Starting phenix.real_space_refine on Fri Jul 3 14:41:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gzm_51727/07_2026/9gzm_51727.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gzm_51727/07_2026/9gzm_51727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gzm_51727/07_2026/9gzm_51727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gzm_51727/07_2026/9gzm_51727.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gzm_51727/07_2026/9gzm_51727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gzm_51727/07_2026/9gzm_51727.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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: 6 Type Number sf(0) Gaussians P 107 5.49 5 Mg 1 5.21 5 S 75 5.16 5 C 8953 2.51 5 N 2626 2.21 5 O 2842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14604 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8483 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1068, 8472 Classifications: {'peptide': 1068} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 68, 'TRANS': 999} Chain breaks: 3 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 50 Conformer: "B" Number of residues, atoms: 1068, 8472 Classifications: {'peptide': 1068} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 68, 'TRANS': 999} Chain breaks: 3 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 50 bond proxies already assigned to first conformer: 8656 Chain: "N" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1039 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "T" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1012 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "B" Number of atoms: 2586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2586 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 21, 'TRANS': 304} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 3, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 46 Chain: "R" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {'GTP': 1} Classifications: {'RNA': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1398 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 8, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 70 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 563 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 563 " occ=0.50 Time building chain proxies: 3.92, per 1000 atoms: 0.27 Number of scatterers: 14604 At special positions: 0 Unit cell: (102.6, 131.4, 143.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 75 16.00 P 107 15.00 Mg 1 11.99 O 2842 8.00 N 2626 7.00 C 8953 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 869.2 milliseconds 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3010 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 12 sheets defined 63.7% alpha, 6.2% beta 43 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 122 through 146 Processing helix chain 'A' and resid 168 through 180 Processing helix chain 'A' and resid 186 through 198 removed outlier: 3.643A pdb=" N ALA A 192 " --> pdb=" O GLU A 188 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLU A 197 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ALA A 198 " --> pdb=" O LEU A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 237 Processing helix chain 'A' and resid 238 through 252 removed outlier: 3.598A pdb=" N ALA A 242 " --> pdb=" O GLN A 238 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 removed outlier: 4.234A pdb=" N LEU A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 274 removed outlier: 3.791A pdb=" N TYR A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 290 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 312 through 326 removed outlier: 4.061A pdb=" N ILE A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 340 through 355 removed outlier: 3.809A pdb=" N VAL A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.613A pdb=" N TYR A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 410 Processing helix chain 'A' and resid 424 through 461 Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 475 through 489 Processing helix chain 'A' and resid 497 through 521 removed outlier: 3.539A pdb=" N GLY A 521 " --> pdb=" O GLN A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 534 removed outlier: 4.064A pdb=" N ALA A 525 " --> pdb=" O GLY A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 557 removed outlier: 3.804A pdb=" N GLY A 557 " --> pdb=" O TRP A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 587 removed outlier: 3.580A pdb=" N THR A 587 " --> pdb=" O LEU A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 635 Processing helix chain 'A' and resid 644 through 646 No H-bonds generated for 'chain 'A' and resid 644 through 646' Processing helix chain 'A' and resid 678 through 687 Processing helix chain 'A' and resid 692 through 704 Processing helix chain 'A' and resid 710 through 723 Processing helix chain 'A' and resid 726 through 730 Processing helix chain 'A' and resid 756 through 789 removed outlier: 4.002A pdb=" N ARG A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU A 761 " --> pdb=" O GLU A 757 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N HIS A 764 " --> pdb=" O ARG A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 824 Processing helix chain 'A' and resid 836 through 850 Processing helix chain 'A' and resid 856 through 867 Processing helix chain 'A' and resid 867 through 877 Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 890 through 907 Processing helix chain 'A' and resid 909 through 912 Processing helix chain 'A' and resid 925 through 936 Processing helix chain 'A' and resid 937 through 944 removed outlier: 3.570A pdb=" N SER A 943 " --> pdb=" O VAL A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 973 removed outlier: 3.993A pdb=" N GLY A 958 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG A 973 " --> pdb=" O GLN A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 981 removed outlier: 3.647A pdb=" N LEU A 981 " --> pdb=" O VAL A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 997 removed outlier: 3.782A pdb=" N VAL A 990 " --> pdb=" O THR A 986 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLN A 992 " --> pdb=" O LYS A 988 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N THR A 993 " --> pdb=" O VAL A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1018 removed outlier: 4.251A pdb=" N SER A1018 " --> pdb=" O LEU A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1023 No H-bonds generated for 'chain 'A' and resid 1021 through 1023' Processing helix chain 'A' and resid 1024 through 1040 Processing helix chain 'A' and resid 1045 through 1064 removed outlier: 4.082A pdb=" N MET A1064 " --> pdb=" O LEU A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1141 Proline residue: A1120 - end of helix removed outlier: 3.759A pdb=" N ILE A1124 " --> pdb=" O PRO A1120 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG A1141 " --> pdb=" O LEU A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1177 removed outlier: 4.046A pdb=" N GLU A1177 " --> pdb=" O ARG A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1191 Processing helix chain 'A' and resid 1197 through 1210 removed outlier: 3.853A pdb=" N ALA A1210 " --> pdb=" O GLU A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1225 removed outlier: 3.678A pdb=" N GLN A1221 " --> pdb=" O ASP A1218 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 89 Processing helix chain 'B' and resid 107 through 117 removed outlier: 3.581A pdb=" N GLY B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 137 removed outlier: 3.733A pdb=" N LEU B 133 " --> pdb=" O PHE B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 154 removed outlier: 3.691A pdb=" N LEU B 154 " --> pdb=" O PHE B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 177 Processing helix chain 'B' and resid 199 through 214 removed outlier: 3.693A pdb=" N TRP B 205 " --> pdb=" O LYS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 220 removed outlier: 3.534A pdb=" N TYR B 218 " --> pdb=" O THR B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 238 Processing helix chain 'B' and resid 248 through 257 Processing helix chain 'B' and resid 267 through 271 removed outlier: 3.594A pdb=" N SER B 270 " --> pdb=" O PRO B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 292 Processing helix chain 'B' and resid 316 through 328 Processing helix chain 'B' and resid 335 through 343 removed outlier: 4.150A pdb=" N SER B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 354 Processing helix chain 'B' and resid 366 through 379 Processing helix chain 'C' and resid 44 through 49 Processing helix chain 'C' and resid 55 through 64 Processing helix chain 'C' and resid 64 through 72 removed outlier: 3.527A pdb=" N PHE C 68 " --> pdb=" O GLN C 64 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 70 " --> pdb=" O PRO C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 91 Processing helix chain 'C' and resid 92 through 121 removed outlier: 3.673A pdb=" N LYS C 96 " --> pdb=" O PRO C 92 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU C 119 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN C 120 " --> pdb=" O ARG C 116 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU C 121 " --> pdb=" O PHE C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 152 Processing helix chain 'C' and resid 160 through 170 Processing helix chain 'C' and resid 180 through 189 removed outlier: 3.810A pdb=" N GLU C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 226 removed outlier: 4.079A pdb=" N LYS C 197 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU C 220 " --> pdb=" O LYS C 216 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET C 222 " --> pdb=" O TRP C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 231 removed outlier: 3.631A pdb=" N LEU C 230 " --> pdb=" O ARG C 227 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 411 through 415 Processing sheet with id=AA2, first strand: chain 'A' and resid 495 through 496 Processing sheet with id=AA3, first strand: chain 'A' and resid 588 through 590 Processing sheet with id=AA4, first strand: chain 'A' and resid 653 through 657 removed outlier: 4.714A pdb=" N TRP A 655 " --> pdb=" O SER A 660 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N SER A 660 " --> pdb=" O TRP A 655 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 707 through 709 Processing sheet with id=AA6, first strand: chain 'A' and resid 798 through 800 Processing sheet with id=AA7, first strand: chain 'A' and resid 831 through 832 removed outlier: 3.612A pdb=" N ARG A 831 " --> pdb=" O SER A 915 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 919 through 922 Processing sheet with id=AA9, first strand: chain 'A' and resid 1069 through 1071 Processing sheet with id=AB1, first strand: chain 'A' and resid 1089 through 1091 removed outlier: 3.533A pdb=" N LYS A1089 " --> pdb=" O TYR A1100 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE A1098 " --> pdb=" O ILE A1091 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 72 through 74 removed outlier: 3.595A pdb=" N LYS B 72 " --> pdb=" O TYR B 274 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR B 74 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 144 through 148 removed outlier: 6.847A pdb=" N VAL B 120 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE B 147 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ALA B 122 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU B 99 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU B 123 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLU B 101 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N MET B 194 " --> pdb=" O CYS B 102 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL B 191 " --> pdb=" O ASN B 226 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N PHE B 228 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLY B 193 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL B 225 " --> pdb=" O MET B 301 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N MET B 301 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS B 264 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLN B 300 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL B 262 " --> pdb=" O GLN B 300 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ILE B 302 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ILE B 260 " --> pdb=" O ILE B 302 " (cutoff:3.500A) 709 hydrogen bonds defined for protein. 2061 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 204 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 3.25 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2173 1.32 - 1.44: 4379 1.44 - 1.56: 8255 1.56 - 1.69: 222 1.69 - 1.81: 118 Bond restraints: 15147 Sorted by residual: bond pdb=" C3' DC T 11 " pdb=" C2' DC T 11 " ideal model delta sigma weight residual 1.516 1.675 -0.159 8.00e-03 1.56e+04 3.97e+02 bond pdb=" C3' DG N 6 " pdb=" C2' DG N 6 " ideal model delta sigma weight residual 1.516 1.640 -0.124 8.00e-03 1.56e+04 2.39e+02 bond pdb=" C3' DT T 47 " pdb=" C2' DT T 47 " ideal model delta sigma weight residual 1.516 1.629 -0.113 8.00e-03 1.56e+04 1.99e+02 bond pdb=" O3' DC N 30 " pdb=" P DA N 31 " ideal model delta sigma weight residual 1.607 1.406 0.201 1.50e-02 4.44e+03 1.79e+02 bond pdb=" C3' DC T 43 " pdb=" C2' DC T 43 " ideal model delta sigma weight residual 1.516 1.621 -0.105 8.00e-03 1.56e+04 1.71e+02 ... (remaining 15142 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.85: 20620 3.85 - 7.71: 287 7.71 - 11.56: 52 11.56 - 15.41: 9 15.41 - 19.26: 2 Bond angle restraints: 20970 Sorted by residual: angle pdb=" C3' DC T 9 " pdb=" O3' DC T 9 " pdb=" P DT T 10 " ideal model delta sigma weight residual 120.20 100.94 19.26 1.50e+00 4.44e-01 1.65e+02 angle pdb=" C3' DA T 31 " pdb=" O3' DA T 31 " pdb=" P DC T 32 " ideal model delta sigma weight residual 120.20 106.72 13.48 1.50e+00 4.44e-01 8.08e+01 angle pdb=" C4' DC T 11 " pdb=" C3' DC T 11 " pdb=" C2' DC T 11 " ideal model delta sigma weight residual 103.10 95.02 8.08 9.00e-01 1.23e+00 8.05e+01 angle pdb=" C3' DC T 11 " pdb=" O3' DC T 11 " pdb=" P DC T 12 " ideal model delta sigma weight residual 120.20 106.84 13.36 1.50e+00 4.44e-01 7.94e+01 angle pdb=" C5' DA N 48 " pdb=" C4' DA N 48 " pdb=" O4' DA N 48 " ideal model delta sigma weight residual 109.30 124.19 -14.89 1.90e+00 2.77e-01 6.14e+01 ... (remaining 20965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.13: 8486 35.13 - 70.26: 474 70.26 - 105.39: 13 105.39 - 140.52: 7 140.52 - 175.65: 2 Dihedral angle restraints: 8982 sinusoidal: 4360 harmonic: 4622 Sorted by residual: dihedral pdb=" O5' GTP R 101 " pdb=" O3A GTP R 101 " pdb=" PA GTP R 101 " pdb=" PB GTP R 101 " ideal model delta sinusoidal sigma weight residual -85.88 89.78 -175.65 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O3B GTP A1301 " pdb=" O3A GTP A1301 " pdb=" PB GTP A1301 " pdb=" PA GTP A1301 " ideal model delta sinusoidal sigma weight residual 291.08 148.86 142.22 1 2.00e+01 2.50e-03 4.30e+01 dihedral pdb=" O5' GTP A1301 " pdb=" O3A GTP A1301 " pdb=" PA GTP A1301 " pdb=" PB GTP A1301 " ideal model delta sinusoidal sigma weight residual -85.88 53.76 -139.63 1 2.00e+01 2.50e-03 4.23e+01 ... (remaining 8979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 2170 0.129 - 0.258: 70 0.258 - 0.387: 8 0.387 - 0.516: 38 0.516 - 0.645: 45 Chirality restraints: 2331 Sorted by residual: chirality pdb=" P DT N 3 " pdb=" OP1 DT N 3 " pdb=" OP2 DT N 3 " pdb=" O5' DT N 3 " both_signs ideal model delta sigma weight residual True 2.34 2.98 -0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" P DA T 0 " pdb=" OP1 DA T 0 " pdb=" OP2 DA T 0 " pdb=" O5' DA T 0 " both_signs ideal model delta sigma weight residual True 2.34 -2.97 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" P A R 102 " pdb=" OP1 A R 102 " pdb=" OP2 A R 102 " pdb=" O5' A R 102 " both_signs ideal model delta sigma weight residual True 2.17 -2.78 -0.61 2.00e-01 2.50e+01 9.29e+00 ... (remaining 2328 not shown) Planarity restraints: 2330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 500 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.50e+00 pdb=" C LEU A 500 " -0.041 2.00e-02 2.50e+03 pdb=" O LEU A 500 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA A 501 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 109 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.08e+00 pdb=" C VAL C 109 " -0.035 2.00e-02 2.50e+03 pdb=" O VAL C 109 " 0.013 2.00e-02 2.50e+03 pdb=" N TYR C 110 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 365 " -0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO A 366 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 366 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 366 " -0.026 5.00e-02 4.00e+02 ... (remaining 2327 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 367 2.70 - 3.25: 13406 3.25 - 3.80: 22652 3.80 - 4.35: 29580 4.35 - 4.90: 47515 Nonbonded interactions: 113520 Sorted by model distance: nonbonded pdb=" OE1 GLN C 64 " pdb=" NH2 ARG C 87 " model vdw 2.149 3.120 nonbonded pdb=" OD1 ASP A 922 " pdb="MG MG A1302 " model vdw 2.207 2.170 nonbonded pdb=" OD2 ASP A1151 " pdb="MG MG A1302 " model vdw 2.269 2.170 nonbonded pdb=" O LYS B 236 " pdb=" OG SER B 251 " model vdw 2.278 3.040 nonbonded pdb=" OD2 ASP A 801 " pdb=" NH1 ARG A 803 " model vdw 2.280 3.120 ... (remaining 113515 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=0.50 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: 0.330 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: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.700 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.040 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 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 : 0.008 0.201 15148 Z= 0.629 Angle : 1.147 19.264 20970 Z= 0.692 Chirality : 0.112 0.645 2331 Planarity : 0.005 0.062 2330 Dihedral : 18.464 175.653 5972 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.56 % Favored : 97.37 % Rotamer: Outliers : 0.45 % Allowed : 0.75 % Favored : 98.79 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.21), residues: 1564 helix: 1.84 (0.17), residues: 921 sheet: -0.38 (0.48), residues: 104 loop : -0.47 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 116 TYR 0.031 0.002 TYR A1100 PHE 0.022 0.002 PHE A1229 TRP 0.016 0.001 TRP C 189 HIS 0.011 0.001 HIS A 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00796 / 0.63 (15147) covalent geometry : angle 1.14696 / 0.69 (20970) hydrogen bonds : bond 0.16824 / 11.24 ( 811) hydrogen bonds : angle 6.00402 / 4.29 ( 2265) Misc. bond : bond 0.02660 / 1.40 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 178 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.8027 (mtt) cc_final: 0.7595 (mtt) REVERT: A 311 GLN cc_start: 0.7918 (tm-30) cc_final: 0.7640 (tm-30) REVERT: A 585 GLN cc_start: 0.8114 (mp10) cc_final: 0.7834 (mp10) REVERT: C 80 LEU cc_start: 0.8825 (mp) cc_final: 0.7902 (mt) REVERT: C 211 TYR cc_start: 0.7127 (m-10) cc_final: 0.6494 (t80) outliers start: 5 outliers final: 3 residues processed: 183 average time/residue: 0.1253 time to fit residues: 32.4393 Evaluate side-chains 157 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 154 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 78 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 50.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.0870 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1080 GLN C 137 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.151899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.108981 restraints weight = 24405.680| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.99 r_work: 0.3083 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15148 Z= 0.156 Angle : 0.656 14.152 20970 Z= 0.362 Chirality : 0.042 0.215 2331 Planarity : 0.006 0.127 2330 Dihedral : 20.889 173.881 2883 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.05 % Favored : 97.89 % Rotamer: Outliers : 1.06 % Allowed : 5.20 % Favored : 93.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.21), residues: 1564 helix: 1.98 (0.17), residues: 931 sheet: -0.30 (0.47), residues: 115 loop : -0.42 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 116 TYR 0.009 0.001 TYR A1100 PHE 0.018 0.002 PHE A1229 TRP 0.010 0.001 TRP C 189 HIS 0.008 0.001 HIS C 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.16 (15147) covalent geometry : angle 0.65636 / 0.36 (20970) hydrogen bonds : bond 0.06356 / 4.31 ( 811) hydrogen bonds : angle 3.99260 / 2.83 ( 2265) Misc. bond : bond 0.00102 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.506 Fit side-chains REVERT: A 263 MET cc_start: 0.8349 (mtt) cc_final: 0.7930 (mtt) REVERT: A 311 GLN cc_start: 0.8138 (tm-30) cc_final: 0.7177 (tm-30) REVERT: B 98 LEU cc_start: 0.8379 (tp) cc_final: 0.8088 (tt) REVERT: B 111 GLN cc_start: 0.7586 (tm-30) cc_final: 0.7352 (tm-30) REVERT: C 82 ARG cc_start: 0.9043 (ptm160) cc_final: 0.8683 (ttp-110) REVERT: C 109 VAL cc_start: 0.8737 (OUTLIER) cc_final: 0.8263 (p) REVERT: C 112 GLU cc_start: 0.8621 (tp30) cc_final: 0.7931 (mt-10) REVERT: C 116 ARG cc_start: 0.8503 (mtm110) cc_final: 0.8245 (mtm-85) REVERT: C 211 TYR cc_start: 0.7580 (m-10) cc_final: 0.6701 (t80) outliers start: 13 outliers final: 5 residues processed: 163 average time/residue: 0.1246 time to fit residues: 28.9695 Evaluate side-chains 153 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 147 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 MET Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 151 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 33 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 48 optimal weight: 0.0670 chunk 38 optimal weight: 5.9990 chunk 153 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.150605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.110583 restraints weight = 40514.015| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.49 r_work: 0.2968 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15148 Z= 0.152 Angle : 0.591 8.048 20970 Z= 0.327 Chirality : 0.040 0.253 2331 Planarity : 0.006 0.117 2330 Dihedral : 20.628 154.973 2883 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.43 % Favored : 97.50 % Rotamer: Outliers : 1.58 % Allowed : 6.56 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.21), residues: 1564 helix: 2.00 (0.17), residues: 936 sheet: -0.26 (0.48), residues: 110 loop : -0.43 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 477 TYR 0.014 0.001 TYR B 247 PHE 0.019 0.002 PHE A 802 TRP 0.011 0.001 TRP A1154 HIS 0.007 0.001 HIS C 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (15147) covalent geometry : angle 0.59084 / 0.33 (20970) hydrogen bonds : bond 0.05731 / 3.85 ( 811) hydrogen bonds : angle 3.68742 / 2.64 ( 2265) Misc. bond : bond 0.00047 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.480 Fit side-chains REVERT: A 263 MET cc_start: 0.8282 (mtt) cc_final: 0.7835 (mtt) REVERT: A 589 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8841 (ptm) REVERT: C 82 ARG cc_start: 0.8919 (ptm160) cc_final: 0.8581 (ttp-110) REVERT: C 83 ARG cc_start: 0.8241 (mtm-85) cc_final: 0.7640 (mtm-85) REVERT: C 87 ARG cc_start: 0.8621 (ptt180) cc_final: 0.8006 (ptt180) REVERT: C 112 GLU cc_start: 0.8599 (tp30) cc_final: 0.7895 (mt-10) REVERT: C 116 ARG cc_start: 0.8521 (mtm110) cc_final: 0.8250 (mtm-85) REVERT: C 211 TYR cc_start: 0.7610 (m-10) cc_final: 0.6685 (t80) REVERT: C 222 MET cc_start: 0.9361 (mmp) cc_final: 0.9078 (mmm) outliers start: 20 outliers final: 11 residues processed: 165 average time/residue: 0.1347 time to fit residues: 31.8626 Evaluate side-chains 162 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 MET Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 151 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 148 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.150027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.108661 restraints weight = 32855.963| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.70 r_work: 0.3014 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15148 Z= 0.161 Angle : 0.602 15.522 20970 Z= 0.332 Chirality : 0.040 0.228 2331 Planarity : 0.005 0.051 2330 Dihedral : 20.369 136.636 2883 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.63 % Favored : 97.31 % Rotamer: Outliers : 1.51 % Allowed : 7.69 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.21), residues: 1564 helix: 2.04 (0.17), residues: 936 sheet: -0.34 (0.48), residues: 110 loop : -0.46 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 803 TYR 0.013 0.001 TYR C 110 PHE 0.028 0.002 PHE C 68 TRP 0.009 0.001 TRP A 553 HIS 0.008 0.001 HIS C 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (15147) covalent geometry : angle 0.60179 / 0.33 (20970) hydrogen bonds : bond 0.05626 / 3.81 ( 811) hydrogen bonds : angle 3.68620 / 2.63 ( 2265) Misc. bond : bond 0.00090 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.503 Fit side-chains REVERT: A 263 MET cc_start: 0.8228 (mtt) cc_final: 0.7779 (mtt) REVERT: A 589 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8867 (ptm) REVERT: A 981 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6741 (pp) REVERT: B 98 LEU cc_start: 0.8200 (tp) cc_final: 0.7961 (tt) REVERT: B 157 ARG cc_start: 0.7542 (mpt180) cc_final: 0.7286 (mmt90) REVERT: C 83 ARG cc_start: 0.8124 (mtm-85) cc_final: 0.7860 (ptm160) REVERT: C 109 VAL cc_start: 0.8628 (OUTLIER) cc_final: 0.8418 (m) REVERT: C 112 GLU cc_start: 0.8576 (tp30) cc_final: 0.7861 (mt-10) REVERT: C 116 ARG cc_start: 0.8524 (mtm110) cc_final: 0.8246 (mtm-85) REVERT: C 148 GLU cc_start: 0.9151 (OUTLIER) cc_final: 0.8663 (pp20) REVERT: C 211 TYR cc_start: 0.7550 (m-10) cc_final: 0.6667 (t80) REVERT: C 222 MET cc_start: 0.9346 (mmp) cc_final: 0.9023 (mmm) outliers start: 19 outliers final: 11 residues processed: 166 average time/residue: 0.1277 time to fit residues: 30.9168 Evaluate side-chains 163 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 MET Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 151 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 78 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 139 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 GLN B 175 ASN ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.152519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.110876 restraints weight = 34261.865| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.90 r_work: 0.3042 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15148 Z= 0.129 Angle : 0.554 8.949 20970 Z= 0.308 Chirality : 0.038 0.238 2331 Planarity : 0.005 0.076 2330 Dihedral : 20.014 116.864 2883 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.43 % Favored : 97.50 % Rotamer: Outliers : 1.66 % Allowed : 7.84 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.22), residues: 1564 helix: 2.23 (0.17), residues: 930 sheet: -0.20 (0.48), residues: 110 loop : -0.37 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 82 TYR 0.018 0.001 TYR C 110 PHE 0.023 0.001 PHE C 117 TRP 0.008 0.001 TRP A1070 HIS 0.007 0.001 HIS C 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.13 (15147) covalent geometry : angle 0.55360 / 0.31 (20970) hydrogen bonds : bond 0.04889 / 3.31 ( 811) hydrogen bonds : angle 3.47165 / 2.48 ( 2265) Misc. bond : bond 0.00082 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 263 MET cc_start: 0.8154 (mtt) cc_final: 0.7695 (mtt) REVERT: A 981 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6687 (pp) REVERT: B 157 ARG cc_start: 0.7517 (mpt180) cc_final: 0.7290 (mmt90) REVERT: C 68 PHE cc_start: 0.6269 (OUTLIER) cc_final: 0.5780 (t80) REVERT: C 112 GLU cc_start: 0.8586 (tp30) cc_final: 0.7812 (mt-10) REVERT: C 116 ARG cc_start: 0.8545 (mtm110) cc_final: 0.8243 (mtm-85) REVERT: C 121 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6726 (pt) REVERT: C 148 GLU cc_start: 0.9121 (OUTLIER) cc_final: 0.8627 (pp20) REVERT: C 211 TYR cc_start: 0.7505 (m-10) cc_final: 0.6637 (t80) REVERT: C 222 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.8986 (mmm) outliers start: 21 outliers final: 11 residues processed: 168 average time/residue: 0.1412 time to fit residues: 34.0300 Evaluate side-chains 167 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1063 HIS Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 222 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 144 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 110 optimal weight: 50.0000 chunk 10 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.151896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.111115 restraints weight = 35731.406| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.97 r_work: 0.3038 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15148 Z= 0.134 Angle : 0.572 11.329 20970 Z= 0.313 Chirality : 0.039 0.243 2331 Planarity : 0.005 0.050 2330 Dihedral : 19.834 117.121 2883 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.24 % Favored : 97.69 % Rotamer: Outliers : 1.81 % Allowed : 8.22 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.22), residues: 1564 helix: 2.26 (0.17), residues: 932 sheet: -0.15 (0.48), residues: 108 loop : -0.41 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG C 82 TYR 0.026 0.001 TYR C 110 PHE 0.018 0.001 PHE C 68 TRP 0.008 0.001 TRP A 553 HIS 0.005 0.001 HIS C 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (15147) covalent geometry : angle 0.57199 / 0.31 (20970) hydrogen bonds : bond 0.04860 / 3.28 ( 811) hydrogen bonds : angle 3.47972 / 2.48 ( 2265) Misc. bond : bond 0.00078 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.552 Fit side-chains REVERT: A 263 MET cc_start: 0.8190 (mtt) cc_final: 0.7759 (mtt) REVERT: A 981 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6652 (pp) REVERT: B 157 ARG cc_start: 0.7494 (mpt180) cc_final: 0.7285 (mmt90) REVERT: C 68 PHE cc_start: 0.6161 (OUTLIER) cc_final: 0.5955 (t80) REVERT: C 83 ARG cc_start: 0.8289 (mtm-85) cc_final: 0.7724 (mtm110) REVERT: C 112 GLU cc_start: 0.8545 (tp30) cc_final: 0.7832 (mt-10) REVERT: C 116 ARG cc_start: 0.8548 (mtm110) cc_final: 0.8249 (mtm-85) REVERT: C 127 MET cc_start: 0.7653 (mmm) cc_final: 0.7021 (ptp) REVERT: C 148 GLU cc_start: 0.9132 (OUTLIER) cc_final: 0.8643 (pp20) REVERT: C 211 TYR cc_start: 0.7500 (m-10) cc_final: 0.6616 (t80) outliers start: 23 outliers final: 16 residues processed: 158 average time/residue: 0.1341 time to fit residues: 30.3218 Evaluate side-chains 167 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1063 HIS Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 151 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 5 optimal weight: 20.0000 chunk 94 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 0 optimal weight: 40.0000 chunk 63 optimal weight: 3.9990 chunk 9 optimal weight: 0.1980 chunk 118 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 249 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.149757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.106218 restraints weight = 25206.329| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.19 r_work: 0.3043 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15148 Z= 0.167 Angle : 0.597 12.376 20970 Z= 0.325 Chirality : 0.040 0.268 2331 Planarity : 0.005 0.049 2330 Dihedral : 19.739 116.781 2881 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.56 % Favored : 97.37 % Rotamer: Outliers : 1.81 % Allowed : 8.60 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.22), residues: 1564 helix: 2.17 (0.17), residues: 932 sheet: -0.33 (0.48), residues: 110 loop : -0.46 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG C 82 TYR 0.026 0.002 TYR C 110 PHE 0.020 0.002 PHE A 802 TRP 0.009 0.001 TRP C 189 HIS 0.006 0.001 HIS A 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (15147) covalent geometry : angle 0.59743 / 0.32 (20970) hydrogen bonds : bond 0.05386 / 3.62 ( 811) hydrogen bonds : angle 3.58385 / 2.57 ( 2265) Misc. bond : bond 0.00077 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 263 MET cc_start: 0.8445 (mtt) cc_final: 0.8002 (mtt) REVERT: A 981 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6668 (pp) REVERT: B 157 ARG cc_start: 0.7640 (mpt180) cc_final: 0.7424 (mmt90) REVERT: C 68 PHE cc_start: 0.6079 (OUTLIER) cc_final: 0.5807 (t80) REVERT: C 112 GLU cc_start: 0.8613 (tp30) cc_final: 0.7890 (mt-10) REVERT: C 116 ARG cc_start: 0.8552 (mtm110) cc_final: 0.8245 (mtm-85) REVERT: C 127 MET cc_start: 0.7722 (mmm) cc_final: 0.7169 (ptp) REVERT: C 148 GLU cc_start: 0.9158 (OUTLIER) cc_final: 0.8669 (pp20) REVERT: C 211 TYR cc_start: 0.7528 (m-10) cc_final: 0.6613 (t80) outliers start: 23 outliers final: 14 residues processed: 163 average time/residue: 0.1367 time to fit residues: 32.0065 Evaluate side-chains 163 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1063 HIS Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 230 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 120 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 157 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 GLN A 679 GLN A1080 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.147993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.107682 restraints weight = 31498.303| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.77 r_work: 0.2974 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15148 Z= 0.218 Angle : 0.651 17.195 20970 Z= 0.349 Chirality : 0.042 0.289 2331 Planarity : 0.005 0.048 2330 Dihedral : 19.771 116.287 2881 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.14 % Favored : 96.80 % Rotamer: Outliers : 1.66 % Allowed : 9.58 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.21), residues: 1564 helix: 1.95 (0.17), residues: 932 sheet: -0.64 (0.50), residues: 102 loop : -0.59 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 82 TYR 0.029 0.002 TYR C 110 PHE 0.025 0.002 PHE A1229 TRP 0.011 0.001 TRP C 189 HIS 0.010 0.001 HIS C 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.22 (15147) covalent geometry : angle 0.65148 / 0.35 (20970) hydrogen bonds : bond 0.06048 / 4.05 ( 811) hydrogen bonds : angle 3.75970 / 2.71 ( 2265) Misc. bond : bond 0.00076 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.359 Fit side-chains REVERT: A 263 MET cc_start: 0.8384 (mtt) cc_final: 0.7974 (mtt) REVERT: A 981 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6771 (pp) REVERT: B 157 ARG cc_start: 0.7512 (mpt180) cc_final: 0.7273 (mmt90) REVERT: C 68 PHE cc_start: 0.6158 (OUTLIER) cc_final: 0.5787 (t80) REVERT: C 83 ARG cc_start: 0.8423 (mtm-85) cc_final: 0.7777 (ttm110) REVERT: C 112 GLU cc_start: 0.8598 (tp30) cc_final: 0.7914 (mt-10) REVERT: C 116 ARG cc_start: 0.8538 (mtm110) cc_final: 0.8256 (mtm-85) REVERT: C 127 MET cc_start: 0.7783 (mmm) cc_final: 0.7238 (ptp) REVERT: C 148 GLU cc_start: 0.9150 (OUTLIER) cc_final: 0.8669 (pp20) REVERT: C 211 TYR cc_start: 0.7519 (m-10) cc_final: 0.6608 (t80) outliers start: 21 outliers final: 14 residues processed: 159 average time/residue: 0.1296 time to fit residues: 30.0311 Evaluate side-chains 164 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1063 HIS Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 300 GLN Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 151 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 136 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1080 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 = 0.3868 r_free = 0.3868 target = 0.152130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.111526 restraints weight = 41382.793| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 3.54 r_work: 0.3005 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15148 Z= 0.131 Angle : 0.582 13.753 20970 Z= 0.321 Chirality : 0.038 0.253 2331 Planarity : 0.005 0.061 2330 Dihedral : 19.663 119.103 2881 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.31 % Favored : 97.63 % Rotamer: Outliers : 1.06 % Allowed : 9.80 % Favored : 89.14 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.22), residues: 1564 helix: 2.29 (0.17), residues: 931 sheet: -0.36 (0.51), residues: 100 loop : -0.50 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 82 TYR 0.037 0.001 TYR C 110 PHE 0.019 0.001 PHE C 68 TRP 0.011 0.001 TRP A1154 HIS 0.008 0.001 HIS C 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.13 (15147) covalent geometry : angle 0.58170 / 0.32 (20970) hydrogen bonds : bond 0.04648 / 3.14 ( 811) hydrogen bonds : angle 3.48228 / 2.50 ( 2265) Misc. bond : bond 0.00075 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 263 MET cc_start: 0.8248 (mtt) cc_final: 0.7815 (mtt) REVERT: A 981 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6647 (pp) REVERT: B 111 GLN cc_start: 0.7521 (tm-30) cc_final: 0.7278 (pt0) REVERT: C 112 GLU cc_start: 0.8579 (tp30) cc_final: 0.7928 (mt-10) REVERT: C 116 ARG cc_start: 0.8481 (mtm110) cc_final: 0.8233 (mtm-85) REVERT: C 126 ILE cc_start: 0.7745 (OUTLIER) cc_final: 0.7214 (pt) REVERT: C 127 MET cc_start: 0.7660 (mmm) cc_final: 0.7092 (ptp) REVERT: C 148 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8627 (pp20) REVERT: C 211 TYR cc_start: 0.7541 (m-10) cc_final: 0.6603 (t80) outliers start: 13 outliers final: 8 residues processed: 154 average time/residue: 0.1258 time to fit residues: 28.0976 Evaluate side-chains 154 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1063 HIS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 300 GLN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 151 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 42 optimal weight: 0.7980 chunk 121 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 162 optimal weight: 6.9990 chunk 148 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 69 optimal weight: 0.5980 chunk 13 optimal weight: 8.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1080 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.149256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.105970 restraints weight = 32885.020| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.62 r_work: 0.2987 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15148 Z= 0.181 Angle : 0.626 14.401 20970 Z= 0.337 Chirality : 0.040 0.215 2331 Planarity : 0.005 0.049 2330 Dihedral : 19.664 117.380 2881 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.82 % Favored : 97.12 % Rotamer: Outliers : 1.21 % Allowed : 9.58 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.22), residues: 1564 helix: 2.16 (0.17), residues: 932 sheet: -0.49 (0.50), residues: 102 loop : -0.56 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 82 TYR 0.028 0.002 TYR C 110 PHE 0.020 0.002 PHE A 802 TRP 0.010 0.001 TRP C 189 HIS 0.008 0.001 HIS C 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (15147) covalent geometry : angle 0.62592 / 0.34 (20970) hydrogen bonds : bond 0.05458 / 3.67 ( 811) hydrogen bonds : angle 3.62641 / 2.59 ( 2265) Misc. bond : bond 0.00076 / 0.04 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 263 MET cc_start: 0.8364 (mtt) cc_final: 0.7923 (mtt) REVERT: A 981 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6777 (pp) REVERT: B 111 GLN cc_start: 0.7562 (tm-30) cc_final: 0.7359 (pt0) REVERT: C 83 ARG cc_start: 0.8264 (mtm-85) cc_final: 0.7894 (ptp90) REVERT: C 87 ARG cc_start: 0.8760 (ptt180) cc_final: 0.8553 (ptt-90) REVERT: C 112 GLU cc_start: 0.8572 (tp30) cc_final: 0.7916 (mt-10) REVERT: C 116 ARG cc_start: 0.8449 (mtm110) cc_final: 0.8214 (mtm-85) REVERT: C 126 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7234 (pt) REVERT: C 127 MET cc_start: 0.7694 (mmm) cc_final: 0.7072 (ptp) REVERT: C 148 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8647 (pp20) REVERT: C 211 TYR cc_start: 0.7537 (m-10) cc_final: 0.6591 (t80) outliers start: 15 outliers final: 10 residues processed: 150 average time/residue: 0.1163 time to fit residues: 25.4688 Evaluate side-chains 154 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1063 HIS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 300 GLN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 151 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 87 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 127 optimal weight: 0.0570 chunk 17 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 110 optimal weight: 50.0000 chunk 98 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 overall best weight: 1.2902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.151947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.108571 restraints weight = 26267.061| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.11 r_work: 0.3074 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15148 Z= 0.133 Angle : 0.578 11.226 20970 Z= 0.316 Chirality : 0.038 0.293 2331 Planarity : 0.005 0.049 2330 Dihedral : 19.536 118.986 2881 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.43 % Favored : 97.50 % Rotamer: Outliers : 1.06 % Allowed : 9.80 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.22), residues: 1564 helix: 2.30 (0.17), residues: 931 sheet: -0.33 (0.51), residues: 100 loop : -0.54 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 82 TYR 0.046 0.001 TYR C 110 PHE 0.011 0.001 PHE C 117 TRP 0.010 0.001 TRP C 189 HIS 0.008 0.001 HIS C 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 (15147) covalent geometry : angle 0.57782 / 0.32 (20970) hydrogen bonds : bond 0.04630 / 3.13 ( 811) hydrogen bonds : angle 3.47663 / 2.49 ( 2265) Misc. bond : bond 0.00079 / 0.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3507.00 seconds wall clock time: 60 minutes 50.84 seconds (3650.84 seconds total)