Starting phenix.real_space_refine on Tue Feb 3 20:58:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xdc_66762/02_2026/9xdc_66762.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xdc_66762/02_2026/9xdc_66762.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xdc_66762/02_2026/9xdc_66762.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xdc_66762/02_2026/9xdc_66762.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xdc_66762/02_2026/9xdc_66762.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xdc_66762/02_2026/9xdc_66762.map" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 4277 2.51 5 N 1166 2.21 5 O 1306 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6763 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4167 Classifications: {'peptide': 544} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 23, 'TRANS': 520} Chain breaks: 1 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 3, 'ARG:plan': 5, 'TYR:plan': 3, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 123 Chain: "B" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2596 Classifications: {'peptide': 344} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 30 Time building chain proxies: 1.17, per 1000 atoms: 0.17 Number of scatterers: 6763 At special positions: 0 Unit cell: (69.72, 84, 166.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 1306 8.00 N 1166 7.00 C 4277 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=0, symmetry=0 Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 270.3 milliseconds 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1612 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 7 sheets defined 12.5% alpha, 31.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 33 through 44 removed outlier: 3.876A pdb=" N LYS A 37 " --> pdb=" O GLY A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 70 removed outlier: 3.840A pdb=" N ALA A 59 " --> pdb=" O ARG A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 127 Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 138 through 156 Processing helix chain 'A' and resid 202 through 208 removed outlier: 3.802A pdb=" N LEU A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 233 removed outlier: 3.804A pdb=" N LEU A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 removed outlier: 3.897A pdb=" N THR A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 1107 through 1111 Processing helix chain 'B' and resid 1139 through 1150 removed outlier: 3.535A pdb=" N SER B1145 " --> pdb=" O GLN B1141 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR B1146 " --> pdb=" O ALA B1142 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B1147 " --> pdb=" O ALA B1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 1159 through 1166 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 108 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 105 through 108 current: chain 'A' and resid 176 through 184 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 190 through 197 removed outlier: 4.837A pdb=" N PHE A 191 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU A 256 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N HIS A 193 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N GLY A 258 " --> pdb=" O HIS A 193 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N THR A 195 " --> pdb=" O GLY A 258 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N VAL A 260 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLU A 197 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 238 " --> pdb=" O SER A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 269 Processing sheet with id=AA5, first strand: chain 'A' and resid 271 through 273 removed outlier: 7.534A pdb=" N LEU B1239 " --> pdb=" O LEU B1235 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B1235 " --> pdb=" O LEU B1239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 297 through 301 removed outlier: 3.674A pdb=" N THR A 299 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 311 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 351 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 367 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 364 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET A 391 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER A 427 " --> pdb=" O GLU A 455 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU A 455 " --> pdb=" O SER A 427 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A 431 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG A 437 " --> pdb=" O PHE A 445 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU A 439 " --> pdb=" O HIS A 443 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N HIS A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR A 450 " --> pdb=" O THR A 501 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR A 501 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 499 " --> pdb=" O GLY A 452 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS A 498 " --> pdb=" O VAL A 526 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 526 " --> pdb=" O LYS A 498 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE A 500 " --> pdb=" O GLU A 524 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER A 522 " --> pdb=" O GLY A 502 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 517 " --> pdb=" O GLY A 541 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N THR A 536 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 559 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 555 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 572 " --> pdb=" O LYS A 552 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 910 through 911 removed outlier: 4.293A pdb=" N ASN B 911 " --> pdb=" O ARG B 914 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG B 914 " --> pdb=" O ASN B 911 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 914 through 917 current: chain 'B' and resid 927 through 935 removed outlier: 3.559A pdb=" N ASP B 933 " --> pdb=" O ARG B 945 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 943 through 950 current: chain 'B' and resid 961 through 973 removed outlier: 7.349A pdb=" N ARG B 962 " --> pdb=" O ALA B 989 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ALA B 989 " --> pdb=" O ARG B 962 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASP B 964 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP B 985 " --> pdb=" O SER B 966 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR B 979 " --> pdb=" O GLU B 972 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY B 982 " --> pdb=" O ASN B1029 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE B1031 " --> pdb=" O GLY B 982 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 984 " --> pdb=" O ILE B1031 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1027 through 1034 current: chain 'B' and resid 1045 through 1048 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1045 through 1048 current: chain 'B' and resid 1062 through 1069 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1062 through 1069 current: chain 'B' and resid 1082 through 1093 removed outlier: 7.239A pdb=" N GLU B1103 " --> pdb=" O ARG B1085 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY B1087 " --> pdb=" O ASN B1101 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASN B1101 " --> pdb=" O GLY B1087 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU B1089 " --> pdb=" O TYR B1099 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N TYR B1099 " --> pdb=" O LEU B1089 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY B1118 " --> pdb=" O PHE B1133 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS B1129 " --> pdb=" O THR B1122 " (cutoff:3.500A) 198 hydrogen bonds defined for protein. 555 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.98 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2274 1.34 - 1.46: 1214 1.46 - 1.57: 3388 1.57 - 1.69: 0 1.69 - 1.80: 28 Bond restraints: 6904 Sorted by residual: bond pdb=" C GLN B1015 " pdb=" N PRO B1016 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.38e+00 bond pdb=" CA VAL A 557 " pdb=" C VAL A 557 " ideal model delta sigma weight residual 1.516 1.525 -0.009 1.11e-02 8.12e+03 7.28e-01 bond pdb=" CA LEU A 349 " pdb=" C LEU A 349 " ideal model delta sigma weight residual 1.522 1.530 -0.008 1.08e-02 8.57e+03 5.46e-01 bond pdb=" N PRO B 958 " pdb=" CA PRO B 958 " ideal model delta sigma weight residual 1.457 1.466 -0.009 1.31e-02 5.83e+03 4.90e-01 bond pdb=" C PRO B 958 " pdb=" O PRO B 958 " ideal model delta sigma weight residual 1.246 1.240 0.006 8.50e-03 1.38e+04 4.70e-01 ... (remaining 6899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 9041 1.13 - 2.25: 274 2.25 - 3.38: 64 3.38 - 4.50: 7 4.50 - 5.63: 4 Bond angle restraints: 9390 Sorted by residual: angle pdb=" CA VAL A 557 " pdb=" C VAL A 557 " pdb=" N PRO A 558 " ideal model delta sigma weight residual 116.57 119.20 -2.63 9.80e-01 1.04e+00 7.18e+00 angle pdb=" N SER A 532 " pdb=" CA SER A 532 " pdb=" C SER A 532 " ideal model delta sigma weight residual 107.93 111.58 -3.65 1.65e+00 3.67e-01 4.90e+00 angle pdb=" N SER B1225 " pdb=" CA SER B1225 " pdb=" C SER B1225 " ideal model delta sigma weight residual 110.30 113.36 -3.06 1.50e+00 4.44e-01 4.17e+00 angle pdb=" C VAL A 557 " pdb=" CA VAL A 557 " pdb=" CB VAL A 557 " ideal model delta sigma weight residual 109.33 111.08 -1.75 9.80e-01 1.04e+00 3.18e+00 angle pdb=" C THR A 276 " pdb=" N ASP A 277 " pdb=" CA ASP A 277 " ideal model delta sigma weight residual 121.54 124.89 -3.35 1.91e+00 2.74e-01 3.08e+00 ... (remaining 9385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3682 18.00 - 36.00: 341 36.00 - 53.99: 53 53.99 - 71.99: 13 71.99 - 89.99: 4 Dihedral angle restraints: 4093 sinusoidal: 1567 harmonic: 2526 Sorted by residual: dihedral pdb=" CA LEU A 553 " pdb=" C LEU A 553 " pdb=" N ASP A 554 " pdb=" CA ASP A 554 " ideal model delta harmonic sigma weight residual -180.00 -161.54 -18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ASP A 528 " pdb=" CB ASP A 528 " pdb=" CG ASP A 528 " pdb=" OD1 ASP A 528 " ideal model delta sinusoidal sigma weight residual -30.00 -88.96 58.96 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA TRP A 235 " pdb=" C TRP A 235 " pdb=" N PHE A 236 " pdb=" CA PHE A 236 " ideal model delta harmonic sigma weight residual 180.00 -163.89 -16.11 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 4090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 653 0.032 - 0.063: 254 0.063 - 0.095: 69 0.095 - 0.126: 71 0.126 - 0.158: 4 Chirality restraints: 1051 Sorted by residual: chirality pdb=" CA ILE A 476 " pdb=" N ILE A 476 " pdb=" C ILE A 476 " pdb=" CB ILE A 476 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.23e-01 chirality pdb=" CA ILE A 392 " pdb=" N ILE A 392 " pdb=" C ILE A 392 " pdb=" CB ILE A 392 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA ILE A 500 " pdb=" N ILE A 500 " pdb=" C ILE A 500 " pdb=" CB ILE A 500 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 ... (remaining 1048 not shown) Planarity restraints: 1236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 546 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.75e+00 pdb=" N PRO A 547 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 547 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 547 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B1015 " -0.021 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO B1016 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B1016 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B1016 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B1236 " 0.018 5.00e-02 4.00e+02 2.68e-02 1.15e+00 pdb=" N PRO B1237 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO B1237 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B1237 " 0.015 5.00e-02 4.00e+02 ... (remaining 1233 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 492 2.74 - 3.28: 6418 3.28 - 3.82: 10043 3.82 - 4.36: 11114 4.36 - 4.90: 20308 Nonbonded interactions: 48375 Sorted by model distance: nonbonded pdb=" OD2 ASP B 875 " pdb=" OG SER B 878 " model vdw 2.199 3.040 nonbonded pdb=" OG SER A 238 " pdb=" OG SER A 261 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR B 974 " pdb=" O LEU B 977 " model vdw 2.297 3.040 nonbonded pdb=" OH TYR A 354 " pdb=" OE1 GLN A 362 " model vdw 2.298 3.040 nonbonded pdb=" O VAL A 241 " pdb=" OG SER B1160 " model vdw 2.300 3.040 ... (remaining 48370 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.010 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 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 : 0.002 0.027 6904 Z= 0.104 Angle : 0.495 5.625 9390 Z= 0.265 Chirality : 0.044 0.158 1051 Planarity : 0.003 0.033 1236 Dihedral : 14.113 89.991 2481 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.16 % Favored : 92.61 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.28), residues: 880 helix: 0.98 (0.56), residues: 85 sheet: -1.44 (0.27), residues: 383 loop : -2.18 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 477 TYR 0.010 0.001 TYR A 479 PHE 0.012 0.001 PHE A 519 TRP 0.016 0.001 TRP A 435 HIS 0.008 0.001 HIS B 994 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 6904) covalent geometry : angle 0.49504 ( 9390) hydrogen bonds : bond 0.26431 ( 198) hydrogen bonds : angle 9.80031 ( 555) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 GLN cc_start: 0.7766 (tp-100) cc_final: 0.7486 (tp-100) REVERT: A 407 ASP cc_start: 0.8003 (p0) cc_final: 0.7648 (p0) REVERT: B 1236 MET cc_start: 0.7641 (ppp) cc_final: 0.7416 (ppp) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1160 time to fit residues: 22.1312 Evaluate side-chains 95 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 0.0770 chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.0000 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS ** B 884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 925 GLN B 994 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.181228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.133781 restraints weight = 9267.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.136622 restraints weight = 5950.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.138608 restraints weight = 4416.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.139873 restraints weight = 3643.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.140249 restraints weight = 3221.968| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6904 Z= 0.129 Angle : 0.612 9.107 9390 Z= 0.313 Chirality : 0.047 0.217 1051 Planarity : 0.004 0.034 1236 Dihedral : 5.493 76.463 965 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.07 % Favored : 91.70 % Rotamer: Outliers : 1.42 % Allowed : 10.24 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.27), residues: 880 helix: 1.53 (0.52), residues: 92 sheet: -1.31 (0.26), residues: 388 loop : -2.38 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 396 TYR 0.023 0.001 TYR A 479 PHE 0.012 0.001 PHE A 429 TRP 0.015 0.001 TRP A 286 HIS 0.003 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 6904) covalent geometry : angle 0.61152 ( 9390) hydrogen bonds : bond 0.04369 ( 198) hydrogen bonds : angle 6.44750 ( 555) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 THR cc_start: 0.8066 (m) cc_final: 0.7858 (p) REVERT: A 366 ASN cc_start: 0.8038 (m-40) cc_final: 0.7778 (m-40) REVERT: B 971 PHE cc_start: 0.7288 (t80) cc_final: 0.6936 (t80) outliers start: 10 outliers final: 7 residues processed: 101 average time/residue: 0.0973 time to fit residues: 12.8104 Evaluate side-chains 88 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 976 ASN Chi-restraints excluded: chain B residue 1031 ILE Chi-restraints excluded: chain B residue 1229 LEU Chi-restraints excluded: chain B residue 1251 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 3.9990 chunk 66 optimal weight: 0.1980 chunk 60 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 52 optimal weight: 0.0070 chunk 80 optimal weight: 2.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 994 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.181997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.135979 restraints weight = 9161.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.138531 restraints weight = 6601.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.139521 restraints weight = 4796.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.140093 restraints weight = 4184.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.140231 restraints weight = 4455.690| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6904 Z= 0.117 Angle : 0.584 10.330 9390 Z= 0.299 Chirality : 0.046 0.211 1051 Planarity : 0.004 0.050 1236 Dihedral : 5.480 76.456 965 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.39 % Favored : 92.50 % Rotamer: Outliers : 2.28 % Allowed : 13.94 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.28), residues: 880 helix: 1.67 (0.53), residues: 93 sheet: -1.13 (0.26), residues: 389 loop : -2.45 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 58 TYR 0.019 0.001 TYR A 479 PHE 0.020 0.001 PHE B 910 TRP 0.006 0.001 TRP A 286 HIS 0.004 0.001 HIS B 994 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 6904) covalent geometry : angle 0.58447 ( 9390) hydrogen bonds : bond 0.03634 ( 198) hydrogen bonds : angle 5.68538 ( 555) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ARG cc_start: 0.8000 (ttt-90) cc_final: 0.7724 (tmt170) REVERT: A 376 GLN cc_start: 0.7793 (tp-100) cc_final: 0.7475 (tp-100) outliers start: 16 outliers final: 10 residues processed: 100 average time/residue: 0.0794 time to fit residues: 10.9490 Evaluate side-chains 85 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 355 TRP Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 976 ASN Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain B residue 1251 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 24 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 76 optimal weight: 0.0870 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 884 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 = 0.4184 r_free = 0.4184 target = 0.181495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.149774 restraints weight = 9272.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.149006 restraints weight = 13403.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.150592 restraints weight = 10106.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.154733 restraints weight = 5996.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.154844 restraints weight = 4079.910| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6904 Z= 0.112 Angle : 0.564 10.247 9390 Z= 0.286 Chirality : 0.046 0.217 1051 Planarity : 0.004 0.039 1236 Dihedral : 5.431 76.330 965 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.84 % Favored : 92.05 % Rotamer: Outliers : 2.84 % Allowed : 16.07 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.28), residues: 880 helix: 1.79 (0.53), residues: 93 sheet: -1.11 (0.26), residues: 392 loop : -2.40 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 58 TYR 0.010 0.001 TYR A 387 PHE 0.015 0.001 PHE B 971 TRP 0.006 0.001 TRP B 936 HIS 0.007 0.001 HIS B 994 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 6904) covalent geometry : angle 0.56377 ( 9390) hydrogen bonds : bond 0.03195 ( 198) hydrogen bonds : angle 5.32917 ( 555) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 98 average time/residue: 0.0886 time to fit residues: 11.7559 Evaluate side-chains 86 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 355 TRP Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 976 ASN Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain B residue 1251 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 82 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 58 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 51 optimal weight: 0.0670 chunk 32 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 884 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 = 0.4170 r_free = 0.4170 target = 0.180100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.133579 restraints weight = 9278.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.136230 restraints weight = 6175.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.137895 restraints weight = 4688.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.139151 restraints weight = 3913.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.139698 restraints weight = 3470.410| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6904 Z= 0.124 Angle : 0.579 10.021 9390 Z= 0.295 Chirality : 0.046 0.234 1051 Planarity : 0.004 0.042 1236 Dihedral : 5.447 76.059 965 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.30 % Favored : 91.59 % Rotamer: Outliers : 2.84 % Allowed : 18.78 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.28), residues: 880 helix: 1.58 (0.53), residues: 92 sheet: -1.16 (0.26), residues: 387 loop : -2.27 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 943 TYR 0.011 0.001 TYR A 387 PHE 0.018 0.001 PHE B 910 TRP 0.008 0.001 TRP A 286 HIS 0.007 0.001 HIS B 994 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 6904) covalent geometry : angle 0.57875 ( 9390) hydrogen bonds : bond 0.03196 ( 198) hydrogen bonds : angle 5.21476 ( 555) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 901 MET cc_start: 0.7232 (ppp) cc_final: 0.7022 (tmm) REVERT: B 992 VAL cc_start: 0.8230 (OUTLIER) cc_final: 0.8022 (p) outliers start: 20 outliers final: 15 residues processed: 100 average time/residue: 0.0805 time to fit residues: 11.0574 Evaluate side-chains 95 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 355 TRP Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 976 ASN Chi-restraints excluded: chain B residue 992 VAL Chi-restraints excluded: chain B residue 1031 ILE Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain B residue 1251 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 57 optimal weight: 20.0000 chunk 83 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 884 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 = 0.4144 r_free = 0.4144 target = 0.177566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.132045 restraints weight = 9396.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.134371 restraints weight = 6717.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.135261 restraints weight = 4981.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.135429 restraints weight = 4412.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.135741 restraints weight = 4531.451| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6904 Z= 0.168 Angle : 0.612 10.338 9390 Z= 0.314 Chirality : 0.047 0.263 1051 Planarity : 0.004 0.045 1236 Dihedral : 5.641 74.990 965 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.75 % Favored : 91.14 % Rotamer: Outliers : 3.70 % Allowed : 19.77 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.28), residues: 880 helix: 1.37 (0.52), residues: 92 sheet: -1.30 (0.26), residues: 378 loop : -2.23 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 474 TYR 0.015 0.002 TYR A 387 PHE 0.030 0.002 PHE B 971 TRP 0.011 0.001 TRP A 453 HIS 0.008 0.001 HIS B 994 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 6904) covalent geometry : angle 0.61151 ( 9390) hydrogen bonds : bond 0.03448 ( 198) hydrogen bonds : angle 5.28215 ( 555) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 913 MET cc_start: 0.8079 (tpp) cc_final: 0.7798 (tpp) REVERT: B 1249 GLN cc_start: 0.7066 (mt0) cc_final: 0.6528 (tt0) outliers start: 26 outliers final: 17 residues processed: 98 average time/residue: 0.0923 time to fit residues: 12.0045 Evaluate side-chains 89 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 123 TYR Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 976 ASN Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1032 VAL Chi-restraints excluded: chain B residue 1040 ILE Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain B residue 1251 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 77 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 0.0070 chunk 45 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 884 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 = 0.4156 r_free = 0.4156 target = 0.179166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.134208 restraints weight = 9149.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.136379 restraints weight = 6431.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.137616 restraints weight = 4979.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.138963 restraints weight = 4237.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.139274 restraints weight = 3775.778| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6904 Z= 0.123 Angle : 0.579 10.416 9390 Z= 0.296 Chirality : 0.046 0.260 1051 Planarity : 0.004 0.043 1236 Dihedral : 5.517 75.984 965 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.73 % Favored : 92.16 % Rotamer: Outliers : 3.98 % Allowed : 19.77 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.28), residues: 880 helix: 1.56 (0.53), residues: 92 sheet: -1.28 (0.26), residues: 377 loop : -2.22 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 477 TYR 0.011 0.001 TYR A 387 PHE 0.015 0.001 PHE A 555 TRP 0.010 0.001 TRP A 235 HIS 0.014 0.002 HIS B 994 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6904) covalent geometry : angle 0.57888 ( 9390) hydrogen bonds : bond 0.03084 ( 198) hydrogen bonds : angle 5.09847 ( 555) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.7715 (tpp-160) cc_final: 0.7353 (tpp-160) REVERT: B 1249 GLN cc_start: 0.6980 (mt0) cc_final: 0.6539 (tt0) outliers start: 28 outliers final: 18 residues processed: 99 average time/residue: 0.0743 time to fit residues: 9.9773 Evaluate side-chains 93 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 355 TRP Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 976 ASN Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1032 VAL Chi-restraints excluded: chain B residue 1040 ILE Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain B residue 1251 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 43 optimal weight: 0.4980 chunk 62 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 0.0170 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 884 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 = 0.4144 r_free = 0.4144 target = 0.177896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.132120 restraints weight = 9348.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.134518 restraints weight = 6305.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.136235 restraints weight = 4856.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.137356 restraints weight = 4065.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.137961 restraints weight = 3608.719| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6904 Z= 0.141 Angle : 0.597 10.230 9390 Z= 0.304 Chirality : 0.046 0.280 1051 Planarity : 0.004 0.043 1236 Dihedral : 5.583 75.967 965 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.98 % Favored : 90.91 % Rotamer: Outliers : 3.13 % Allowed : 20.48 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.28), residues: 880 helix: 1.49 (0.53), residues: 92 sheet: -1.22 (0.27), residues: 371 loop : -2.27 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 396 TYR 0.013 0.001 TYR A 387 PHE 0.019 0.001 PHE B 971 TRP 0.009 0.001 TRP A 453 HIS 0.013 0.002 HIS B 994 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 6904) covalent geometry : angle 0.59701 ( 9390) hydrogen bonds : bond 0.03156 ( 198) hydrogen bonds : angle 5.07129 ( 555) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 913 MET cc_start: 0.7973 (tpp) cc_final: 0.7395 (tpp) outliers start: 22 outliers final: 20 residues processed: 92 average time/residue: 0.0933 time to fit residues: 11.5116 Evaluate side-chains 95 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 355 TRP Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 976 ASN Chi-restraints excluded: chain B residue 1032 VAL Chi-restraints excluded: chain B residue 1040 ILE Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain B residue 1251 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 72 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 71 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 8 optimal weight: 0.0570 chunk 86 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN ** B 884 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 = 0.4156 r_free = 0.4156 target = 0.179106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.132929 restraints weight = 9305.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.134819 restraints weight = 6107.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.136052 restraints weight = 5200.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.138231 restraints weight = 3948.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.138434 restraints weight = 3619.544| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6904 Z= 0.116 Angle : 0.584 10.526 9390 Z= 0.297 Chirality : 0.046 0.290 1051 Planarity : 0.004 0.039 1236 Dihedral : 5.478 76.652 965 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.05 % Favored : 92.84 % Rotamer: Outliers : 3.56 % Allowed : 20.20 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.28), residues: 880 helix: 1.61 (0.53), residues: 93 sheet: -1.14 (0.27), residues: 366 loop : -2.24 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 396 TYR 0.010 0.001 TYR A 387 PHE 0.017 0.001 PHE A 555 TRP 0.008 0.001 TRP A 235 HIS 0.012 0.002 HIS B 994 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 6904) covalent geometry : angle 0.58377 ( 9390) hydrogen bonds : bond 0.02949 ( 198) hydrogen bonds : angle 4.93581 ( 555) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 TYR cc_start: 0.6928 (m-80) cc_final: 0.6698 (m-80) REVERT: B 913 MET cc_start: 0.7970 (tpp) cc_final: 0.7419 (tpp) REVERT: B 1249 GLN cc_start: 0.7037 (mt0) cc_final: 0.6457 (tt0) outliers start: 25 outliers final: 24 residues processed: 94 average time/residue: 0.0865 time to fit residues: 10.9854 Evaluate side-chains 98 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 355 TRP Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 976 ASN Chi-restraints excluded: chain B residue 1031 ILE Chi-restraints excluded: chain B residue 1032 VAL Chi-restraints excluded: chain B residue 1040 ILE Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain B residue 1251 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 69 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 43 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN ** B 884 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 = 0.4140 r_free = 0.4140 target = 0.177370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.132902 restraints weight = 9317.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.134919 restraints weight = 6201.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.135511 restraints weight = 4479.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.135755 restraints weight = 4383.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.135871 restraints weight = 4336.988| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6904 Z= 0.156 Angle : 0.612 10.757 9390 Z= 0.313 Chirality : 0.047 0.310 1051 Planarity : 0.004 0.039 1236 Dihedral : 5.582 76.334 965 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.98 % Favored : 90.91 % Rotamer: Outliers : 3.70 % Allowed : 20.48 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.28), residues: 880 helix: 1.58 (0.53), residues: 92 sheet: -1.23 (0.27), residues: 371 loop : -2.22 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 477 TYR 0.014 0.001 TYR A 387 PHE 0.022 0.001 PHE B 971 TRP 0.011 0.001 TRP A 453 HIS 0.012 0.002 HIS B 994 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 6904) covalent geometry : angle 0.61163 ( 9390) hydrogen bonds : bond 0.03144 ( 198) hydrogen bonds : angle 5.00405 ( 555) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.7931 (tpp-160) cc_final: 0.7590 (tpp-160) REVERT: B 913 MET cc_start: 0.7957 (tpp) cc_final: 0.7686 (tpp) REVERT: B 1129 LYS cc_start: 0.6475 (ttpt) cc_final: 0.6120 (tttp) REVERT: B 1249 GLN cc_start: 0.7041 (mt0) cc_final: 0.6537 (tt0) outliers start: 26 outliers final: 26 residues processed: 93 average time/residue: 0.0858 time to fit residues: 10.7891 Evaluate side-chains 99 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 355 TRP Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 976 ASN Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1031 ILE Chi-restraints excluded: chain B residue 1032 VAL Chi-restraints excluded: chain B residue 1040 ILE Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain B residue 1251 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 57 optimal weight: 30.0000 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 884 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 = 0.4141 r_free = 0.4141 target = 0.177613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.134556 restraints weight = 9364.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.134998 restraints weight = 6990.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.135480 restraints weight = 5240.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.135722 restraints weight = 4707.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.136007 restraints weight = 4463.545| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6904 Z= 0.136 Angle : 0.600 10.742 9390 Z= 0.306 Chirality : 0.046 0.309 1051 Planarity : 0.004 0.040 1236 Dihedral : 5.561 76.466 965 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.18 % Favored : 91.70 % Rotamer: Outliers : 3.84 % Allowed : 20.77 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.28), residues: 880 helix: 1.54 (0.53), residues: 93 sheet: -1.23 (0.26), residues: 378 loop : -2.18 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 396 TYR 0.012 0.001 TYR A 387 PHE 0.008 0.001 PHE B 910 TRP 0.009 0.001 TRP A 286 HIS 0.012 0.002 HIS B 994 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6904) covalent geometry : angle 0.60027 ( 9390) hydrogen bonds : bond 0.03060 ( 198) hydrogen bonds : angle 4.96371 ( 555) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1499.42 seconds wall clock time: 26 minutes 27.87 seconds (1587.87 seconds total)