Starting phenix.real_space_refine on Thu Aug 6 09:37:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gzm_51727/08_2026/9gzm_51727.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gzm_51727/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9gzm_51727/08_2026/9gzm_51727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gzm_51727/08_2026/9gzm_51727.map" model { file = "/net/cci-nas-00/data/ceres_data/9gzm_51727/08_2026/9gzm_51727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gzm_51727/08_2026/9gzm_51727.cif" } 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-2.2rc3-6140/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: 4.58, per 1000 atoms: 0.31 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: 1.34 Conformation dependent library (CDL) restraints added in 696.1 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: 1.38 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: 3.12 Time building geometry restraints manager: 1.75 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=" O3' DC N 30 " pdb=" P DA N 31 " ideal model delta sigma weight residual 1.607 1.406 0.201 1.20e-02 6.94e+03 2.80e+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=" 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 - 3.75: 20597 3.75 - 7.51: 306 7.51 - 11.26: 54 11.26 - 15.01: 10 15.01 - 18.76: 3 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 119.70 100.94 18.76 1.20e+00 6.94e-01 2.45e+02 angle pdb=" C3' DA T 31 " pdb=" O3' DA T 31 " pdb=" P DC T 32 " ideal model delta sigma weight residual 119.70 106.72 12.98 1.20e+00 6.94e-01 1.17e+02 angle pdb=" C3' DC T 11 " pdb=" O3' DC T 11 " pdb=" P DC T 12 " ideal model delta sigma weight residual 119.70 106.84 12.86 1.20e+00 6.94e-01 1.15e+02 angle pdb=" C3' DC T 41 " pdb=" O3' DC T 41 " pdb=" P DC T 42 " ideal model delta sigma weight residual 119.70 131.33 -11.63 1.20e+00 6.94e-01 9.40e+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 ... (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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.310 Find NCS groups from input model: 0.080 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.950 ------------------------------------------------------------------------------- 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= 0.639 Angle : 1.143 18.764 20970 Z= 0.707 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 / 0.64 (15147) covalent geometry : angle 1.14288 / 0.71 (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 : 0.514 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: 0.1347 time to fit residues: 35.1587 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 : 0.508 ------------------------------------------------------------------------------- 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: 10.0000 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1080 GLN B 175 ASN C 137 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.151950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.108410 restraints weight = 24393.945| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.23 r_work: 0.3044 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15148 Z= 0.160 Angle : 0.653 13.619 20970 Z= 0.360 Chirality : 0.042 0.207 2331 Planarity : 0.006 0.128 2330 Dihedral : 20.873 173.953 2883 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.99 % Favored : 97.95 % Rotamer: Outliers : 1.13 % Allowed : 5.13 % 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 0.008 0.000 ARG C 116 TYR 0.009 0.001 TYR A1100 PHE 0.017 0.002 PHE A1229 TRP 0.012 0.001 TRP C 189 HIS 0.008 0.001 HIS C 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.16 (15147) covalent geometry : angle 0.65278 / 0.36 (20970) hydrogen bonds : bond 0.06344 / 4.30 ( 811) hydrogen bonds : angle 3.98492 / 2.82 ( 2265) Misc. bond : bond 0.00167 / 0.09 ( 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 172 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.477 Fit side-chains REVERT: A 263 MET cc_start: 0.8196 (mtt) cc_final: 0.7767 (mtt) REVERT: A 311 GLN cc_start: 0.8120 (tm-30) cc_final: 0.7183 (tm-30) REVERT: B 98 LEU cc_start: 0.8214 (tp) cc_final: 0.7905 (tt) REVERT: C 82 ARG cc_start: 0.9036 (ptm160) cc_final: 0.8798 (ttp80) REVERT: C 109 VAL cc_start: 0.8708 (OUTLIER) cc_final: 0.8240 (p) REVERT: C 112 GLU cc_start: 0.8607 (tp30) cc_final: 0.7911 (mt-10) REVERT: C 116 ARG cc_start: 0.8497 (mtm110) cc_final: 0.8240 (mtm-85) REVERT: C 211 TYR cc_start: 0.7567 (m-10) cc_final: 0.6701 (t80) outliers start: 14 outliers final: 6 residues processed: 164 average time/residue: 0.1289 time to fit residues: 29.8819 Evaluate side-chains 154 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 147 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 67 ILE 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: 0.9990 chunk 105 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 39 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 48 optimal weight: 0.0470 chunk 38 optimal weight: 5.9990 chunk 153 optimal weight: 20.0000 chunk 49 optimal weight: 0.3980 overall best weight: 0.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 GLN A 893 GLN ** A1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.153883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.114536 restraints weight = 40913.812| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 3.60 r_work: 0.3033 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 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 = 0.3039 r_free = 0.3039 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: 0.3039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 15148 Z= 0.130 Angle : 0.572 8.960 20970 Z= 0.318 Chirality : 0.039 0.269 2331 Planarity : 0.006 0.121 2330 Dihedral : 20.505 155.246 2883 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.50 % Favored : 97.44 % Rotamer: Outliers : 1.43 % Allowed : 6.26 % Favored : 92.31 % 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 (0.21), residues: 1564 helix: 2.21 (0.17), residues: 927 sheet: -0.05 (0.47), residues: 110 loop : -0.35 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 477 TYR 0.022 0.001 TYR C 110 PHE 0.010 0.001 PHE A 802 TRP 0.013 0.001 TRP A1154 HIS 0.006 0.001 HIS C 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.13 (15147) covalent geometry : angle 0.57248 / 0.32 (20970) hydrogen bonds : bond 0.05023 / 3.38 ( 811) hydrogen bonds : angle 3.53365 / 2.52 ( 2265) Misc. bond : bond 0.00070 / 0.04 ( 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 182 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 263 MET cc_start: 0.8218 (mtt) cc_final: 0.7757 (mtt) REVERT: A 342 GLU cc_start: 0.8167 (tp30) cc_final: 0.7956 (tp30) REVERT: A 589 MET cc_start: 0.9082 (ttp) cc_final: 0.8808 (ptm) REVERT: B 225 VAL cc_start: 0.8757 (OUTLIER) cc_final: 0.8555 (p) REVERT: C 82 ARG cc_start: 0.8889 (ptm160) cc_final: 0.8537 (ttp-110) REVERT: C 83 ARG cc_start: 0.8181 (mtm-85) cc_final: 0.7693 (ptt180) REVERT: C 87 ARG cc_start: 0.8591 (ptt180) cc_final: 0.8387 (ptt-90) REVERT: C 112 GLU cc_start: 0.8582 (tp30) cc_final: 0.7819 (mt-10) REVERT: C 116 ARG cc_start: 0.8522 (mtm110) cc_final: 0.8140 (mtm-85) REVERT: C 211 TYR cc_start: 0.7536 (m-10) cc_final: 0.6677 (t80) REVERT: C 222 MET cc_start: 0.9359 (mmp) cc_final: 0.9077 (mmm) outliers start: 18 outliers final: 11 residues processed: 171 average time/residue: 0.1155 time to fit residues: 28.0226 Evaluate side-chains 159 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 1103 ASN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 225 VAL 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 Chi-restraints excluded: chain C residue 230 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 148 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 893 GLN B 235 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.152921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.111850 restraints weight = 32951.535| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.82 r_work: 0.3060 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15148 Z= 0.135 Angle : 0.576 15.589 20970 Z= 0.314 Chirality : 0.039 0.228 2331 Planarity : 0.005 0.050 2330 Dihedral : 20.187 135.244 2883 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.37 % Favored : 97.57 % Rotamer: Outliers : 1.36 % Allowed : 7.47 % Favored : 91.18 % 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: 1.86 (0.21), residues: 1564 helix: 2.27 (0.17), residues: 930 sheet: -0.03 (0.47), residues: 110 loop : -0.37 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 83 TYR 0.029 0.001 TYR C 110 PHE 0.022 0.001 PHE C 117 TRP 0.009 0.001 TRP A 553 HIS 0.006 0.001 HIS C 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 (15147) covalent geometry : angle 0.57573 / 0.31 (20970) hydrogen bonds : bond 0.04959 / 3.36 ( 811) hydrogen bonds : angle 3.51393 / 2.51 ( 2265) Misc. bond : bond 0.00098 / 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 167 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.8175 (mtt) cc_final: 0.7735 (mtt) REVERT: A 589 MET cc_start: 0.9085 (ttp) cc_final: 0.8817 (ptm) REVERT: A 981 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6654 (pp) REVERT: B 157 ARG cc_start: 0.7528 (mpt180) cc_final: 0.7284 (mmt90) REVERT: C 112 GLU cc_start: 0.8520 (tp30) cc_final: 0.7828 (mt-10) REVERT: C 116 ARG cc_start: 0.8518 (mtm110) cc_final: 0.8227 (mtm-85) REVERT: C 148 GLU cc_start: 0.9127 (OUTLIER) cc_final: 0.8640 (pp20) REVERT: C 211 TYR cc_start: 0.7518 (m-10) cc_final: 0.6658 (t80) REVERT: C 222 MET cc_start: 0.9306 (mmp) cc_final: 0.9019 (mmm) outliers start: 17 outliers final: 9 residues processed: 156 average time/residue: 0.1365 time to fit residues: 30.7267 Evaluate side-chains 153 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 390 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 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: 4.9990 chunk 10 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 161 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 23 optimal weight: 0.4980 chunk 139 optimal weight: 8.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 249 HIS ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.148944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.109094 restraints weight = 34308.163| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.95 r_work: 0.2983 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15148 Z= 0.196 Angle : 0.628 9.962 20970 Z= 0.343 Chirality : 0.042 0.258 2331 Planarity : 0.005 0.049 2330 Dihedral : 20.010 115.244 2883 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.88 % Favored : 97.05 % Rotamer: Outliers : 1.73 % Allowed : 7.99 % Favored : 90.27 % 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: 1.58 (0.21), residues: 1564 helix: 2.07 (0.17), residues: 930 sheet: -0.35 (0.48), residues: 110 loop : -0.50 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 82 TYR 0.018 0.002 TYR B 247 PHE 0.027 0.002 PHE A1229 TRP 0.011 0.001 TRP A 553 HIS 0.010 0.002 HIS C 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (15147) covalent geometry : angle 0.62843 / 0.34 (20970) hydrogen bonds : bond 0.06000 / 4.03 ( 811) hydrogen bonds : angle 3.69471 / 2.66 ( 2265) Misc. bond : bond 0.00056 / 0.03 ( 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 179 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.508 Fit side-chains REVERT: A 263 MET cc_start: 0.8327 (mtt) cc_final: 0.7924 (mtt) REVERT: A 589 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8905 (ptm) REVERT: A 981 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6641 (pp) REVERT: B 157 ARG cc_start: 0.7564 (mpt180) cc_final: 0.7292 (mmt90) REVERT: C 83 ARG cc_start: 0.8034 (mtm-85) cc_final: 0.7679 (ptp-170) REVERT: C 112 GLU cc_start: 0.8550 (tp30) cc_final: 0.7947 (mt-10) REVERT: C 116 ARG cc_start: 0.8529 (mtm110) cc_final: 0.8244 (mtm-85) REVERT: C 148 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.8660 (pp20) REVERT: C 211 TYR cc_start: 0.7519 (m-10) cc_final: 0.6642 (t80) outliers start: 22 outliers final: 11 residues processed: 165 average time/residue: 0.1260 time to fit residues: 30.2706 Evaluate side-chains 162 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 144 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 110 optimal weight: 50.0000 chunk 10 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 GLN 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 = 0.149727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.108845 restraints weight = 36614.517| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.29 r_work: 0.2970 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1832 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= 0.161 Angle : 0.601 10.979 20970 Z= 0.326 Chirality : 0.040 0.256 2331 Planarity : 0.005 0.048 2330 Dihedral : 19.888 116.647 2883 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.50 % Favored : 97.44 % Rotamer: Outliers : 1.51 % Allowed : 8.75 % Favored : 89.74 % 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: 1.61 (0.21), residues: 1564 helix: 2.10 (0.17), residues: 932 sheet: -0.28 (0.49), residues: 108 loop : -0.49 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 82 TYR 0.026 0.001 TYR C 110 PHE 0.018 0.002 PHE A1229 TRP 0.009 0.001 TRP A 885 HIS 0.006 0.001 HIS C 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (15147) covalent geometry : angle 0.60109 / 0.33 (20970) hydrogen bonds : bond 0.05498 / 3.69 ( 811) hydrogen bonds : angle 3.60675 / 2.59 ( 2265) Misc. bond : bond 0.00053 / 0.03 ( 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 169 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 263 MET cc_start: 0.8337 (mtt) cc_final: 0.7895 (mtt) REVERT: A 981 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6650 (pp) REVERT: B 157 ARG cc_start: 0.7599 (mpt180) cc_final: 0.7338 (mmt90) REVERT: C 110 TYR cc_start: 0.8344 (t80) cc_final: 0.8118 (t80) REVERT: C 112 GLU cc_start: 0.8556 (tp30) cc_final: 0.7986 (mt-10) REVERT: C 116 ARG cc_start: 0.8511 (mtm110) cc_final: 0.8182 (mtm-85) REVERT: C 127 MET cc_start: 0.7857 (mmm) cc_final: 0.7003 (ptp) REVERT: C 148 GLU cc_start: 0.9150 (OUTLIER) cc_final: 0.8672 (pp20) REVERT: C 211 TYR cc_start: 0.7516 (m-10) cc_final: 0.6628 (t80) outliers start: 19 outliers final: 12 residues processed: 158 average time/residue: 0.1245 time to fit residues: 28.7043 Evaluate side-chains 160 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 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 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 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: 10.0000 chunk 94 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 63 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 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 = 0.3842 r_free = 0.3842 target = 0.149849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.105832 restraints weight = 25416.153| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.34 r_work: 0.2993 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 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 = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1947 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= 0.158 Angle : 0.613 17.265 20970 Z= 0.330 Chirality : 0.040 0.275 2331 Planarity : 0.005 0.049 2330 Dihedral : 19.751 116.825 2881 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.75 % Favored : 97.18 % Rotamer: Outliers : 1.51 % Allowed : 9.13 % Favored : 89.37 % 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: 2.12 (0.17), residues: 932 sheet: -0.32 (0.49), residues: 108 loop : -0.51 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 83 TYR 0.016 0.001 TYR C 57 PHE 0.020 0.002 PHE C 68 TRP 0.008 0.001 TRP A 885 HIS 0.006 0.001 HIS C 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (15147) covalent geometry : angle 0.61284 / 0.33 (20970) hydrogen bonds : bond 0.05371 / 3.60 ( 811) hydrogen bonds : angle 3.58745 / 2.57 ( 2265) Misc. bond : bond 0.00063 / 0.03 ( 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 169 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 263 MET cc_start: 0.8322 (mtt) cc_final: 0.7867 (mtt) REVERT: A 981 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6664 (pp) REVERT: B 157 ARG cc_start: 0.7517 (mpt180) cc_final: 0.7314 (mmt90) REVERT: C 112 GLU cc_start: 0.8512 (tp30) cc_final: 0.7955 (mt-10) REVERT: C 116 ARG cc_start: 0.8479 (mtm110) cc_final: 0.8189 (mtm-85) REVERT: C 127 MET cc_start: 0.7768 (mmm) cc_final: 0.6927 (ptp) REVERT: C 148 GLU cc_start: 0.9119 (OUTLIER) cc_final: 0.8655 (pp20) REVERT: C 211 TYR cc_start: 0.7504 (m-10) cc_final: 0.6602 (t80) outliers start: 19 outliers final: 13 residues processed: 159 average time/residue: 0.1239 time to fit residues: 28.3117 Evaluate side-chains 160 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 997 VAL Chi-restraints excluded: chain A residue 1063 HIS 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 300 GLN 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 149 LEU Chi-restraints excluded: chain C residue 151 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 120 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 152 optimal weight: 0.2980 chunk 28 optimal weight: 9.9990 chunk 127 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 157 optimal weight: 20.0000 chunk 94 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 74 optimal weight: 0.0570 overall best weight: 1.8702 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.151324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.108491 restraints weight = 31699.776| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.52 r_work: 0.3036 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 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: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15148 Z= 0.137 Angle : 0.588 15.850 20970 Z= 0.317 Chirality : 0.039 0.284 2331 Planarity : 0.005 0.049 2330 Dihedral : 19.679 117.894 2881 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.31 % Favored : 97.63 % Rotamer: Outliers : 1.36 % Allowed : 9.28 % Favored : 89.37 % 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: 1.72 (0.22), residues: 1564 helix: 2.21 (0.17), residues: 932 sheet: -0.37 (0.50), residues: 102 loop : -0.48 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 83 TYR 0.031 0.001 TYR C 110 PHE 0.033 0.001 PHE C 68 TRP 0.010 0.001 TRP C 218 HIS 0.005 0.001 HIS C 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.14 (15147) covalent geometry : angle 0.58793 / 0.32 (20970) hydrogen bonds : bond 0.04926 / 3.31 ( 811) hydrogen bonds : angle 3.49559 / 2.51 ( 2265) Misc. bond : bond 0.00064 / 0.03 ( 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 165 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: A 263 MET cc_start: 0.8230 (mtt) cc_final: 0.7799 (mtt) REVERT: A 981 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6658 (pp) REVERT: C 112 GLU cc_start: 0.8460 (tp30) cc_final: 0.7926 (mt-10) REVERT: C 116 ARG cc_start: 0.8425 (mtm110) cc_final: 0.8169 (mtm-85) REVERT: C 148 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8626 (pp20) REVERT: C 211 TYR cc_start: 0.7499 (m-10) cc_final: 0.6607 (t80) outliers start: 17 outliers final: 14 residues processed: 155 average time/residue: 0.1310 time to fit residues: 29.7986 Evaluate side-chains 156 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 997 VAL Chi-restraints excluded: chain A residue 1063 HIS 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 300 GLN 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 149 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 230 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 136 optimal weight: 0.0040 chunk 29 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- 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 = 0.3877 r_free = 0.3877 target = 0.152642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.112149 restraints weight = 40920.505| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.52 r_work: 0.3023 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 15148 Z= 0.122 Angle : 0.569 14.426 20970 Z= 0.308 Chirality : 0.037 0.173 2331 Planarity : 0.005 0.050 2330 Dihedral : 19.572 118.898 2881 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.63 % Favored : 97.31 % Rotamer: Outliers : 1.21 % Allowed : 9.35 % Favored : 89.44 % 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: 1.84 (0.22), residues: 1564 helix: 2.33 (0.17), residues: 931 sheet: -0.27 (0.50), residues: 100 loop : -0.49 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 82 TYR 0.015 0.001 TYR C 110 PHE 0.015 0.001 PHE C 68 TRP 0.010 0.001 TRP C 218 HIS 0.005 0.001 HIS C 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.12 (15147) covalent geometry : angle 0.56934 / 0.31 (20970) hydrogen bonds : bond 0.04462 / 3.01 ( 811) hydrogen bonds : angle 3.37146 / 2.42 ( 2265) Misc. bond : bond 0.00073 / 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 163 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 263 MET cc_start: 0.8214 (mtt) cc_final: 0.7796 (mtt) REVERT: A 981 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6627 (pp) REVERT: C 87 ARG cc_start: 0.8731 (ptt180) cc_final: 0.7952 (ptt180) REVERT: C 112 GLU cc_start: 0.8516 (tp30) cc_final: 0.7973 (mt-10) REVERT: C 116 ARG cc_start: 0.8423 (mtm110) cc_final: 0.8192 (mtm-85) REVERT: C 127 MET cc_start: 0.7362 (mmm) cc_final: 0.6481 (ptp) REVERT: C 148 GLU cc_start: 0.9131 (OUTLIER) cc_final: 0.8619 (pp20) REVERT: C 211 TYR cc_start: 0.7522 (m-10) cc_final: 0.6577 (t80) outliers start: 15 outliers final: 12 residues processed: 154 average time/residue: 0.1308 time to fit residues: 29.8944 Evaluate side-chains 155 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 133 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 42 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 86 optimal weight: 9.9990 chunk 162 optimal weight: 6.9990 chunk 148 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 152 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 679 GLN B 111 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.151330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.108140 restraints weight = 32802.600| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.57 r_work: 0.3026 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15148 Z= 0.140 Angle : 0.581 14.695 20970 Z= 0.313 Chirality : 0.038 0.196 2331 Planarity : 0.005 0.049 2330 Dihedral : 19.534 118.395 2881 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.63 % Favored : 97.31 % Rotamer: Outliers : 1.21 % Allowed : 9.28 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.77 (0.22), residues: 1564 helix: 2.26 (0.17), residues: 931 sheet: -0.36 (0.49), residues: 102 loop : -0.48 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 82 TYR 0.027 0.001 TYR C 110 PHE 0.017 0.002 PHE A 802 TRP 0.010 0.001 TRP C 218 HIS 0.011 0.001 HIS C 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (15147) covalent geometry : angle 0.58148 / 0.31 (20970) hydrogen bonds : bond 0.04801 / 3.24 ( 811) hydrogen bonds : angle 3.43103 / 2.46 ( 2265) Misc. bond : bond 0.00073 / 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 152 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: A 263 MET cc_start: 0.8279 (mtt) cc_final: 0.7830 (mtt) REVERT: A 981 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6633 (pp) REVERT: C 112 GLU cc_start: 0.8451 (tp30) cc_final: 0.7949 (mt-10) REVERT: C 116 ARG cc_start: 0.8401 (mtm110) cc_final: 0.8167 (mtm-85) REVERT: C 127 MET cc_start: 0.7381 (mmm) cc_final: 0.6424 (ptp) REVERT: C 148 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8610 (pp20) REVERT: C 211 TYR cc_start: 0.7493 (m-10) cc_final: 0.6565 (t80) outliers start: 15 outliers final: 12 residues processed: 144 average time/residue: 0.1315 time to fit residues: 28.0308 Evaluate side-chains 150 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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 133 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 87 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 110 optimal weight: 50.0000 chunk 98 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 = 0.150217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.105904 restraints weight = 25984.728| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.14 r_work: 0.3032 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 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 = 0.3037 r_free = 0.3037 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: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15148 Z= 0.170 Angle : 0.605 15.682 20970 Z= 0.325 Chirality : 0.039 0.180 2331 Planarity : 0.005 0.048 2330 Dihedral : 19.515 117.839 2881 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.95 % Favored : 96.99 % Rotamer: Outliers : 1.13 % Allowed : 9.50 % Favored : 89.37 % 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: 1.65 (0.22), residues: 1564 helix: 2.17 (0.17), residues: 932 sheet: -0.38 (0.50), residues: 100 loop : -0.56 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 477 TYR 0.054 0.002 TYR C 110 PHE 0.019 0.002 PHE A 802 TRP 0.011 0.001 TRP C 218 HIS 0.009 0.001 HIS C 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (15147) covalent geometry : angle 0.60488 / 0.32 (20970) hydrogen bonds : bond 0.05208 / 3.49 ( 811) hydrogen bonds : angle 3.54703 / 2.55 ( 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: 3168.98 seconds wall clock time: 54 minutes 57.02 seconds (3297.02 seconds total)