: 0.2979 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7893 Z= 0.092 Angle : 0.447 6.869 10699 Z= 0.237 Chirality : 0.043 0.138 1116 Planarity : 0.004 0.043 1404 Dihedral : 7.185 58.297 1123 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.70 % Allowed : 12.97 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.22 (0.28), residues: 939 helix: 2.24 (0.56), residues: 93 sheet: 0.05 (0.26), residues: 410 loop : -0.80 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 469 TYR 0.014 0.001 TYR A 112 PHE 0.007 0.001 PHE B 123 TRP 0.005 0.001 TRP A 125 HIS 0.004 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 7887) covalent geometry : angle 0.44681 (10693) SS BOND : bond 0.00080 ( 3) SS BOND : angle 0.43721 ( 6) hydrogen bonds : bond 0.02860 ( 274) hydrogen bonds : angle 4.71504 ( 777) Misc. bond : bond 0.00068 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 142 MET cc_start: 0.9109 (mmp) cc_final: 0.8723 (mmt) REVERT: A 202 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7372 (mtm180) REVERT: A 301 GLU cc_start: 0.8431 (mm-30) cc_final: 0.7826 (mt-10) REVERT: A 691 ARG cc_start: 0.7645 (pmt170) cc_final: 0.7078 (tpp-160) REVERT: D 70 TYR cc_start: 0.8976 (m-80) cc_final: 0.8695 (m-80) outliers start: 14 outliers final: 11 residues processed: 103 average time/residue: 0.0994 time to fit residues: 13.6489 Evaluate side-chains 103 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 167 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 0 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 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 = 0.3491 r_free = 0.3491 target = 0.108416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.080033 restraints weight = 12056.822| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.28 r_work: 0.2956 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7893 Z= 0.111 Angle : 0.458 6.716 10699 Z= 0.242 Chirality : 0.044 0.137 1116 Planarity : 0.004 0.046 1404 Dihedral : 7.175 57.436 1123 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.33 % Allowed : 13.09 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.08 (0.28), residues: 939 helix: 2.87 (0.55), residues: 87 sheet: 0.08 (0.25), residues: 413 loop : -0.73 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 225 TYR 0.014 0.001 TYR A 112 PHE 0.007 0.001 PHE B 126 TRP 0.005 0.001 TRP A 311 HIS 0.004 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 7887) covalent geometry : angle 0.45833 (10693) SS BOND : bond 0.00098 ( 3) SS BOND : angle 0.46899 ( 6) hydrogen bonds : bond 0.02970 ( 274) hydrogen bonds : angle 4.74128 ( 777) Misc. bond : bond 0.00077 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 202 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7392 (mtm180) REVERT: A 301 GLU cc_start: 0.8467 (mm-30) cc_final: 0.7817 (mt-10) REVERT: A 691 ARG cc_start: 0.7643 (pmt170) cc_final: 0.7012 (tpp-160) REVERT: D 70 TYR cc_start: 0.8958 (m-80) cc_final: 0.8661 (m-80) outliers start: 11 outliers final: 10 residues processed: 104 average time/residue: 0.0923 time to fit residues: 12.7386 Evaluate side-chains 103 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 167 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 46 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.106427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.078330 restraints weight = 12173.977| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.15 r_work: 0.2926 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7893 Z= 0.179 Angle : 0.499 6.500 10699 Z= 0.264 Chirality : 0.045 0.136 1116 Planarity : 0.004 0.046 1404 Dihedral : 7.345 56.503 1123 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.45 % Allowed : 12.85 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.29 (0.28), residues: 939 helix: 2.07 (0.56), residues: 95 sheet: -0.02 (0.26), residues: 410 loop : -0.82 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 225 TYR 0.013 0.001 TYR A 244 PHE 0.011 0.001 PHE B 123 TRP 0.006 0.001 TRP A 180 HIS 0.003 0.001 HIS A 745 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 7887) covalent geometry : angle 0.49862 (10693) SS BOND : bond 0.00145 ( 3) SS BOND : angle 0.63123 ( 6) hydrogen bonds : bond 0.03516 ( 274) hydrogen bonds : angle 4.99208 ( 777) Misc. bond : bond 0.00106 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2001.97 seconds wall clock time: 34 minutes 49.49 seconds (2089.49 seconds total)