Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:40:26 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdh_13338/11_2022/7pdh_13338.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdh_13338/11_2022/7pdh_13338.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdh_13338/11_2022/7pdh_13338.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdh_13338/11_2022/7pdh_13338.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdh_13338/11_2022/7pdh_13338.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdh_13338/11_2022/7pdh_13338.pdb" } resolution = 4.0 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 ------------------------------------------------------------------------------- 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= 0.000 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 392": "OE1" <-> "OE2" Residue "A TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 130": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 4516 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3550 Classifications: {'peptide': 449} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 439} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 966 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Time building chain proxies: 3.33, per 1000 atoms: 0.74 Number of scatterers: 4516 At special positions: 0 Unit cell: (95.598, 77.97, 77.97, 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 33 16.00 O 864 8.00 N 772 7.00 C 2847 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 - 3.50 Amino acid : False - 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: 1.98 Conformation dependent library (CDL) restraints added in 674.7 milliseconds 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1058 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 4 sheets defined 49.7% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 320 through 336 removed outlier: 3.688A pdb=" N GLU A 324 " --> pdb=" O GLY A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 351 through 359 Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 413 through 434 Processing helix chain 'A' and resid 457 through 481 Processing helix chain 'A' and resid 511 through 523 removed outlier: 4.101A pdb=" N ASN A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 537 Processing helix chain 'A' and resid 1021 through 1037 Processing helix chain 'A' and resid 1038 through 1046 removed outlier: 3.581A pdb=" N LYS A1046 " --> pdb=" O ALA A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1072 Processing helix chain 'A' and resid 1079 through 1097 removed outlier: 3.924A pdb=" N TYR A1083 " --> pdb=" O GLY A1079 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A1097 " --> pdb=" O PHE A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1157 removed outlier: 4.308A pdb=" N GLN A1137 " --> pdb=" O GLN A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1201 removed outlier: 4.063A pdb=" N ASN A1193 " --> pdb=" O GLY A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1219 removed outlier: 4.192A pdb=" N LYS A1219 " --> pdb=" O ARG A1215 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 25 removed outlier: 3.587A pdb=" N LYS B 16 " --> pdb=" O SER B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 35 removed outlier: 3.688A pdb=" N VAL B 30 " --> pdb=" O GLN B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 58 Processing helix chain 'B' and resid 59 through 70 Processing helix chain 'B' and resid 82 through 91 Processing helix chain 'B' and resid 92 through 101 Processing helix chain 'B' and resid 115 through 123 removed outlier: 3.735A pdb=" N LEU B 119 " --> pdb=" O THR B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 133 removed outlier: 4.157A pdb=" N ALA B 129 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 436 through 441 removed outlier: 3.788A pdb=" N ILE A 438 " --> pdb=" O TYR A 446 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N TYR A 446 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N THR A 440 " --> pdb=" O CYS A 444 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N CYS A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER A 394 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N GLY A 493 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER A 394 " --> pdb=" O HIS A 491 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N HIS A 491 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU A 396 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY A 489 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA A 398 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ARG A 487 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE A 400 " --> pdb=" O ASN A 485 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASN A 485 " --> pdb=" O ILE A 400 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 441 removed outlier: 3.788A pdb=" N ILE A 438 " --> pdb=" O TYR A 446 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N TYR A 446 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N THR A 440 " --> pdb=" O CYS A 444 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N CYS A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER A 394 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N GLY A 493 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER A 394 " --> pdb=" O HIS A 491 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N HIS A 491 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU A 396 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY A 489 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA A 398 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ARG A 487 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE A 400 " --> pdb=" O ASN A 485 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASN A 485 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N HIS A 530 " --> pdb=" O MET A 486 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL A 488 " --> pdb=" O HIS A 530 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N SER A 532 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N VAL A 490 " --> pdb=" O SER A 532 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1105 through 1109 removed outlier: 7.386A pdb=" N MET A1116 " --> pdb=" O ILE A1108 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER A1119 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY A1059 " --> pdb=" O SER A1119 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER A1057 " --> pdb=" O GLY A1171 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLY A1171 " --> pdb=" O SER A1057 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLY A1059 " --> pdb=" O ASN A1169 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN A1169 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE A1061 " --> pdb=" O GLY A1167 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY A1167 " --> pdb=" O ILE A1061 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA A1063 " --> pdb=" O ARG A1165 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG A1165 " --> pdb=" O ALA A1063 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1105 through 1109 removed outlier: 7.386A pdb=" N MET A1116 " --> pdb=" O ILE A1108 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER A1119 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY A1059 " --> pdb=" O SER A1119 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER A1057 " --> pdb=" O GLY A1171 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLY A1171 " --> pdb=" O SER A1057 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLY A1059 " --> pdb=" O ASN A1169 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN A1169 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE A1061 " --> pdb=" O GLY A1167 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY A1167 " --> pdb=" O ILE A1061 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA A1063 " --> pdb=" O ARG A1165 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG A1165 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR A1241 " --> pdb=" O VAL A1209 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY A1228 " --> pdb=" O THR A1240 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU A1242 " --> pdb=" O TYR A1226 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N TYR A1226 " --> pdb=" O LEU A1242 " (cutoff:3.500A) 251 hydrogen bonds defined for protein. 723 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: 1.54 Time building geometry restraints manager: 2.14 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: 1515 1.34 - 1.46: 958 1.46 - 1.58: 2068 1.58 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 4595 Sorted by residual: bond pdb=" C CYS A 451 " pdb=" N PRO A 452 " ideal model delta sigma weight residual 1.336 1.356 -0.020 1.20e-02 6.94e+03 2.79e+00 bond pdb=" C ILE A 334 " pdb=" N HIS A 335 " ideal model delta sigma weight residual 1.334 1.321 0.013 1.38e-02 5.25e+03 8.76e-01 bond pdb=" CG GLU A 431 " pdb=" CD GLU A 431 " ideal model delta sigma weight residual 1.516 1.494 0.022 2.50e-02 1.60e+03 7.77e-01 bond pdb=" CD GLU A 432 " pdb=" OE1 GLU A 432 " ideal model delta sigma weight residual 1.249 1.232 0.017 1.90e-02 2.77e+03 7.58e-01 bond pdb=" CG LEU A1032 " pdb=" CD2 LEU A1032 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.41e-01 ... (remaining 4590 not shown) Histogram of bond angle deviations from ideal: 98.13 - 105.30: 57 105.30 - 112.47: 2321 112.47 - 119.64: 1587 119.64 - 126.80: 2176 126.80 - 133.97: 48 Bond angle restraints: 6189 Sorted by residual: angle pdb=" N VAL A 337 " pdb=" CA VAL A 337 " pdb=" C VAL A 337 " ideal model delta sigma weight residual 113.20 109.42 3.78 9.60e-01 1.09e+00 1.55e+01 angle pdb=" C ILE A 334 " pdb=" N HIS A 335 " pdb=" CA HIS A 335 " ideal model delta sigma weight residual 121.18 114.78 6.40 1.98e+00 2.55e-01 1.05e+01 angle pdb=" N GLU A 431 " pdb=" CA GLU A 431 " pdb=" CB GLU A 431 " ideal model delta sigma weight residual 110.12 114.84 -4.72 1.47e+00 4.63e-01 1.03e+01 angle pdb=" N GLU A1141 " pdb=" CA GLU A1141 " pdb=" CB GLU A1141 " ideal model delta sigma weight residual 110.01 114.55 -4.54 1.45e+00 4.76e-01 9.81e+00 angle pdb=" C THR A1181 " pdb=" N LYS A1182 " pdb=" CA LYS A1182 " ideal model delta sigma weight residual 122.59 127.41 -4.82 1.57e+00 4.06e-01 9.43e+00 ... (remaining 6184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 2461 17.46 - 34.92: 251 34.92 - 52.38: 31 52.38 - 69.84: 1 69.84 - 87.30: 8 Dihedral angle restraints: 2752 sinusoidal: 1102 harmonic: 1650 Sorted by residual: dihedral pdb=" CA TRP A1159 " pdb=" C TRP A1159 " pdb=" N PHE A1160 " pdb=" CA PHE A1160 " ideal model delta harmonic sigma weight residual 180.00 161.10 18.90 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA THR A1180 " pdb=" C THR A1180 " pdb=" N THR A1181 " pdb=" CA THR A1181 " ideal model delta harmonic sigma weight residual -180.00 -163.24 -16.76 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA MET A 338 " pdb=" C MET A 338 " pdb=" N PRO A 339 " pdb=" CA PRO A 339 " ideal model delta harmonic sigma weight residual -180.00 -163.30 -16.70 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 2749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 409 0.031 - 0.062: 170 0.062 - 0.093: 60 0.093 - 0.123: 32 0.123 - 0.154: 9 Chirality restraints: 680 Sorted by residual: chirality pdb=" CA PRO A 339 " pdb=" N PRO A 339 " pdb=" C PRO A 339 " pdb=" CB PRO A 339 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" CA ASP A 541 " pdb=" N ASP A 541 " pdb=" C ASP A 541 " pdb=" CB ASP A 541 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA GLU A1141 " pdb=" N GLU A1141 " pdb=" C GLU A1141 " pdb=" CB GLU A1141 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 677 not shown) Planarity restraints: 803 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 56 " 0.017 2.00e-02 2.50e+03 1.34e-02 4.52e+00 pdb=" CG TRP B 56 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP B 56 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP B 56 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 56 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 56 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 56 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 56 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 56 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 56 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A1037 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO A1038 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A1038 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1038 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1141 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.84e+00 pdb=" C GLU A1141 " 0.029 2.00e-02 2.50e+03 pdb=" O GLU A1141 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE A1142 " -0.010 2.00e-02 2.50e+03 ... (remaining 800 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 196 2.72 - 3.26: 4863 3.26 - 3.81: 7475 3.81 - 4.35: 8807 4.35 - 4.90: 14458 Nonbonded interactions: 35799 Sorted by model distance: nonbonded pdb=" ND2 ASN A 420 " pdb=" O ILE A1178 " model vdw 2.169 2.520 nonbonded pdb=" O ASP A 351 " pdb=" OG SER A 354 " model vdw 2.233 2.440 nonbonded pdb=" O ALA A 534 " pdb=" NZ LYS A 537 " model vdw 2.241 2.520 nonbonded pdb=" O SER A 532 " pdb=" OG1 THR A 535 " model vdw 2.251 2.440 nonbonded pdb=" OG1 THR B 49 " pdb=" ND1 HIS B 52 " model vdw 2.267 2.520 ... (remaining 35794 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 2847 2.51 5 N 772 2.21 5 O 864 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.970 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: 11.550 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.040 Process input model: 17.110 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 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 4595 Z= 0.202 Angle : 0.697 7.456 6189 Z= 0.379 Chirality : 0.044 0.154 680 Planarity : 0.004 0.049 803 Dihedral : 14.156 87.304 1694 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.35), residues: 567 helix: 0.05 (0.32), residues: 273 sheet: -0.78 (0.45), residues: 104 loop : -1.63 (0.45), residues: 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1565 time to fit residues: 14.4218 Evaluate side-chains 54 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.580 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 4595 Z= 0.176 Angle : 0.613 6.502 6189 Z= 0.323 Chirality : 0.043 0.147 680 Planarity : 0.004 0.058 803 Dihedral : 4.738 17.279 615 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.34), residues: 567 helix: 0.16 (0.31), residues: 274 sheet: -0.56 (0.48), residues: 94 loop : -1.53 (0.44), residues: 199 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.566 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 56 average time/residue: 0.1784 time to fit residues: 13.0149 Evaluate side-chains 53 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.557 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0518 time to fit residues: 1.1177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 55 optimal weight: 0.0570 chunk 45 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 4595 Z= 0.144 Angle : 0.566 6.565 6189 Z= 0.295 Chirality : 0.041 0.142 680 Planarity : 0.003 0.055 803 Dihedral : 4.522 20.444 615 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.34), residues: 567 helix: 0.35 (0.30), residues: 281 sheet: -0.54 (0.51), residues: 88 loop : -1.53 (0.43), residues: 198 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 66 average time/residue: 0.1588 time to fit residues: 13.8783 Evaluate side-chains 58 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.445 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0719 time to fit residues: 1.1343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 24 optimal weight: 0.0170 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 4595 Z= 0.142 Angle : 0.578 6.673 6189 Z= 0.301 Chirality : 0.041 0.145 680 Planarity : 0.003 0.051 803 Dihedral : 4.445 20.805 615 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.35), residues: 567 helix: 0.47 (0.31), residues: 281 sheet: -0.46 (0.51), residues: 88 loop : -1.52 (0.44), residues: 198 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 59 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 70 average time/residue: 0.1493 time to fit residues: 13.9510 Evaluate side-chains 62 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.589 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0601 time to fit residues: 1.4629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 4595 Z= 0.182 Angle : 0.608 6.820 6189 Z= 0.316 Chirality : 0.042 0.148 680 Planarity : 0.004 0.051 803 Dihedral : 4.617 22.620 615 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.35), residues: 567 helix: 0.58 (0.31), residues: 270 sheet: -0.72 (0.47), residues: 100 loop : -1.28 (0.47), residues: 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.571 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 60 average time/residue: 0.1584 time to fit residues: 12.7346 Evaluate side-chains 58 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.593 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0684 time to fit residues: 0.9569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 30 optimal weight: 0.0670 chunk 39 optimal weight: 4.9990 overall best weight: 1.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1054 ASN ** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 4595 Z= 0.241 Angle : 0.656 8.261 6189 Z= 0.343 Chirality : 0.043 0.152 680 Planarity : 0.004 0.059 803 Dihedral : 4.920 23.567 615 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.35), residues: 567 helix: 0.22 (0.31), residues: 275 sheet: -0.66 (0.49), residues: 93 loop : -1.46 (0.46), residues: 199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 62 average time/residue: 0.1656 time to fit residues: 13.4989 Evaluate side-chains 60 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.560 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1003 time to fit residues: 1.4557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 0.0010 chunk 45 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 4595 Z= 0.150 Angle : 0.621 9.804 6189 Z= 0.314 Chirality : 0.042 0.207 680 Planarity : 0.003 0.057 803 Dihedral : 4.583 21.132 615 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.35), residues: 567 helix: 0.56 (0.31), residues: 269 sheet: -0.60 (0.48), residues: 98 loop : -1.37 (0.47), residues: 200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 61 average time/residue: 0.1648 time to fit residues: 13.4672 Evaluate side-chains 56 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.574 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0485 time to fit residues: 0.9190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1054 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 4595 Z= 0.187 Angle : 0.636 9.761 6189 Z= 0.325 Chirality : 0.042 0.188 680 Planarity : 0.004 0.058 803 Dihedral : 4.680 22.054 615 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.35), residues: 567 helix: 0.35 (0.31), residues: 276 sheet: -0.62 (0.49), residues: 93 loop : -1.25 (0.47), residues: 198 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 58 average time/residue: 0.1654 time to fit residues: 12.7093 Evaluate side-chains 57 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.568 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0589 time to fit residues: 1.0598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 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 : 0.004 0.032 4595 Z= 0.250 Angle : 0.713 10.129 6189 Z= 0.366 Chirality : 0.045 0.250 680 Planarity : 0.004 0.061 803 Dihedral : 5.083 23.526 615 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.35), residues: 567 helix: 0.18 (0.31), residues: 269 sheet: -0.83 (0.49), residues: 94 loop : -1.36 (0.46), residues: 204 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 59 average time/residue: 0.1609 time to fit residues: 12.6680 Evaluate side-chains 57 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.546 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1303 time to fit residues: 1.4281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 47 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4595 Z= 0.168 Angle : 0.659 9.904 6189 Z= 0.333 Chirality : 0.042 0.159 680 Planarity : 0.004 0.059 803 Dihedral : 4.716 21.117 615 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.35), residues: 567 helix: 0.19 (0.31), residues: 281 sheet: -0.70 (0.52), residues: 83 loop : -1.45 (0.44), residues: 203 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 59 average time/residue: 0.1650 time to fit residues: 13.1600 Evaluate side-chains 54 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.548 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 0.3980 chunk 39 optimal weight: 0.6980 chunk 2 optimal weight: 0.1980 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4185 r_free = 0.4185 target = 0.102766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.074801 restraints weight = 16452.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.076829 restraints weight = 11427.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.078098 restraints weight = 8969.845| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 4595 Z= 0.157 Angle : 0.654 9.309 6189 Z= 0.329 Chirality : 0.041 0.154 680 Planarity : 0.003 0.060 803 Dihedral : 4.495 20.604 615 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.35), residues: 567 helix: 0.35 (0.31), residues: 282 sheet: -0.69 (0.52), residues: 83 loop : -1.42 (0.45), residues: 202 =============================================================================== Job complete usr+sys time: 1303.25 seconds wall clock time: 25 minutes 19.60 seconds (1519.60 seconds total)