Starting phenix.real_space_refine on Tue Feb 3 20:03:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xdd_66763/02_2026/9xdd_66763.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xdd_66763/02_2026/9xdd_66763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xdd_66763/02_2026/9xdd_66763.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xdd_66763/02_2026/9xdd_66763.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xdd_66763/02_2026/9xdd_66763.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xdd_66763/02_2026/9xdd_66763.map" } resolution = 3.82 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= 0.013 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 12 5.16 5 C 4085 2.51 5 N 1123 2.21 5 O 1238 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s 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: 6458 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4238 Classifications: {'peptide': 544} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 23, 'TRANS': 520} Chain breaks: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 4, 'TYR:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 2220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2220 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 277} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 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: 1.47, per 1000 atoms: 0.23 Number of scatterers: 6458 At special positions: 0 Unit cell: (69.72, 82.32, 168.84, 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 12 16.00 O 1238 8.00 N 1123 7.00 C 4085 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: 0.58 Conformation dependent library (CDL) restraints added in 231.1 milliseconds 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1526 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 9 sheets defined 15.0% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 33 through 44 removed outlier: 3.719A pdb=" N LYS A 37 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 72 removed outlier: 4.195A pdb=" N ALA A 59 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG A 60 " --> pdb=" O ARG A 56 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU A 72 " --> pdb=" O GLY A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 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 removed outlier: 3.500A pdb=" N LYS A 147 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 209 removed outlier: 4.228A pdb=" N GLN A 207 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 232 removed outlier: 3.887A pdb=" N LEU A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 removed outlier: 3.582A pdb=" N THR A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 421 removed outlier: 3.657A pdb=" N TRP A 420 " --> pdb=" O ASN A 417 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY A 421 " --> pdb=" O THR A 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 417 through 421' Processing helix chain 'A' and resid 458 through 462 Processing helix chain 'A' and resid 463 through 467 Processing helix chain 'B' and resid 1107 through 1111 Processing helix chain 'B' and resid 1139 through 1150 removed outlier: 3.804A pdb=" N SER B1145 " --> pdb=" O GLN B1141 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR B1146 " --> pdb=" O ALA B1142 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B1147 " --> pdb=" O ALA B1143 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG B1149 " --> pdb=" O SER B1145 " (cutoff:3.500A) Processing helix chain 'B' and resid 1159 through 1166 removed outlier: 3.829A pdb=" N MET B1163 " --> pdb=" O ASP B1159 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29 removed outlier: 7.465A pdb=" N GLN A 27 " --> pdb=" O ALA A 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 106 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 105 through 106 current: chain 'A' and resid 176 through 181 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: 5.823A pdb=" N LEU A 254 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N HIS A 193 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR A 195 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR A 257 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL A 241 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A 259 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL A 239 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER A 261 " --> pdb=" O ASN A 237 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 273 through 274 removed outlier: 3.654A pdb=" N ALA A 556 " --> pdb=" O GLN A 568 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR A 570 " --> pdb=" O ASP A 554 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASP A 554 " --> pdb=" O TYR A 570 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N GLY A 572 " --> pdb=" O LYS A 552 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LYS A 552 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY A 537 " --> pdb=" O ASP A 521 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 517 " --> pdb=" O GLY A 541 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLY A 516 " --> pdb=" O ASN A 509 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ASN A 509 " --> pdb=" O GLY A 516 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL A 518 " --> pdb=" O GLN A 507 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N GLN A 507 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 282 through 288 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 297 through 304 current: chain 'A' and resid 327 through 339 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 342 through 344 current: chain 'A' and resid 370 through 376 Processing sheet with id=AA6, first strand: chain 'A' and resid 365 through 367 removed outlier: 3.583A pdb=" N GLY A 389 " --> pdb=" O ASN A 366 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR A 450 " --> pdb=" O THR A 501 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 393 through 395 removed outlier: 3.618A pdb=" N ARG A 394 " --> pdb=" O GLN A 409 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 438 through 439 Processing sheet with id=AA9, first strand: chain 'B' and resid 914 through 915 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 914 through 915 current: chain 'B' and resid 927 through 935 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 944 through 949 current: chain 'B' and resid 961 through 973 removed outlier: 7.173A pdb=" N ARG B 962 " --> pdb=" O ALA B 989 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ALA B 989 " --> pdb=" O ARG B 962 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASP B 964 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B1031 " --> pdb=" O GLY B 982 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS B1033 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 986 " --> pdb=" O HIS B1033 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1026 through 1034 current: chain 'B' and resid 1061 through 1070 removed outlier: 3.510A pdb=" N GLY B1066 " --> pdb=" O PHE B1091 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE B1091 " --> pdb=" O GLY B1066 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY B1087 " --> pdb=" O ILE B1070 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N VAL B1084 " --> pdb=" O ILE B1105 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE B1105 " --> pdb=" O VAL B1084 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS B1086 " --> pdb=" O GLU B1103 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY B1123 " --> pdb=" O LEU B1100 " (cutoff:3.500A) 162 hydrogen bonds defined for protein. 411 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: 0.94 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: 2168 1.34 - 1.46: 1269 1.46 - 1.57: 3140 1.57 - 1.69: 0 1.69 - 1.80: 24 Bond restraints: 6601 Sorted by residual: bond pdb=" C TRP A 290 " pdb=" N MET A 291 " ideal model delta sigma weight residual 1.332 1.320 0.013 1.40e-02 5.10e+03 8.22e-01 bond pdb=" CA VAL B 993 " pdb=" C VAL B 993 " ideal model delta sigma weight residual 1.523 1.534 -0.011 1.27e-02 6.20e+03 8.03e-01 bond pdb=" CG LEU A 113 " pdb=" CD1 LEU A 113 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.34e-01 bond pdb=" N GLY A 523 " pdb=" CA GLY A 523 " ideal model delta sigma weight residual 1.454 1.447 0.008 9.90e-03 1.02e+04 5.95e-01 bond pdb=" C TYR A 183 " pdb=" N ASN A 184 " ideal model delta sigma weight residual 1.332 1.322 0.010 1.31e-02 5.83e+03 5.84e-01 ... (remaining 6596 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 8652 1.25 - 2.51: 270 2.51 - 3.76: 49 3.76 - 5.01: 7 5.01 - 6.26: 3 Bond angle restraints: 8981 Sorted by residual: angle pdb=" C ASP A 473 " pdb=" N ARG A 474 " pdb=" CA ARG A 474 " ideal model delta sigma weight residual 121.54 125.96 -4.42 1.91e+00 2.74e-01 5.35e+00 angle pdb=" CA VAL B1003 " pdb=" C VAL B1003 " pdb=" N SER B1004 " ideal model delta sigma weight residual 116.60 119.85 -3.25 1.45e+00 4.76e-01 5.02e+00 angle pdb=" CA ARG A 353 " pdb=" CB ARG A 353 " pdb=" CG ARG A 353 " ideal model delta sigma weight residual 114.10 118.47 -4.37 2.00e+00 2.50e-01 4.78e+00 angle pdb=" CA GLY A 537 " pdb=" C GLY A 537 " pdb=" N THR A 538 " ideal model delta sigma weight residual 115.09 117.89 -2.80 1.29e+00 6.01e-01 4.72e+00 angle pdb=" N VAL B1003 " pdb=" CA VAL B1003 " pdb=" C VAL B1003 " ideal model delta sigma weight residual 109.34 113.59 -4.25 2.08e+00 2.31e-01 4.17e+00 ... (remaining 8976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 3484 16.97 - 33.94: 342 33.94 - 50.90: 55 50.90 - 67.87: 12 67.87 - 84.84: 8 Dihedral angle restraints: 3901 sinusoidal: 1511 harmonic: 2390 Sorted by residual: dihedral pdb=" CA ARG A 202 " pdb=" C ARG A 202 " pdb=" N ASP A 203 " pdb=" CA ASP A 203 " ideal model delta harmonic sigma weight residual -180.00 -158.60 -21.40 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ASP A 414 " pdb=" CB ASP A 414 " pdb=" CG ASP A 414 " pdb=" OD1 ASP A 414 " ideal model delta sinusoidal sigma weight residual -30.00 -88.00 58.00 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP A 407 " pdb=" CB ASP A 407 " pdb=" CG ASP A 407 " pdb=" OD1 ASP A 407 " ideal model delta sinusoidal sigma weight residual -30.00 -87.81 57.81 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 3898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 607 0.032 - 0.063: 249 0.063 - 0.095: 74 0.095 - 0.126: 61 0.126 - 0.158: 7 Chirality restraints: 998 Sorted by residual: 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 2.59 -0.16 2.00e-01 2.50e+01 6.23e-01 chirality pdb=" CA ILE B1024 " pdb=" N ILE B1024 " pdb=" C ILE B1024 " pdb=" CB ILE B1024 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-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 4.54e-01 ... (remaining 995 not shown) Planarity restraints: 1179 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 958 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO B 959 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 959 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 959 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 986 " 0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO B 987 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 993 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" C VAL B 993 " 0.023 2.00e-02 2.50e+03 pdb=" O VAL B 993 " -0.009 2.00e-02 2.50e+03 pdb=" N HIS B 994 " -0.008 2.00e-02 2.50e+03 ... (remaining 1176 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 216 2.71 - 3.26: 6145 3.26 - 3.80: 9539 3.80 - 4.35: 11092 4.35 - 4.90: 19653 Nonbonded interactions: 46645 Sorted by model distance: nonbonded pdb=" OD2 ASP B 875 " pdb=" OG SER B 878 " model vdw 2.158 3.040 nonbonded pdb=" OG SER A 305 " pdb=" O GLU A 308 " model vdw 2.161 3.040 nonbonded pdb=" OG1 THR A 302 " pdb=" O THR A 310 " model vdw 2.194 3.040 nonbonded pdb=" OG1 THR B 974 " pdb=" O LEU B 977 " model vdw 2.211 3.040 nonbonded pdb=" O LYS A 156 " pdb=" NH2 ARG A 188 " model vdw 2.225 3.120 ... (remaining 46640 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: 5.020 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.690 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6601 Z= 0.157 Angle : 0.546 6.263 8981 Z= 0.294 Chirality : 0.044 0.158 998 Planarity : 0.004 0.051 1179 Dihedral : 13.982 84.838 2375 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.47 % Favored : 93.41 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.28), residues: 835 helix: -0.07 (0.59), residues: 74 sheet: -0.84 (0.28), residues: 362 loop : -1.59 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 114 TYR 0.014 0.002 TYR A 218 PHE 0.012 0.001 PHE A 429 TRP 0.020 0.002 TRP A 355 HIS 0.004 0.001 HIS B 994 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 6601) covalent geometry : angle 0.54619 ( 8981) hydrogen bonds : bond 0.28503 ( 162) hydrogen bonds : angle 11.46104 ( 411) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 361 TRP cc_start: 0.7386 (m100) cc_final: 0.6953 (m100) REVERT: B 897 MET cc_start: 0.7692 (mmm) cc_final: 0.7420 (mmt) REVERT: B 942 TRP cc_start: 0.6763 (p-90) cc_final: 0.6535 (p90) REVERT: B 980 LEU cc_start: 0.9181 (tp) cc_final: 0.8965 (tt) REVERT: B 1166 MET cc_start: 0.6412 (tmm) cc_final: 0.6196 (tmm) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.0917 time to fit residues: 15.6986 Evaluate side-chains 79 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.0020 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 overall best weight: 1.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 376 GLN A 381 ASN B1076 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.161042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3713 r_free = 0.3713 target = 0.126284 restraints weight = 11011.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.124700 restraints weight = 14404.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.125722 restraints weight = 12734.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.123615 restraints weight = 10544.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.123999 restraints weight = 11155.778| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6601 Z= 0.220 Angle : 0.672 8.487 8981 Z= 0.352 Chirality : 0.048 0.167 998 Planarity : 0.005 0.052 1179 Dihedral : 4.808 22.918 914 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.78 % Favored : 92.10 % Rotamer: Outliers : 1.92 % Allowed : 10.32 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.28), residues: 835 helix: 0.40 (0.59), residues: 82 sheet: -0.92 (0.28), residues: 346 loop : -1.66 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 188 TYR 0.019 0.002 TYR A 411 PHE 0.019 0.002 PHE B 882 TRP 0.019 0.002 TRP A 369 HIS 0.007 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00498 ( 6601) covalent geometry : angle 0.67216 ( 8981) hydrogen bonds : bond 0.05320 ( 162) hydrogen bonds : angle 7.83297 ( 411) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.7081 (mmt90) cc_final: 0.6862 (tpp80) REVERT: A 291 MET cc_start: 0.8366 (tpp) cc_final: 0.7991 (mmm) REVERT: B 882 PHE cc_start: 0.7145 (m-10) cc_final: 0.6940 (m-10) outliers start: 13 outliers final: 10 residues processed: 90 average time/residue: 0.0816 time to fit residues: 9.8004 Evaluate side-chains 86 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 923 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 81 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4120 r_free = 0.4120 target = 0.163670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.128515 restraints weight = 10802.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.125742 restraints weight = 12271.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.122143 restraints weight = 8412.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.122112 restraints weight = 8536.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.122223 restraints weight = 8422.451| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6601 Z= 0.130 Angle : 0.566 7.908 8981 Z= 0.294 Chirality : 0.046 0.156 998 Planarity : 0.004 0.053 1179 Dihedral : 4.506 22.016 914 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.27 % Favored : 94.61 % Rotamer: Outliers : 2.65 % Allowed : 12.83 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.29), residues: 835 helix: 0.44 (0.58), residues: 82 sheet: -0.79 (0.28), residues: 361 loop : -1.64 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 188 TYR 0.009 0.001 TYR A 411 PHE 0.009 0.001 PHE B 899 TRP 0.016 0.002 TRP A 369 HIS 0.004 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6601) covalent geometry : angle 0.56613 ( 8981) hydrogen bonds : bond 0.04165 ( 162) hydrogen bonds : angle 6.69311 ( 411) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.7189 (mmt90) cc_final: 0.6944 (tpp80) REVERT: A 361 TRP cc_start: 0.7430 (m100) cc_final: 0.7027 (m100) REVERT: A 570 TYR cc_start: 0.5793 (OUTLIER) cc_final: 0.4096 (m-80) REVERT: B 882 PHE cc_start: 0.7671 (m-10) cc_final: 0.7384 (m-10) outliers start: 18 outliers final: 9 residues processed: 94 average time/residue: 0.0700 time to fit residues: 8.8823 Evaluate side-chains 85 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain A residue 570 TYR Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 923 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 24 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 55 optimal weight: 0.0050 chunk 66 optimal weight: 0.7980 chunk 17 optimal weight: 0.0370 chunk 63 optimal weight: 1.9990 overall best weight: 0.5072 ------------------------------------------------------------------------------- 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 = 0.4142 r_free = 0.4142 target = 0.165753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 117)---------------| | r_work = 0.3638 r_free = 0.3638 target = 0.122607 restraints weight = 10682.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.123140 restraints weight = 8660.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.123453 restraints weight = 7860.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.123629 restraints weight = 7355.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.123821 restraints weight = 7251.178| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6601 Z= 0.104 Angle : 0.555 8.337 8981 Z= 0.283 Chirality : 0.045 0.148 998 Planarity : 0.004 0.050 1179 Dihedral : 4.330 20.554 914 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.79 % Favored : 95.09 % Rotamer: Outliers : 2.36 % Allowed : 14.90 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.29), residues: 835 helix: 0.59 (0.58), residues: 82 sheet: -0.78 (0.28), residues: 356 loop : -1.57 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 130 TYR 0.018 0.001 TYR A 274 PHE 0.017 0.001 PHE B 899 TRP 0.023 0.001 TRP B 942 HIS 0.003 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 6601) covalent geometry : angle 0.55545 ( 8981) hydrogen bonds : bond 0.03584 ( 162) hydrogen bonds : angle 6.15615 ( 411) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.7131 (mmt90) cc_final: 0.6901 (tpp80) REVERT: A 204 GLU cc_start: 0.6515 (OUTLIER) cc_final: 0.6088 (tp30) REVERT: A 361 TRP cc_start: 0.7378 (m100) cc_final: 0.7025 (m100) REVERT: A 415 TYR cc_start: 0.7417 (t80) cc_final: 0.6923 (m-80) REVERT: B 882 PHE cc_start: 0.7954 (m-10) cc_final: 0.7638 (m-10) REVERT: B 971 PHE cc_start: 0.7043 (t80) cc_final: 0.6804 (t80) REVERT: B 1166 MET cc_start: 0.6153 (tmm) cc_final: 0.5810 (tmm) outliers start: 16 outliers final: 12 residues processed: 93 average time/residue: 0.0813 time to fit residues: 9.9497 Evaluate side-chains 88 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 960 MET Chi-restraints excluded: chain B residue 1032 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 62 optimal weight: 5.9990 chunk 67 optimal weight: 0.0270 chunk 59 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 25 optimal weight: 0.0470 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- 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 = 0.4148 r_free = 0.4148 target = 0.166562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.122580 restraints weight = 10970.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.123580 restraints weight = 8437.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.124058 restraints weight = 7144.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.123879 restraints weight = 6477.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.124136 restraints weight = 6741.129| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6601 Z= 0.097 Angle : 0.540 7.904 8981 Z= 0.277 Chirality : 0.045 0.145 998 Planarity : 0.004 0.050 1179 Dihedral : 4.264 20.142 914 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.91 % Favored : 94.97 % Rotamer: Outliers : 2.21 % Allowed : 16.37 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.29), residues: 835 helix: 0.76 (0.59), residues: 82 sheet: -0.74 (0.29), residues: 330 loop : -1.50 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 130 TYR 0.006 0.001 TYR A 411 PHE 0.022 0.001 PHE B 899 TRP 0.017 0.001 TRP A 369 HIS 0.003 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 6601) covalent geometry : angle 0.53981 ( 8981) hydrogen bonds : bond 0.03454 ( 162) hydrogen bonds : angle 5.87499 ( 411) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8537 (t0) cc_final: 0.8259 (t0) REVERT: A 204 GLU cc_start: 0.6293 (OUTLIER) cc_final: 0.5988 (tp30) REVERT: A 361 TRP cc_start: 0.7348 (m100) cc_final: 0.7055 (m100) REVERT: A 415 TYR cc_start: 0.7383 (t80) cc_final: 0.6847 (m-80) REVERT: A 570 TYR cc_start: 0.5551 (OUTLIER) cc_final: 0.4026 (m-80) REVERT: B 882 PHE cc_start: 0.7977 (m-10) cc_final: 0.7706 (m-10) REVERT: B 971 PHE cc_start: 0.7203 (t80) cc_final: 0.6902 (t80) REVERT: B 972 GLU cc_start: 0.8299 (mp0) cc_final: 0.7909 (mp0) REVERT: B 1131 GLU cc_start: 0.6781 (pm20) cc_final: 0.6559 (pm20) outliers start: 15 outliers final: 10 residues processed: 93 average time/residue: 0.0829 time to fit residues: 10.2080 Evaluate side-chains 94 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain A residue 570 TYR Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 960 MET Chi-restraints excluded: chain B residue 1032 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 29 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 69 optimal weight: 0.3980 chunk 35 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4140 r_free = 0.4140 target = 0.165462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3648 r_free = 0.3648 target = 0.122427 restraints weight = 10651.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.122154 restraints weight = 9792.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.123189 restraints weight = 8070.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.123669 restraints weight = 7074.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.124392 restraints weight = 6557.708| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6601 Z= 0.122 Angle : 0.547 7.715 8981 Z= 0.281 Chirality : 0.046 0.147 998 Planarity : 0.004 0.050 1179 Dihedral : 4.283 19.968 914 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.75 % Favored : 94.13 % Rotamer: Outliers : 2.36 % Allowed : 16.96 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.29), residues: 835 helix: 0.82 (0.58), residues: 81 sheet: -0.80 (0.29), residues: 341 loop : -1.45 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 188 TYR 0.016 0.001 TYR A 274 PHE 0.009 0.001 PHE B 899 TRP 0.026 0.002 TRP B 942 HIS 0.003 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 6601) covalent geometry : angle 0.54658 ( 8981) hydrogen bonds : bond 0.03565 ( 162) hydrogen bonds : angle 5.74754 ( 411) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 204 GLU cc_start: 0.6261 (OUTLIER) cc_final: 0.5954 (tp30) REVERT: A 338 ASP cc_start: 0.7408 (t0) cc_final: 0.7187 (t0) REVERT: A 361 TRP cc_start: 0.7373 (m100) cc_final: 0.7066 (m100) REVERT: A 415 TYR cc_start: 0.7362 (t80) cc_final: 0.6852 (m-80) REVERT: A 570 TYR cc_start: 0.5704 (OUTLIER) cc_final: 0.4179 (m-80) REVERT: B 882 PHE cc_start: 0.7815 (m-10) cc_final: 0.7586 (m-10) REVERT: B 972 GLU cc_start: 0.8210 (mp0) cc_final: 0.7820 (mp0) REVERT: B 1166 MET cc_start: 0.6200 (tmm) cc_final: 0.5921 (tmm) outliers start: 16 outliers final: 11 residues processed: 93 average time/residue: 0.0882 time to fit residues: 10.8345 Evaluate side-chains 91 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain A residue 570 TYR Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 1032 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.4127 r_free = 0.4127 target = 0.164205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.135718 restraints weight = 10679.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.122264 restraints weight = 15564.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.122702 restraints weight = 14730.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.123080 restraints weight = 11469.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.123391 restraints weight = 10365.714| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6601 Z= 0.143 Angle : 0.572 7.093 8981 Z= 0.293 Chirality : 0.046 0.150 998 Planarity : 0.004 0.051 1179 Dihedral : 4.409 20.443 914 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.35 % Favored : 93.53 % Rotamer: Outliers : 2.51 % Allowed : 17.99 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.29), residues: 835 helix: 0.81 (0.59), residues: 81 sheet: -0.96 (0.29), residues: 331 loop : -1.43 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 56 TYR 0.015 0.001 TYR A 274 PHE 0.010 0.001 PHE B 910 TRP 0.019 0.001 TRP A 369 HIS 0.003 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 6601) covalent geometry : angle 0.57164 ( 8981) hydrogen bonds : bond 0.03590 ( 162) hydrogen bonds : angle 5.67757 ( 411) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 204 GLU cc_start: 0.6296 (OUTLIER) cc_final: 0.6080 (tp30) REVERT: A 361 TRP cc_start: 0.7398 (m100) cc_final: 0.7044 (m100) REVERT: A 415 TYR cc_start: 0.7387 (t80) cc_final: 0.6971 (m-80) REVERT: A 570 TYR cc_start: 0.5826 (OUTLIER) cc_final: 0.4184 (m-80) REVERT: B 1131 GLU cc_start: 0.7193 (pm20) cc_final: 0.6483 (pm20) REVERT: B 1166 MET cc_start: 0.6293 (tmm) cc_final: 0.6081 (tmm) outliers start: 17 outliers final: 14 residues processed: 94 average time/residue: 0.0755 time to fit residues: 9.2438 Evaluate side-chains 96 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain A residue 570 TYR Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 1032 VAL Chi-restraints excluded: chain B residue 1103 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 13 optimal weight: 0.2980 chunk 12 optimal weight: 0.2980 chunk 19 optimal weight: 0.1980 chunk 82 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4150 r_free = 0.4150 target = 0.166456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.137416 restraints weight = 10583.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.124932 restraints weight = 13654.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.125270 restraints weight = 14019.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.125764 restraints weight = 10810.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.125933 restraints weight = 9409.762| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6601 Z= 0.110 Angle : 0.562 7.525 8981 Z= 0.289 Chirality : 0.046 0.148 998 Planarity : 0.004 0.051 1179 Dihedral : 4.291 20.382 914 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.39 % Favored : 94.49 % Rotamer: Outliers : 2.51 % Allowed : 19.03 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.29), residues: 835 helix: 0.82 (0.58), residues: 83 sheet: -0.77 (0.29), residues: 332 loop : -1.52 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 58 TYR 0.014 0.001 TYR A 274 PHE 0.014 0.001 PHE B 971 TRP 0.020 0.001 TRP A 369 HIS 0.003 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 6601) covalent geometry : angle 0.56182 ( 8981) hydrogen bonds : bond 0.03389 ( 162) hydrogen bonds : angle 5.53815 ( 411) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 361 TRP cc_start: 0.7138 (m100) cc_final: 0.6840 (m100) REVERT: A 415 TYR cc_start: 0.7318 (t80) cc_final: 0.6935 (m-80) REVERT: A 501 THR cc_start: 0.7871 (t) cc_final: 0.6432 (p) REVERT: A 570 TYR cc_start: 0.5712 (OUTLIER) cc_final: 0.4229 (m-80) REVERT: B 1131 GLU cc_start: 0.7231 (pm20) cc_final: 0.6447 (pm20) REVERT: B 1166 MET cc_start: 0.6251 (tmm) cc_final: 0.6045 (tmm) outliers start: 17 outliers final: 14 residues processed: 99 average time/residue: 0.0740 time to fit residues: 9.6964 Evaluate side-chains 96 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain A residue 570 TYR Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 1032 VAL Chi-restraints excluded: chain B residue 1100 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 1 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 9 optimal weight: 0.1980 chunk 0 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 51 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4152 r_free = 0.4152 target = 0.166597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.122493 restraints weight = 10746.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.123906 restraints weight = 8356.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.124674 restraints weight = 7070.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.124681 restraints weight = 6435.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.125116 restraints weight = 6422.988| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6601 Z= 0.113 Angle : 0.570 7.142 8981 Z= 0.293 Chirality : 0.045 0.150 998 Planarity : 0.004 0.050 1179 Dihedral : 4.291 18.094 914 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.39 % Favored : 94.49 % Rotamer: Outliers : 2.51 % Allowed : 19.62 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.29), residues: 835 helix: 0.80 (0.57), residues: 83 sheet: -0.84 (0.29), residues: 345 loop : -1.50 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1106 TYR 0.015 0.001 TYR B 929 PHE 0.038 0.001 PHE B 882 TRP 0.020 0.001 TRP A 369 HIS 0.003 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 6601) covalent geometry : angle 0.57016 ( 8981) hydrogen bonds : bond 0.03373 ( 162) hydrogen bonds : angle 5.44424 ( 411) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 361 TRP cc_start: 0.7362 (m100) cc_final: 0.7068 (m100) REVERT: A 415 TYR cc_start: 0.7336 (t80) cc_final: 0.6861 (m-80) REVERT: B 1003 VAL cc_start: 0.8865 (OUTLIER) cc_final: 0.8637 (t) outliers start: 17 outliers final: 15 residues processed: 92 average time/residue: 0.0667 time to fit residues: 8.2873 Evaluate side-chains 94 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 477 ARG Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1032 VAL Chi-restraints excluded: chain B residue 1100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 78 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4154 r_free = 0.4154 target = 0.166559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.133546 restraints weight = 10429.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.126294 restraints weight = 15592.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.125747 restraints weight = 11599.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.125617 restraints weight = 12019.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.125863 restraints weight = 9810.529| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6601 Z= 0.115 Angle : 0.573 8.114 8981 Z= 0.295 Chirality : 0.046 0.144 998 Planarity : 0.004 0.050 1179 Dihedral : 4.279 14.871 914 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.63 % Favored : 94.25 % Rotamer: Outliers : 2.36 % Allowed : 20.50 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.29), residues: 835 helix: 0.78 (0.57), residues: 83 sheet: -0.88 (0.29), residues: 345 loop : -1.48 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1106 TYR 0.019 0.001 TYR B 929 PHE 0.014 0.001 PHE A 519 TRP 0.021 0.001 TRP A 369 HIS 0.003 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 6601) covalent geometry : angle 0.57269 ( 8981) hydrogen bonds : bond 0.03354 ( 162) hydrogen bonds : angle 5.37276 ( 411) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 361 TRP cc_start: 0.7342 (m100) cc_final: 0.7059 (m100) REVERT: A 384 MET cc_start: 0.6661 (tmm) cc_final: 0.6340 (tmm) REVERT: A 415 TYR cc_start: 0.7322 (t80) cc_final: 0.6939 (m-80) REVERT: B 1003 VAL cc_start: 0.8925 (OUTLIER) cc_final: 0.8696 (t) REVERT: B 1112 GLU cc_start: 0.6874 (mm-30) cc_final: 0.6477 (mm-30) outliers start: 16 outliers final: 13 residues processed: 90 average time/residue: 0.0843 time to fit residues: 9.9013 Evaluate side-chains 93 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1032 VAL Chi-restraints excluded: chain B residue 1100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 80 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 57 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4140 r_free = 0.4140 target = 0.165526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.134352 restraints weight = 10451.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.122526 restraints weight = 14320.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.123448 restraints weight = 12681.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.123906 restraints weight = 9464.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.124113 restraints weight = 8271.542| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6601 Z= 0.131 Angle : 0.592 8.275 8981 Z= 0.302 Chirality : 0.046 0.146 998 Planarity : 0.004 0.050 1179 Dihedral : 4.369 15.817 914 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.23 % Favored : 93.65 % Rotamer: Outliers : 2.21 % Allowed : 20.35 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.29), residues: 835 helix: 0.74 (0.58), residues: 81 sheet: -0.96 (0.28), residues: 362 loop : -1.40 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 477 TYR 0.011 0.001 TYR A 411 PHE 0.015 0.001 PHE A 519 TRP 0.020 0.001 TRP A 369 HIS 0.004 0.001 HIS B 994 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 6601) covalent geometry : angle 0.59205 ( 8981) hydrogen bonds : bond 0.03383 ( 162) hydrogen bonds : angle 5.33072 ( 411) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1314.65 seconds wall clock time: 23 minutes 14.75 seconds (1394.75 seconds total)