Starting phenix.real_space_refine on Thu Sep 18 06:18:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gzm_51727/09_2025/9gzm_51727.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gzm_51727/09_2025/9gzm_51727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gzm_51727/09_2025/9gzm_51727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gzm_51727/09_2025/9gzm_51727.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gzm_51727/09_2025/9gzm_51727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gzm_51727/09_2025/9gzm_51727.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 107 5.49 5 Mg 1 5.21 5 S 75 5.16 5 C 8953 2.51 5 N 2626 2.21 5 O 2842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 1.23 Conformation dependent library (CDL) restraints added in 850.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.98 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: 3.38 Time building geometry restraints manager: 1.64 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=" O3' DC N 30 " pdb=" P DA N 31 " ideal model delta sigma weight residual 1.607 1.406 0.201 1.50e-02 4.44e+03 1.79e+02 bond pdb=" C3' DC T 11 " pdb=" C2' DC T 11 " ideal model delta sigma weight residual 1.525 1.675 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" O3' DA N 17 " pdb=" P DC N 18 " ideal model delta sigma weight residual 1.607 1.704 -0.097 1.50e-02 4.44e+03 4.22e+01 bond pdb=" O3' DA N 48 " pdb=" P DA N 49 " ideal model delta sigma weight residual 1.607 1.518 0.089 1.50e-02 4.44e+03 3.49e+01 bond pdb=" C3' DG N 6 " pdb=" C2' DG N 6 " ideal model delta sigma weight residual 1.525 1.640 -0.115 2.00e-02 2.50e+03 3.28e+01 ... (remaining 15142 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.85: 20635 3.85 - 7.71: 273 7.71 - 11.56: 52 11.56 - 15.41: 9 15.41 - 19.26: 1 Bond angle restraints: 20970 Sorted by residual: angle pdb=" C3' DC T 9 " pdb=" O3' DC T 9 " pdb=" P DT T 10 " ideal model delta sigma weight residual 120.20 100.94 19.26 1.50e+00 4.44e-01 1.65e+02 angle pdb=" C5' DA N 48 " pdb=" C4' DA N 48 " pdb=" O4' DA N 48 " ideal model delta sigma weight residual 109.40 124.19 -14.79 1.50e+00 4.44e-01 9.72e+01 angle pdb=" O3' DC N 18 " pdb=" C3' DC N 18 " pdb=" C2' DC N 18 " ideal model delta sigma weight residual 111.50 97.38 14.12 1.50e+00 4.44e-01 8.87e+01 angle pdb=" O3' DT T 5 " pdb=" C3' DT T 5 " pdb=" C2' DT T 5 " ideal model delta sigma weight residual 111.50 125.12 -13.62 1.50e+00 4.44e-01 8.24e+01 angle pdb=" C3' DA T 31 " pdb=" O3' DA T 31 " pdb=" P DC T 32 " ideal model delta sigma weight residual 120.20 106.72 13.48 1.50e+00 4.44e-01 8.08e+01 ... (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 - 0.127: 2167 0.127 - 0.254: 75 0.254 - 0.381: 7 0.381 - 0.508: 37 0.508 - 0.635: 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 2.35 2.98 -0.63 2.00e-01 2.50e+01 1.01e+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 2.35 -2.97 -0.63 2.00e-01 2.50e+01 9.78e+00 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: 0.350 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 17.980 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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= 0.424 Angle : 1.140 19.264 20970 Z= 0.646 Chirality : 0.109 0.635 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 aren 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 covalent geometry : bond 0.00764 (15147) covalent geometry : angle 1.13979 (20970) hydrogen bonds : bond 0.16824 ( 811) hydrogen bonds : angle 6.00402 ( 2265) Misc. bond : bond 0.02660 ( 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 : 0.548 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: 0.1475 time to fit residues: 38.0917 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 : 0.507 ------------------------------------------------------------------------------- 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: 20.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.0770 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: 4.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.152118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.108633 restraints weight = 24427.355| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.07 r_work: 0.3077 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15148 Z= 0.148 Angle : 0.610 12.875 20970 Z= 0.327 Chirality : 0.037 0.191 2331 Planarity : 0.006 0.167 2330 Dihedral : 20.661 164.077 2883 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.18 % Favored : 97.76 % Rotamer: Outliers : 0.75 % Allowed : 5.20 % Favored : 94.04 % 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 aren not related in a simple way. whole: 1.59 (0.21), residues: 1564 helix: 2.04 (0.17), residues: 931 sheet: -0.34 (0.47), residues: 115 loop : -0.41 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 116 TYR 0.009 0.001 TYR B 247 PHE 0.015 0.001 PHE A1229 TRP 0.010 0.001 TRP C 189 HIS 0.008 0.001 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00309 (15147) covalent geometry : angle 0.60956 (20970) hydrogen bonds : bond 0.05827 ( 811) hydrogen bonds : angle 3.84032 ( 2265) Misc. bond : bond 0.00045 ( 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 170 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 161 time to evaluate : 0.565 Fit side-chains REVERT: A 263 MET cc_start: 0.8155 (mtt) cc_final: 0.7691 (mtt) REVERT: A 342 GLU cc_start: 0.8099 (tp30) cc_final: 0.7877 (tp30) REVERT: B 98 LEU cc_start: 0.8147 (tp) cc_final: 0.7777 (tt) REVERT: B 396 ARG cc_start: 0.7698 (ttm170) cc_final: 0.7302 (ttp80) REVERT: C 82 ARG cc_start: 0.8923 (ptm160) cc_final: 0.8661 (ttp80) REVERT: C 83 ARG cc_start: 0.8335 (mtm-85) cc_final: 0.7542 (mtm-85) REVERT: C 87 ARG cc_start: 0.7781 (ptt-90) cc_final: 0.7512 (ptt180) REVERT: C 112 GLU cc_start: 0.8521 (tp30) cc_final: 0.7817 (mt-10) REVERT: C 116 ARG cc_start: 0.8469 (mtm110) cc_final: 0.8219 (mtm-85) REVERT: C 211 TYR cc_start: 0.7524 (m-10) cc_final: 0.6660 (t80) outliers start: 9 outliers final: 4 residues processed: 164 average time/residue: 0.1523 time to fit residues: 34.9897 Evaluate side-chains 153 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 149 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 105 optimal weight: 0.7980 chunk 100 optimal weight: 9.9990 chunk 39 optimal weight: 0.4980 chunk 101 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 38 optimal weight: 6.9990 chunk 153 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN A 893 GLN ** A1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.153828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.116178 restraints weight = 40779.239| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 3.65 r_work: 0.3034 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 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 = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15148 Z= 0.132 Angle : 0.555 8.300 20970 Z= 0.299 Chirality : 0.036 0.172 2331 Planarity : 0.005 0.055 2330 Dihedral : 20.057 134.396 2883 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.37 % Favored : 97.57 % Rotamer: Outliers : 1.43 % Allowed : 6.33 % Favored : 92.23 % 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 aren not related in a simple way. whole: 1.87 (0.21), residues: 1564 helix: 2.27 (0.17), residues: 927 sheet: -0.10 (0.48), residues: 110 loop : -0.32 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 83 TYR 0.010 0.001 TYR B 247 PHE 0.012 0.001 PHE A 802 TRP 0.010 0.001 TRP A1154 HIS 0.005 0.001 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00274 (15147) covalent geometry : angle 0.55500 (20970) hydrogen bonds : bond 0.04786 ( 811) hydrogen bonds : angle 3.46850 ( 2265) Misc. bond : bond 0.00057 ( 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 181 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.524 Fit side-chains REVERT: A 263 MET cc_start: 0.8207 (mtt) cc_final: 0.7771 (mtt) REVERT: A 342 GLU cc_start: 0.8254 (tp30) cc_final: 0.8011 (tp30) REVERT: A 589 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8851 (ptm) REVERT: B 157 ARG cc_start: 0.7648 (mpt180) cc_final: 0.7425 (mmt90) REVERT: C 83 ARG cc_start: 0.8283 (mtm-85) cc_final: 0.7311 (ptt180) REVERT: C 112 GLU cc_start: 0.8572 (tp30) cc_final: 0.7848 (mt-10) REVERT: C 116 ARG cc_start: 0.8488 (mtm110) cc_final: 0.8230 (mtm-85) REVERT: C 148 GLU cc_start: 0.9192 (OUTLIER) cc_final: 0.8610 (pp20) REVERT: C 211 TYR cc_start: 0.7562 (m-10) cc_final: 0.6669 (t80) REVERT: C 222 MET cc_start: 0.9340 (mmp) cc_final: 0.9035 (mmm) outliers start: 18 outliers final: 10 residues processed: 170 average time/residue: 0.1428 time to fit residues: 34.2471 Evaluate side-chains 155 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 589 MET Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 151 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 148 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 165 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN A 893 GLN ** A1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.152890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.111558 restraints weight = 33123.774| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.80 r_work: 0.3051 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1809 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= 0.131 Angle : 0.559 12.833 20970 Z= 0.298 Chirality : 0.036 0.200 2331 Planarity : 0.005 0.049 2330 Dihedral : 19.541 117.002 2883 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.31 % Favored : 97.63 % Rotamer: Outliers : 1.81 % Allowed : 7.24 % Favored : 90.95 % 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 aren not related in a simple way. whole: 1.91 (0.22), residues: 1564 helix: 2.32 (0.17), residues: 930 sheet: -0.03 (0.47), residues: 110 loop : -0.35 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 82 TYR 0.018 0.001 TYR C 110 PHE 0.020 0.001 PHE C 68 TRP 0.009 0.001 TRP A 553 HIS 0.005 0.001 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00283 (15147) covalent geometry : angle 0.55949 (20970) hydrogen bonds : bond 0.04654 ( 811) hydrogen bonds : angle 3.37492 ( 2265) Misc. bond : bond 0.00059 ( 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 178 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 263 MET cc_start: 0.8234 (mtt) cc_final: 0.7768 (mtt) REVERT: A 342 GLU cc_start: 0.8238 (tp30) cc_final: 0.8028 (tp30) REVERT: A 981 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6676 (pp) REVERT: B 157 ARG cc_start: 0.7528 (mpt180) cc_final: 0.7317 (mmt90) REVERT: C 83 ARG cc_start: 0.7964 (mtm-85) cc_final: 0.7524 (ptp-170) REVERT: C 112 GLU cc_start: 0.8546 (tp30) cc_final: 0.7660 (mt-10) REVERT: C 116 ARG cc_start: 0.8443 (mtm110) cc_final: 0.8226 (mtm-85) REVERT: C 127 MET cc_start: 0.7680 (mmm) cc_final: 0.6876 (ptp) REVERT: C 148 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.8589 (pp20) REVERT: C 211 TYR cc_start: 0.7524 (m-10) cc_final: 0.6622 (t80) REVERT: C 222 MET cc_start: 0.9255 (mmp) cc_final: 0.8936 (mmm) outliers start: 23 outliers final: 12 residues processed: 164 average time/residue: 0.1382 time to fit residues: 33.0646 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 : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain 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 80 LEU Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 230 LEU Rotamers are restrained with sigma=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: 4.9990 chunk 98 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS ** A1080 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 = 0.3847 r_free = 0.3847 target = 0.150171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.108303 restraints weight = 34358.021| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.88 r_work: 0.2998 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15148 Z= 0.170 Angle : 0.586 9.687 20970 Z= 0.312 Chirality : 0.038 0.176 2331 Planarity : 0.005 0.048 2330 Dihedral : 19.454 116.869 2881 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.43 % Favored : 97.50 % Rotamer: Outliers : 1.58 % Allowed : 8.07 % Favored : 90.35 % 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 aren not related in a simple way. whole: 1.79 (0.22), residues: 1564 helix: 2.23 (0.17), residues: 930 sheet: -0.09 (0.48), residues: 109 loop : -0.42 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 82 TYR 0.024 0.002 TYR C 110 PHE 0.020 0.002 PHE A 802 TRP 0.009 0.001 TRP A 885 HIS 0.008 0.001 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00397 (15147) covalent geometry : angle 0.58570 (20970) hydrogen bonds : bond 0.05282 ( 811) hydrogen bonds : angle 3.51352 ( 2265) Misc. bond : bond 0.00062 ( 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 173 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.571 Fit side-chains REVERT: A 263 MET cc_start: 0.8335 (mtt) cc_final: 0.7908 (mtt) REVERT: A 981 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6631 (pp) REVERT: B 157 ARG cc_start: 0.7545 (mpt180) cc_final: 0.7320 (mmt90) REVERT: B 388 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8741 (mp) REVERT: C 87 ARG cc_start: 0.8707 (ptt180) cc_final: 0.8403 (ptt-90) REVERT: C 112 GLU cc_start: 0.8561 (tp30) cc_final: 0.7766 (mt-10) REVERT: C 116 ARG cc_start: 0.8455 (mtm110) cc_final: 0.8214 (mtm-85) REVERT: C 127 MET cc_start: 0.7528 (mmm) cc_final: 0.6775 (ptp) REVERT: C 148 GLU cc_start: 0.9176 (OUTLIER) cc_final: 0.8610 (pp20) REVERT: C 211 TYR cc_start: 0.7553 (m-10) cc_final: 0.6619 (t80) outliers start: 20 outliers final: 11 residues processed: 163 average time/residue: 0.1409 time to fit residues: 33.0669 Evaluate side-chains 159 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1063 HIS Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 388 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 144 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 110 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 41 optimal weight: 0.0870 overall best weight: 2.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.151619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.109933 restraints weight = 35576.938| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.97 r_work: 0.3019 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15148 Z= 0.143 Angle : 0.574 16.372 20970 Z= 0.303 Chirality : 0.037 0.364 2331 Planarity : 0.005 0.049 2330 Dihedral : 19.316 118.571 2881 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.43 % Favored : 97.50 % Rotamer: Outliers : 1.43 % Allowed : 8.67 % Favored : 89.89 % 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 aren not related in a simple way. whole: 1.78 (0.22), residues: 1564 helix: 2.25 (0.17), residues: 932 sheet: -0.24 (0.50), residues: 100 loop : -0.45 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 82 TYR 0.029 0.001 TYR C 110 PHE 0.023 0.002 PHE C 68 TRP 0.009 0.001 TRP A 885 HIS 0.006 0.001 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00322 (15147) covalent geometry : angle 0.57354 (20970) hydrogen bonds : bond 0.04803 ( 811) hydrogen bonds : angle 3.43148 ( 2265) Misc. bond : bond 0.00060 ( 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 171 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.604 Fit side-chains REVERT: A 263 MET cc_start: 0.8256 (mtt) cc_final: 0.7813 (mtt) REVERT: A 981 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6636 (pp) REVERT: B 388 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8677 (mp) REVERT: C 87 ARG cc_start: 0.8798 (ptt180) cc_final: 0.8286 (ptt-90) REVERT: C 112 GLU cc_start: 0.8555 (tp30) cc_final: 0.7924 (mt-10) REVERT: C 116 ARG cc_start: 0.8491 (mtm110) cc_final: 0.8258 (mtm-85) REVERT: C 127 MET cc_start: 0.7530 (mmm) cc_final: 0.6800 (ptp) REVERT: C 148 GLU cc_start: 0.9169 (OUTLIER) cc_final: 0.8594 (pp20) REVERT: C 211 TYR cc_start: 0.7580 (m-10) cc_final: 0.6579 (t80) REVERT: C 222 MET cc_start: 0.9118 (mmp) cc_final: 0.8799 (mmm) outliers start: 18 outliers final: 11 residues processed: 162 average time/residue: 0.1461 time to fit residues: 33.9105 Evaluate side-chains 156 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1063 HIS Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 388 LEU 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 80 LEU Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 151 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 5 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 40.0000 chunk 63 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 118 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.152665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.109106 restraints weight = 25516.627| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.16 r_work: 0.3052 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 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 : 0.003 0.034 15148 Z= 0.128 Angle : 0.563 13.019 20970 Z= 0.298 Chirality : 0.036 0.328 2331 Planarity : 0.005 0.049 2330 Dihedral : 19.198 119.094 2881 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.43 % Favored : 97.50 % Rotamer: Outliers : 1.58 % Allowed : 9.65 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.22), residues: 1564 helix: 2.32 (0.17), residues: 931 sheet: -0.19 (0.50), residues: 100 loop : -0.45 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 82 TYR 0.025 0.001 TYR C 110 PHE 0.034 0.001 PHE C 68 TRP 0.008 0.001 TRP A 885 HIS 0.006 0.001 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00278 (15147) covalent geometry : angle 0.56273 (20970) hydrogen bonds : bond 0.04404 ( 811) hydrogen bonds : angle 3.36722 ( 2265) Misc. bond : bond 0.00056 ( 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: 20 poor density : 149 time to evaluate : 0.542 Fit side-chains REVERT: A 263 MET cc_start: 0.8194 (mtt) cc_final: 0.7748 (mtt) REVERT: A 981 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6623 (pp) REVERT: B 388 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8607 (mp) REVERT: C 87 ARG cc_start: 0.8759 (ptt180) cc_final: 0.8373 (ptt-90) REVERT: C 117 PHE cc_start: 0.4812 (t80) cc_final: 0.4551 (t80) REVERT: C 148 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8555 (pp20) REVERT: C 211 TYR cc_start: 0.7493 (m-10) cc_final: 0.6531 (t80) REVERT: C 222 MET cc_start: 0.9042 (mmp) cc_final: 0.8625 (mmm) outliers start: 20 outliers final: 13 residues processed: 158 average time/residue: 0.1539 time to fit residues: 34.4485 Evaluate side-chains 158 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 129 PHE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 230 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 120 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 152 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 127 optimal weight: 0.2980 chunk 4 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 GLN A 679 GLN A1080 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.149154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.108621 restraints weight = 31868.325| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.73 r_work: 0.2992 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 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 = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15148 Z= 0.190 Angle : 0.616 11.567 20970 Z= 0.325 Chirality : 0.039 0.252 2331 Planarity : 0.005 0.047 2330 Dihedral : 19.282 117.003 2881 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.20 % Favored : 96.73 % Rotamer: Outliers : 1.51 % Allowed : 9.58 % Favored : 88.91 % 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 aren not related in a simple way. whole: 1.56 (0.21), residues: 1564 helix: 2.09 (0.17), residues: 932 sheet: -0.42 (0.50), residues: 100 loop : -0.57 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 82 TYR 0.034 0.002 TYR C 110 PHE 0.035 0.002 PHE C 68 TRP 0.013 0.001 TRP A 885 HIS 0.007 0.001 HIS A 798 Details of bonding type rmsd covalent geometry : bond 0.00450 (15147) covalent geometry : angle 0.61608 (20970) hydrogen bonds : bond 0.05553 ( 811) hydrogen bonds : angle 3.61585 ( 2265) Misc. bond : bond 0.00056 ( 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 164 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 263 MET cc_start: 0.8393 (mtt) cc_final: 0.7962 (mtt) REVERT: A 981 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6693 (pp) REVERT: B 111 GLN cc_start: 0.7509 (tm-30) cc_final: 0.7261 (pt0) REVERT: C 127 MET cc_start: 0.6726 (mmp) cc_final: 0.5435 (ptp) REVERT: C 148 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.8598 (pp20) REVERT: C 211 TYR cc_start: 0.7540 (m-10) cc_final: 0.6575 (t80) REVERT: C 222 MET cc_start: 0.9045 (mmp) cc_final: 0.8588 (mmm) REVERT: C 231 LEU cc_start: 0.7726 (mt) cc_final: 0.7495 (mp) outliers start: 19 outliers final: 13 residues processed: 153 average time/residue: 0.1389 time to fit residues: 30.9516 Evaluate side-chains 157 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1063 HIS Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 300 GLN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 230 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 50 optimal weight: 0.0570 chunk 9 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 94 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.152866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.112254 restraints weight = 41017.119| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 3.56 r_work: 0.3014 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15148 Z= 0.127 Angle : 0.564 17.241 20970 Z= 0.297 Chirality : 0.036 0.272 2331 Planarity : 0.005 0.049 2330 Dihedral : 19.121 119.740 2881 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.69 % Favored : 97.25 % Rotamer: Outliers : 1.21 % Allowed : 9.88 % Favored : 88.91 % 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 aren not related in a simple way. whole: 1.80 (0.22), residues: 1564 helix: 2.29 (0.17), residues: 931 sheet: -0.35 (0.50), residues: 100 loop : -0.49 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 82 TYR 0.037 0.001 TYR C 110 PHE 0.033 0.001 PHE C 68 TRP 0.010 0.001 TRP A1070 HIS 0.005 0.001 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00276 (15147) covalent geometry : angle 0.56421 (20970) hydrogen bonds : bond 0.04357 ( 811) hydrogen bonds : angle 3.36992 ( 2265) Misc. bond : bond 0.00058 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: A 263 MET cc_start: 0.8252 (mtt) cc_final: 0.7828 (mtt) REVERT: A 981 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6652 (pp) REVERT: B 111 GLN cc_start: 0.7560 (tm-30) cc_final: 0.7241 (pt0) REVERT: B 114 LEU cc_start: 0.8086 (mm) cc_final: 0.7879 (mt) REVERT: C 127 MET cc_start: 0.6701 (mmp) cc_final: 0.5546 (ptp) REVERT: C 148 GLU cc_start: 0.9141 (OUTLIER) cc_final: 0.8603 (pp20) REVERT: C 220 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8375 (tm-30) REVERT: C 222 MET cc_start: 0.9047 (mmp) cc_final: 0.8653 (mmm) REVERT: C 231 LEU cc_start: 0.7751 (mt) cc_final: 0.7535 (mp) outliers start: 15 outliers final: 13 residues processed: 153 average time/residue: 0.1425 time to fit residues: 31.3346 Evaluate side-chains 154 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1063 HIS Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 300 GLN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 230 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 42 optimal weight: 0.0050 chunk 121 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 chunk 148 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 152 optimal weight: 30.0000 chunk 69 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.151969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.108504 restraints weight = 33048.927| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.65 r_work: 0.3026 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 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 = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2446 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= 0.135 Angle : 0.572 15.127 20970 Z= 0.298 Chirality : 0.036 0.230 2331 Planarity : 0.005 0.050 2330 Dihedral : 19.096 118.323 2881 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.82 % Favored : 97.12 % Rotamer: Outliers : 1.21 % Allowed : 9.88 % Favored : 88.91 % 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 aren not related in a simple way. whole: 1.80 (0.22), residues: 1564 helix: 2.30 (0.17), residues: 931 sheet: -0.36 (0.50), residues: 100 loop : -0.49 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 116 TYR 0.041 0.001 TYR C 110 PHE 0.033 0.001 PHE C 68 TRP 0.009 0.001 TRP A 885 HIS 0.004 0.001 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00299 (15147) covalent geometry : angle 0.57229 (20970) hydrogen bonds : bond 0.04513 ( 811) hydrogen bonds : angle 3.37325 ( 2265) Misc. bond : bond 0.00053 ( 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 155 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 263 MET cc_start: 0.8279 (mtt) cc_final: 0.7831 (mtt) REVERT: A 981 LEU cc_start: 0.7064 (OUTLIER) cc_final: 0.6603 (pp) REVERT: C 84 ILE cc_start: 0.8772 (mt) cc_final: 0.8567 (mp) REVERT: C 87 ARG cc_start: 0.8574 (ptt180) cc_final: 0.8214 (ptt-90) REVERT: C 127 MET cc_start: 0.6610 (mmp) cc_final: 0.5480 (ptp) REVERT: C 148 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8591 (pp20) REVERT: C 220 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8308 (tm-30) REVERT: C 231 LEU cc_start: 0.7822 (mt) cc_final: 0.7606 (mp) outliers start: 15 outliers final: 13 residues processed: 147 average time/residue: 0.1440 time to fit residues: 30.6100 Evaluate side-chains 153 residues out of total 1391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1063 HIS Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 300 GLN Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain C residue 54 VAL 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: 5.9990 chunk 123 optimal weight: 7.9990 chunk 127 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 110 optimal weight: 20.0000 chunk 98 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.153833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.110282 restraints weight = 26194.006| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.18 r_work: 0.3085 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2562 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= 0.122 Angle : 0.572 15.047 20970 Z= 0.296 Chirality : 0.036 0.256 2331 Planarity : 0.005 0.058 2330 Dihedral : 19.023 119.483 2881 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.56 % Favored : 97.37 % Rotamer: Outliers : 1.21 % Allowed : 10.03 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.22), residues: 1564 helix: 2.36 (0.17), residues: 931 sheet: -0.29 (0.50), residues: 100 loop : -0.44 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 116 TYR 0.031 0.001 TYR C 110 PHE 0.038 0.001 PHE C 68 TRP 0.021 0.001 TRP C 218 HIS 0.011 0.001 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00261 (15147) covalent geometry : angle 0.57190 (20970) hydrogen bonds : bond 0.04115 ( 811) hydrogen bonds : angle 3.30327 ( 2265) Misc. bond : bond 0.00054 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3712.83 seconds wall clock time: 64 minutes 15.49 seconds (3855.49 seconds total)