Starting phenix.real_space_refine on Thu Jan 18 15:05:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cp6_16778/01_2024/8cp6_16778.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cp6_16778/01_2024/8cp6_16778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cp6_16778/01_2024/8cp6_16778.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cp6_16778/01_2024/8cp6_16778.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cp6_16778/01_2024/8cp6_16778.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cp6_16778/01_2024/8cp6_16778.pdb" } resolution = 2.45 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= 0.002 sd= 0.024 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 15 5.16 5 C 5535 2.51 5 N 1685 2.21 5 O 1664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 821": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 842": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 8899 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 121 Classifications: {'peptide': 18} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 16} Chain: "B" Number of atoms: 8614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8614 Classifications: {'peptide': 1084} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1031} Chain breaks: 1 Chain: "C" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 164 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 25} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 5.19, per 1000 atoms: 0.58 Number of scatterers: 8899 At special positions: 0 Unit cell: (79.206, 80.127, 116.967, 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 15 16.00 O 1664 8.00 N 1685 7.00 C 5535 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.22 Conformation dependent library (CDL) restraints added in 1.9 seconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1998 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 8 sheets defined 6.0% alpha, 37.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'B' and resid 152 through 156 Processing helix chain 'B' and resid 159 through 164 removed outlier: 3.612A pdb=" N GLN B 163 " --> pdb=" O PRO B 159 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR B 164 " --> pdb=" O ALA B 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 159 through 164' Processing helix chain 'B' and resid 207 through 209 No H-bonds generated for 'chain 'B' and resid 207 through 209' Processing helix chain 'B' and resid 360 through 364 removed outlier: 3.509A pdb=" N ARG B 364 " --> pdb=" O GLY B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 removed outlier: 4.185A pdb=" N GLY B 406 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 407' Processing helix chain 'B' and resid 1035 through 1049 Processing helix chain 'B' and resid 1053 through 1057 removed outlier: 3.704A pdb=" N VAL B1057 " --> pdb=" O ALA B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1147 Processing helix chain 'B' and resid 1154 through 1158 Processing helix chain 'C' and resid 1180 through 1186 Processing helix chain 'C' and resid 1187 through 1193 removed outlier: 3.688A pdb=" N GLU C1193 " --> pdb=" O GLY C1189 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35 removed outlier: 3.586A pdb=" N LEU A 34 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY B 119 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 57 through 62 removed outlier: 4.193A pdb=" N GLU B 60 " --> pdb=" O ARG B 76 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ARG B 76 " --> pdb=" O GLU B 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 85 through 86 removed outlier: 3.639A pdb=" N GLY B 89 " --> pdb=" O GLY B 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 128 through 131 removed outlier: 6.100A pdb=" N TYR B 177 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER B 193 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N HIS B 179 " --> pdb=" O GLN B 191 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 202 through 205 removed outlier: 5.360A pdb=" N THR B 212 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER B 221 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY B 243 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN B 227 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LEU B 241 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 10.022A pdb=" N ARG B 240 " --> pdb=" O PHE B 272 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N PHE B 272 " --> pdb=" O ARG B 240 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N PHE B 242 " --> pdb=" O TYR B 270 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR B 270 " --> pdb=" O PHE B 242 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 268 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU B 246 " --> pdb=" O TRP B 266 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP B 266 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ILE B 279 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL B 291 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL B 281 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG B 295 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU B 299 " --> pdb=" O ARG B 295 " (cutoff:3.500A) removed outlier: 10.654A pdb=" N MET B 298 " --> pdb=" O TRP B 314 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N TRP B 314 " --> pdb=" O MET B 298 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N VAL B 300 " --> pdb=" O TYR B 312 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS B 325 " --> pdb=" O GLU B 313 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N VAL B 324 " --> pdb=" O PHE B 336 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA B 358 " --> pdb=" O TRP B 366 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N TRP B 366 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 9.553A pdb=" N ARG B 365 " --> pdb=" O TYR B 381 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N TYR B 381 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N THR B 367 " --> pdb=" O PHE B 379 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N VAL B 388 " --> pdb=" O ARG B 400 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N VAL B 431 " --> pdb=" O PHE B 443 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N THR B 452 " --> pdb=" O TYR B 463 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ARG B 486 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU B 498 " --> pdb=" O ARG B 486 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLU B 488 " --> pdb=" O ALA B 496 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ALA B 496 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N VAL B 517 " --> pdb=" O ARG B 529 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ILE B 538 " --> pdb=" O TYR B 550 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA B 547 " --> pdb=" O ASP B 563 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASP B 563 " --> pdb=" O ALA B 547 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N SER B 549 " --> pdb=" O ILE B 561 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE B 561 " --> pdb=" O SER B 549 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLU B 551 " --> pdb=" O THR B 559 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N THR B 559 " --> pdb=" O PHE B 571 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU B 570 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL B 582 " --> pdb=" O LEU B 570 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N SER B 572 " --> pdb=" O ALA B 580 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ALA B 580 " --> pdb=" O TYR B 592 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N VAL B 601 " --> pdb=" O PHE B 613 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU B 623 " --> pdb=" O ARG B 614 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N VAL B 622 " --> pdb=" O TYR B 634 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ILE B 643 " --> pdb=" O TYR B 655 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N GLU B 652 " --> pdb=" O VAL B 668 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N VAL B 668 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR B 654 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ILE B 666 " --> pdb=" O THR B 654 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA B 656 " --> pdb=" O ALA B 664 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ALA B 664 " --> pdb=" O TYR B 681 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ALA B 690 " --> pdb=" O TYR B 701 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ARG B 710 " --> pdb=" O HIS B 726 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N SER B 723 " --> pdb=" O TYR B 739 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N TYR B 739 " --> pdb=" O SER B 723 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLU B 725 " --> pdb=" O SER B 737 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER B 737 " --> pdb=" O GLU B 725 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER B 727 " --> pdb=" O GLN B 735 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLN B 735 " --> pdb=" O TRP B 747 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA B 746 " --> pdb=" O ALA B 758 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA B 758 " --> pdb=" O ALA B 746 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU B 748 " --> pdb=" O HIS B 756 " (cutoff:3.500A) removed outlier: 11.456A pdb=" N HIS B 754 " --> pdb=" O ARG B 769 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N ARG B 769 " --> pdb=" O HIS B 754 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N HIS B 756 " --> pdb=" O PHE B 767 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLU B 764 " --> pdb=" O ALA B 780 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA B 780 " --> pdb=" O GLU B 764 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA B 766 " --> pdb=" O ARG B 778 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG B 778 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLU B 768 " --> pdb=" O VAL B 776 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N VAL B 776 " --> pdb=" O ARG B 794 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE B 790 " --> pdb=" O ALA B 780 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR B 791 " --> pdb=" O LEU B 807 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU B 807 " --> pdb=" O THR B 791 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU B 793 " --> pdb=" O SER B 805 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N SER B 805 " --> pdb=" O GLU B 793 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLN B 795 " --> pdb=" O GLN B 803 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N GLN B 803 " --> pdb=" O TYR B 819 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL B 828 " --> pdb=" O TYR B 840 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ARG B 839 " --> pdb=" O SER B 851 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER B 851 " --> pdb=" O ARG B 839 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU B 841 " --> pdb=" O LEU B 849 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 862 through 863 removed outlier: 4.309A pdb=" N ARG B 862 " --> pdb=" O LEU B 870 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 919 through 920 removed outlier: 4.927A pdb=" N VAL B 934 " --> pdb=" O LEU B 946 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N VAL B 955 " --> pdb=" O TYR B 971 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ILE B 980 " --> pdb=" O PHE B 995 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ARG B 994 " --> pdb=" O GLU B1005 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU B1005 " --> pdb=" O ARG B 994 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLY B 996 " --> pdb=" O CYS B1003 " (cutoff:3.500A) removed outlier: 9.944A pdb=" N ARG B1001 " --> pdb=" O HIS B1016 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N HIS B1016 " --> pdb=" O ARG B1001 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N CYS B1003 " --> pdb=" O THR B1014 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU B1024 " --> pdb=" O PHE B1068 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU B1077 " --> pdb=" O GLN B1089 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLN B1089 " --> pdb=" O LEU B1077 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU B1079 " --> pdb=" O ARG B1087 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1109 through 1110 297 hydrogen bonds defined for protein. 810 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.78 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3173 1.34 - 1.46: 2000 1.46 - 1.57: 3911 1.57 - 1.69: 0 1.69 - 1.81: 21 Bond restraints: 9105 Sorted by residual: bond pdb=" C TRP B 205 " pdb=" N SER B 206 " ideal model delta sigma weight residual 1.332 1.324 0.008 1.40e-02 5.10e+03 3.59e-01 bond pdb=" C GLY C1176 " pdb=" O GLY C1176 " ideal model delta sigma weight residual 1.239 1.235 0.004 7.10e-03 1.98e+04 3.23e-01 bond pdb=" CB VAL B 582 " pdb=" CG2 VAL B 582 " ideal model delta sigma weight residual 1.521 1.502 0.019 3.30e-02 9.18e+02 3.17e-01 bond pdb=" CA HIS B1069 " pdb=" CB HIS B1069 " ideal model delta sigma weight residual 1.531 1.513 0.018 3.28e-02 9.30e+02 2.92e-01 bond pdb=" CA PHE B 74 " pdb=" C PHE B 74 " ideal model delta sigma weight residual 1.526 1.520 0.006 1.20e-02 6.94e+03 2.35e-01 ... (remaining 9100 not shown) Histogram of bond angle deviations from ideal: 100.81 - 107.44: 359 107.44 - 114.08: 4737 114.08 - 120.71: 3636 120.71 - 127.34: 3490 127.34 - 133.98: 116 Bond angle restraints: 12338 Sorted by residual: angle pdb=" CA GLY C1176 " pdb=" C GLY C1176 " pdb=" N ALA C1177 " ideal model delta sigma weight residual 118.95 116.70 2.25 1.06e+00 8.90e-01 4.52e+00 angle pdb=" C ARG B1096 " pdb=" N ALA B1097 " pdb=" CA ALA B1097 " ideal model delta sigma weight residual 121.54 125.47 -3.93 1.91e+00 2.74e-01 4.23e+00 angle pdb=" C GLY B 406 " pdb=" N ARG B 407 " pdb=" CA ARG B 407 " ideal model delta sigma weight residual 121.54 125.32 -3.78 1.91e+00 2.74e-01 3.93e+00 angle pdb=" N GLY C1176 " pdb=" CA GLY C1176 " pdb=" C GLY C1176 " ideal model delta sigma weight residual 115.80 112.62 3.18 1.74e+00 3.30e-01 3.34e+00 angle pdb=" CA LEU B 957 " pdb=" CB LEU B 957 " pdb=" CG LEU B 957 " ideal model delta sigma weight residual 116.30 122.50 -6.20 3.50e+00 8.16e-02 3.14e+00 ... (remaining 12333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 5154 17.14 - 34.28: 190 34.28 - 51.42: 26 51.42 - 68.57: 3 68.57 - 85.71: 2 Dihedral angle restraints: 5375 sinusoidal: 2198 harmonic: 3177 Sorted by residual: dihedral pdb=" N GLU B 135 " pdb=" CA GLU B 135 " pdb=" CB GLU B 135 " pdb=" CG GLU B 135 " ideal model delta sinusoidal sigma weight residual -180.00 -121.99 -58.01 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" N VAL B1098 " pdb=" CA VAL B1098 " pdb=" CB VAL B1098 " pdb=" CG1 VAL B1098 " ideal model delta sinusoidal sigma weight residual 180.00 128.41 51.59 3 1.50e+01 4.44e-03 9.03e+00 dihedral pdb=" CA GLU B1048 " pdb=" CB GLU B1048 " pdb=" CG GLU B1048 " pdb=" CD GLU B1048 " ideal model delta sinusoidal sigma weight residual 60.00 111.37 -51.37 3 1.50e+01 4.44e-03 9.01e+00 ... (remaining 5372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 715 0.026 - 0.051: 347 0.051 - 0.077: 90 0.077 - 0.103: 53 0.103 - 0.129: 44 Chirality restraints: 1249 Sorted by residual: chirality pdb=" CA ILE B 666 " pdb=" N ILE B 666 " pdb=" C ILE B 666 " pdb=" CB ILE B 666 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA ILE B 561 " pdb=" N ILE B 561 " pdb=" C ILE B 561 " pdb=" CB ILE B 561 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA VAL B 214 " pdb=" N VAL B 214 " pdb=" C VAL B 214 " pdb=" CB VAL B 214 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.64e-01 ... (remaining 1246 not shown) Planarity restraints: 1678 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 521 " -0.026 5.00e-02 4.00e+02 3.87e-02 2.40e+00 pdb=" N PRO B 522 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 522 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 522 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 797 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO B 798 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 798 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 798 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 183 " -0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO B 184 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 184 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 184 " -0.020 5.00e-02 4.00e+02 ... (remaining 1675 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 706 2.74 - 3.28: 7861 3.28 - 3.82: 14579 3.82 - 4.36: 18907 4.36 - 4.90: 32783 Nonbonded interactions: 74836 Sorted by model distance: nonbonded pdb=" OH TYR B 199 " pdb=" OD1 ASP B 472 " model vdw 2.203 2.440 nonbonded pdb=" O ALA B 67 " pdb=" NH2 ARG B 220 " model vdw 2.235 2.520 nonbonded pdb=" O ARG B 154 " pdb=" OH TYR B 177 " model vdw 2.240 2.440 nonbonded pdb=" OD2 ASP B 63 " pdb=" OH TYR B 270 " model vdw 2.263 2.440 nonbonded pdb=" OG SER B 727 " pdb=" OG1 THR B 736 " model vdw 2.281 2.440 ... (remaining 74831 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.840 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: 3.440 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 29.190 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 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 : 0.003 0.023 9105 Z= 0.198 Angle : 0.424 6.204 12338 Z= 0.223 Chirality : 0.040 0.129 1249 Planarity : 0.004 0.039 1678 Dihedral : 9.140 85.707 3377 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.46 % Allowed : 2.75 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.62 (0.25), residues: 1121 helix: -0.90 (0.98), residues: 33 sheet: 0.75 (0.28), residues: 351 loop : 0.41 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 93 HIS 0.002 0.000 HIS B 129 PHE 0.007 0.001 PHE B 790 TYR 0.009 0.001 TYR B1130 ARG 0.003 0.000 ARG B1136 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 1.064 Fit side-chains REVERT: A 37 ARG cc_start: 0.8088 (ttp80) cc_final: 0.7885 (ttm-80) REVERT: B 135 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7975 (mm-30) REVERT: B 149 GLN cc_start: 0.8975 (mt0) cc_final: 0.8766 (mt0) REVERT: B 204 ARG cc_start: 0.7597 (ttm110) cc_final: 0.7376 (ttm110) REVERT: B 298 MET cc_start: 0.9173 (mmp) cc_final: 0.8941 (mmp) REVERT: B 360 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7317 (mm-30) REVERT: B 402 ARG cc_start: 0.7622 (mtp85) cc_final: 0.7304 (mtt-85) REVERT: B 411 GLU cc_start: 0.8334 (tt0) cc_final: 0.8134 (tt0) REVERT: B 420 ARG cc_start: 0.8020 (mtp85) cc_final: 0.7620 (mtp85) REVERT: B 421 LYS cc_start: 0.8292 (tttt) cc_final: 0.7804 (ttmp) REVERT: B 1103 GLN cc_start: 0.7912 (pm20) cc_final: 0.7611 (pm20) REVERT: B 1118 GLU cc_start: 0.8477 (tt0) cc_final: 0.7807 (tm-30) outliers start: 4 outliers final: 2 residues processed: 76 average time/residue: 1.8189 time to fit residues: 145.3669 Evaluate side-chains 53 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 1098 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 0.0000 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 GLN B 260 GLN B 405 GLN B 803 GLN B 956 HIS B1078 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9105 Z= 0.282 Angle : 0.490 7.091 12338 Z= 0.259 Chirality : 0.042 0.131 1249 Planarity : 0.005 0.038 1678 Dihedral : 4.035 49.845 1321 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.95 % Allowed : 4.81 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.50 (0.25), residues: 1121 helix: -0.29 (1.01), residues: 33 sheet: 0.68 (0.28), residues: 335 loop : 0.29 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 93 HIS 0.003 0.001 HIS B 594 PHE 0.010 0.001 PHE B 790 TYR 0.009 0.001 TYR B 636 ARG 0.005 0.000 ARG B 440 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 53 time to evaluate : 1.072 Fit side-chains REVERT: B 135 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7814 (mm-30) REVERT: B 149 GLN cc_start: 0.8979 (mt0) cc_final: 0.8758 (mt0) REVERT: B 202 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7676 (mt-10) REVERT: B 411 GLU cc_start: 0.8163 (tt0) cc_final: 0.7905 (tt0) REVERT: B 420 ARG cc_start: 0.7993 (mtp85) cc_final: 0.7743 (mtp85) REVERT: B 421 LYS cc_start: 0.8199 (tttt) cc_final: 0.7829 (ttmp) REVERT: B 563 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.7966 (p0) REVERT: B 781 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.6968 (mtp85) REVERT: B 1103 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7599 (pm20) REVERT: B 1118 GLU cc_start: 0.8508 (tt0) cc_final: 0.7793 (tm-30) outliers start: 17 outliers final: 8 residues processed: 64 average time/residue: 1.5586 time to fit residues: 106.2398 Evaluate side-chains 64 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 51 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain B residue 786 ASP Chi-restraints excluded: chain B residue 787 ASP Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 963 ASP Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1103 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 68 optimal weight: 0.0470 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 109 optimal weight: 0.0050 chunk 89 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 overall best weight: 1.5696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 GLN B 816 GLN B1078 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9105 Z= 0.275 Angle : 0.474 6.878 12338 Z= 0.249 Chirality : 0.042 0.134 1249 Planarity : 0.004 0.040 1678 Dihedral : 4.050 49.342 1321 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.17 % Allowed : 5.38 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 (0.25), residues: 1121 helix: 0.12 (1.05), residues: 33 sheet: 0.68 (0.27), residues: 329 loop : 0.21 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 93 HIS 0.003 0.001 HIS B 956 PHE 0.010 0.001 PHE B 120 TYR 0.008 0.001 TYR B1130 ARG 0.005 0.000 ARG B 204 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 50 time to evaluate : 1.078 Fit side-chains REVERT: B 149 GLN cc_start: 0.8941 (mt0) cc_final: 0.8722 (mt0) REVERT: B 411 GLU cc_start: 0.8143 (tt0) cc_final: 0.7810 (tt0) REVERT: B 420 ARG cc_start: 0.8000 (mtp85) cc_final: 0.7643 (mtp85) REVERT: B 421 LYS cc_start: 0.8184 (tttt) cc_final: 0.7792 (ttmp) REVERT: B 563 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.7937 (p0) REVERT: B 781 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7049 (mtp85) REVERT: B 1048 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6623 (mt-10) REVERT: B 1103 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7650 (pm20) outliers start: 19 outliers final: 8 residues processed: 62 average time/residue: 1.6722 time to fit residues: 109.8972 Evaluate side-chains 60 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 48 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain B residue 786 ASP Chi-restraints excluded: chain B residue 787 ASP Chi-restraints excluded: chain B residue 963 ASP Chi-restraints excluded: chain B residue 1048 GLU Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1103 GLN Chi-restraints excluded: chain C residue 1175 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 0.2980 chunk 96 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 GLN B1078 GLN B1125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9105 Z= 0.211 Angle : 0.452 6.631 12338 Z= 0.237 Chirality : 0.041 0.133 1249 Planarity : 0.004 0.041 1678 Dihedral : 3.965 50.273 1321 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.60 % Allowed : 6.52 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.45 (0.25), residues: 1121 helix: -0.01 (1.04), residues: 34 sheet: 0.74 (0.27), residues: 329 loop : 0.18 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 93 HIS 0.002 0.001 HIS B 956 PHE 0.011 0.001 PHE B 790 TYR 0.008 0.001 TYR B1130 ARG 0.004 0.000 ARG B 204 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 53 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: B 149 GLN cc_start: 0.8937 (mt0) cc_final: 0.8718 (mt0) REVERT: B 411 GLU cc_start: 0.8117 (tt0) cc_final: 0.7786 (tt0) REVERT: B 420 ARG cc_start: 0.8011 (mtp85) cc_final: 0.7720 (mtp85) REVERT: B 421 LYS cc_start: 0.8160 (tttt) cc_final: 0.7737 (ttmp) REVERT: B 563 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.7934 (p0) REVERT: B 1048 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6559 (mt-10) REVERT: B 1103 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7629 (pm20) outliers start: 14 outliers final: 8 residues processed: 62 average time/residue: 1.4303 time to fit residues: 94.7417 Evaluate side-chains 63 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 52 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 786 ASP Chi-restraints excluded: chain B residue 787 ASP Chi-restraints excluded: chain B residue 963 ASP Chi-restraints excluded: chain B residue 1048 GLU Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1103 GLN Chi-restraints excluded: chain C residue 1175 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 27 optimal weight: 0.0010 chunk 36 optimal weight: 0.7980 chunk 21 optimal weight: 0.0070 overall best weight: 0.4806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 GLN B1078 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 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 : 0.002 0.026 9105 Z= 0.122 Angle : 0.423 5.932 12338 Z= 0.223 Chirality : 0.040 0.133 1249 Planarity : 0.004 0.041 1678 Dihedral : 3.798 53.729 1321 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.60 % Allowed : 6.86 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.54 (0.25), residues: 1121 helix: 0.11 (1.06), residues: 34 sheet: 0.80 (0.27), residues: 346 loop : 0.24 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 93 HIS 0.001 0.000 HIS B 317 PHE 0.009 0.001 PHE B 790 TYR 0.007 0.001 TYR B1130 ARG 0.009 0.000 ARG B 204 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 1.115 Fit side-chains REVERT: B 149 GLN cc_start: 0.8929 (mt0) cc_final: 0.8716 (mt0) REVERT: B 183 CYS cc_start: 0.8650 (m) cc_final: 0.8092 (m) REVERT: B 411 GLU cc_start: 0.8158 (tt0) cc_final: 0.7864 (OUTLIER) REVERT: B 420 ARG cc_start: 0.8005 (mtp85) cc_final: 0.7711 (mtp85) REVERT: B 563 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7916 (p0) REVERT: B 963 ASP cc_start: 0.9051 (OUTLIER) cc_final: 0.8746 (p0) REVERT: B 1048 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6591 (mt-10) REVERT: B 1103 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7611 (pm20) outliers start: 14 outliers final: 9 residues processed: 64 average time/residue: 1.4388 time to fit residues: 98.8259 Evaluate side-chains 66 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 54 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain B residue 786 ASP Chi-restraints excluded: chain B residue 963 ASP Chi-restraints excluded: chain B residue 1048 GLU Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1103 GLN Chi-restraints excluded: chain C residue 1175 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 8 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 12 optimal weight: 0.0060 chunk 61 optimal weight: 4.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 GLN B1078 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9105 Z= 0.180 Angle : 0.439 6.197 12338 Z= 0.230 Chirality : 0.040 0.132 1249 Planarity : 0.004 0.047 1678 Dihedral : 3.832 52.981 1321 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.95 % Allowed : 6.86 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.56 (0.25), residues: 1121 helix: 0.11 (1.06), residues: 34 sheet: 0.87 (0.27), residues: 339 loop : 0.23 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 93 HIS 0.002 0.001 HIS B 956 PHE 0.010 0.001 PHE B 790 TYR 0.007 0.001 TYR B1130 ARG 0.009 0.000 ARG B 204 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 52 time to evaluate : 1.127 Fit side-chains revert: symmetry clash REVERT: B 149 GLN cc_start: 0.8927 (mt0) cc_final: 0.8711 (mt0) REVERT: B 183 CYS cc_start: 0.8592 (m) cc_final: 0.8045 (m) REVERT: B 298 MET cc_start: 0.9021 (mmt) cc_final: 0.8808 (mmt) REVERT: B 401 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.5765 (mtt90) REVERT: B 411 GLU cc_start: 0.8144 (tt0) cc_final: 0.7857 (OUTLIER) REVERT: B 420 ARG cc_start: 0.8016 (mtp85) cc_final: 0.7714 (mtp85) REVERT: B 563 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7930 (p0) REVERT: B 963 ASP cc_start: 0.9062 (OUTLIER) cc_final: 0.8760 (p0) REVERT: B 1048 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6593 (mt-10) REVERT: B 1103 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7632 (pm20) outliers start: 17 outliers final: 12 residues processed: 62 average time/residue: 1.5131 time to fit residues: 100.1327 Evaluate side-chains 69 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 53 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 401 ARG Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 786 ASP Chi-restraints excluded: chain B residue 787 ASP Chi-restraints excluded: chain B residue 963 ASP Chi-restraints excluded: chain B residue 1048 GLU Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1103 GLN Chi-restraints excluded: chain C residue 1169 ILE Chi-restraints excluded: chain C residue 1175 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 GLN B1078 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9105 Z= 0.240 Angle : 0.461 6.325 12338 Z= 0.241 Chirality : 0.041 0.133 1249 Planarity : 0.004 0.050 1678 Dihedral : 3.919 50.060 1321 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.17 % Allowed : 6.64 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.53 (0.25), residues: 1121 helix: 0.11 (1.05), residues: 34 sheet: 0.86 (0.27), residues: 329 loop : 0.21 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 93 HIS 0.003 0.001 HIS B 956 PHE 0.011 0.001 PHE B 790 TYR 0.008 0.001 TYR B1130 ARG 0.012 0.000 ARG B 204 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 53 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: B 149 GLN cc_start: 0.8936 (mt0) cc_final: 0.8713 (mt0) REVERT: B 183 CYS cc_start: 0.8608 (m) cc_final: 0.8035 (m) REVERT: B 401 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.5795 (mtt90) REVERT: B 411 GLU cc_start: 0.8124 (tt0) cc_final: 0.7832 (OUTLIER) REVERT: B 420 ARG cc_start: 0.8021 (mtp85) cc_final: 0.7712 (mtp85) REVERT: B 421 LYS cc_start: 0.8197 (tttt) cc_final: 0.7763 (ttmp) REVERT: B 563 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7925 (p0) REVERT: B 1048 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6512 (mt-10) REVERT: B 1103 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7670 (pm20) outliers start: 19 outliers final: 12 residues processed: 65 average time/residue: 1.5128 time to fit residues: 105.0246 Evaluate side-chains 69 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 54 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 401 ARG Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 779 ASP Chi-restraints excluded: chain B residue 786 ASP Chi-restraints excluded: chain B residue 787 ASP Chi-restraints excluded: chain B residue 963 ASP Chi-restraints excluded: chain B residue 1048 GLU Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1103 GLN Chi-restraints excluded: chain C residue 1169 ILE Chi-restraints excluded: chain C residue 1175 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 GLN B1078 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9105 Z= 0.265 Angle : 0.470 6.332 12338 Z= 0.245 Chirality : 0.041 0.133 1249 Planarity : 0.004 0.056 1678 Dihedral : 3.973 49.386 1321 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.17 % Allowed : 6.86 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.53 (0.25), residues: 1121 helix: 0.10 (1.05), residues: 34 sheet: 0.80 (0.27), residues: 334 loop : 0.24 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 93 HIS 0.003 0.001 HIS B 956 PHE 0.011 0.001 PHE B 790 TYR 0.008 0.001 TYR B1130 ARG 0.012 0.000 ARG B 204 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 54 time to evaluate : 1.132 Fit side-chains REVERT: B 149 GLN cc_start: 0.8935 (mt0) cc_final: 0.8716 (mt0) REVERT: B 183 CYS cc_start: 0.8609 (m) cc_final: 0.8064 (m) REVERT: B 411 GLU cc_start: 0.8083 (tt0) cc_final: 0.7774 (OUTLIER) REVERT: B 420 ARG cc_start: 0.8015 (mtp85) cc_final: 0.7710 (mtp85) REVERT: B 421 LYS cc_start: 0.8194 (tttt) cc_final: 0.7759 (ttmp) REVERT: B 563 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7910 (p0) REVERT: B 1009 ARG cc_start: 0.8089 (mmt180) cc_final: 0.7039 (mmp-170) REVERT: B 1048 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6553 (mt-10) REVERT: B 1103 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7662 (pm20) outliers start: 19 outliers final: 13 residues processed: 64 average time/residue: 1.4087 time to fit residues: 96.4912 Evaluate side-chains 70 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 55 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 779 ASP Chi-restraints excluded: chain B residue 786 ASP Chi-restraints excluded: chain B residue 787 ASP Chi-restraints excluded: chain B residue 963 ASP Chi-restraints excluded: chain B residue 1048 GLU Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1103 GLN Chi-restraints excluded: chain C residue 1169 ILE Chi-restraints excluded: chain C residue 1175 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 0.0770 chunk 99 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 GLN B1078 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9105 Z= 0.157 Angle : 0.441 5.993 12338 Z= 0.230 Chirality : 0.040 0.135 1249 Planarity : 0.004 0.055 1678 Dihedral : 3.832 52.233 1321 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.83 % Allowed : 7.32 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.61 (0.25), residues: 1121 helix: 0.17 (1.06), residues: 34 sheet: 0.74 (0.26), residues: 355 loop : 0.34 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 93 HIS 0.002 0.000 HIS B 956 PHE 0.010 0.001 PHE B 790 TYR 0.008 0.001 TYR B1130 ARG 0.014 0.000 ARG B 204 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 55 time to evaluate : 1.029 Fit side-chains REVERT: B 149 GLN cc_start: 0.8926 (mt0) cc_final: 0.8699 (mt0) REVERT: B 183 CYS cc_start: 0.8587 (m) cc_final: 0.8182 (m) REVERT: B 260 GLN cc_start: 0.9213 (mm-40) cc_final: 0.9003 (mm-40) REVERT: B 411 GLU cc_start: 0.8123 (tt0) cc_final: 0.7832 (OUTLIER) REVERT: B 420 ARG cc_start: 0.8013 (mtp85) cc_final: 0.7717 (mtp85) REVERT: B 563 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7925 (p0) REVERT: B 1048 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6560 (mt-10) REVERT: B 1103 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7663 (pm20) outliers start: 16 outliers final: 12 residues processed: 64 average time/residue: 1.4718 time to fit residues: 100.4344 Evaluate side-chains 67 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 53 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 786 ASP Chi-restraints excluded: chain B residue 963 ASP Chi-restraints excluded: chain B residue 1048 GLU Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1103 GLN Chi-restraints excluded: chain C residue 1175 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 101 optimal weight: 0.3980 chunk 88 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 26 optimal weight: 0.0770 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1078 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9105 Z= 0.140 Angle : 0.441 6.355 12338 Z= 0.230 Chirality : 0.040 0.133 1249 Planarity : 0.004 0.060 1678 Dihedral : 3.801 53.327 1321 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.60 % Allowed : 7.78 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.25), residues: 1121 helix: 0.21 (1.07), residues: 34 sheet: 0.83 (0.26), residues: 353 loop : 0.34 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 93 HIS 0.002 0.000 HIS B 956 PHE 0.010 0.001 PHE B 790 TYR 0.007 0.001 TYR B1130 ARG 0.015 0.000 ARG B 204 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 55 time to evaluate : 1.110 Fit side-chains REVERT: B 183 CYS cc_start: 0.8566 (m) cc_final: 0.8207 (m) REVERT: B 204 ARG cc_start: 0.7488 (ttm110) cc_final: 0.6900 (ttp-110) REVERT: B 295 ARG cc_start: 0.8338 (mmm-85) cc_final: 0.7724 (ttp-110) REVERT: B 411 GLU cc_start: 0.8123 (tt0) cc_final: 0.7848 (OUTLIER) REVERT: B 420 ARG cc_start: 0.8012 (mtp85) cc_final: 0.7717 (mtp85) REVERT: B 440 ARG cc_start: 0.8075 (mtt90) cc_final: 0.7568 (mtt90) REVERT: B 563 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.7931 (p0) REVERT: B 1048 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6537 (mt-10) REVERT: B 1103 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7648 (pm20) outliers start: 14 outliers final: 9 residues processed: 64 average time/residue: 1.5134 time to fit residues: 103.3611 Evaluate side-chains 64 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 53 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 786 ASP Chi-restraints excluded: chain B residue 963 ASP Chi-restraints excluded: chain B residue 1048 GLU Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1103 GLN Chi-restraints excluded: chain C residue 1175 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 11 optimal weight: 0.0040 chunk 16 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 GLN B1078 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.090714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.068328 restraints weight = 12408.338| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.71 r_work: 0.2674 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9105 Z= 0.208 Angle : 0.465 10.427 12338 Z= 0.240 Chirality : 0.041 0.131 1249 Planarity : 0.004 0.060 1678 Dihedral : 3.855 52.029 1319 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.49 % Allowed : 8.24 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.25), residues: 1121 helix: 0.19 (1.06), residues: 34 sheet: 0.82 (0.27), residues: 344 loop : 0.33 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 93 HIS 0.003 0.001 HIS B 956 PHE 0.011 0.001 PHE B 790 TYR 0.007 0.001 TYR B1130 ARG 0.014 0.000 ARG B 204 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3067.03 seconds wall clock time: 55 minutes 18.34 seconds (3318.34 seconds total)