Starting phenix.real_space_refine on Wed Jan 17 16:12:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdh_13338/01_2024/7pdh_13338.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdh_13338/01_2024/7pdh_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_13338/01_2024/7pdh_13338.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdh_13338/01_2024/7pdh_13338.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdh_13338/01_2024/7pdh_13338.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdh_13338/01_2024/7pdh_13338.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.000 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 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. 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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 2.84, per 1000 atoms: 0.63 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: 1.93 Conformation dependent library (CDL) restraints added in 959.1 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: 0.57 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: 1.35 Time building geometry restraints manager: 2.10 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 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: 2.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 11.110 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 17.510 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 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 : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP B 56 HIS 0.003 0.001 HIS B 59 PHE 0.010 0.002 PHE A 507 TYR 0.011 0.001 TYR A 445 ARG 0.003 0.000 ARG B 31 *********************** 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 : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1145 GLU cc_start: 0.8781 (mp0) cc_final: 0.8507 (mp0) REVERT: A 1157 MET cc_start: 0.7946 (tmm) cc_final: 0.7725 (tmm) REVERT: A 1238 MET cc_start: 0.8753 (tpp) cc_final: 0.8424 (tpp) REVERT: B 78 TRP cc_start: 0.7358 (t60) cc_final: 0.7155 (t60) REVERT: B 101 LYS cc_start: 0.7836 (mmpt) cc_final: 0.7627 (mmtm) REVERT: B 109 GLN cc_start: 0.7076 (pt0) cc_final: 0.6852 (mt0) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1559 time to fit residues: 14.2431 Evaluate side-chains 55 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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: 10.0000 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7008 moved from start: 0.1073 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= 0.168 Angle : 0.604 6.505 6189 Z= 0.317 Chirality : 0.042 0.149 680 Planarity : 0.004 0.059 803 Dihedral : 4.671 16.906 615 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.83 % Allowed : 10.42 % Favored : 88.75 % 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: -1.00 (0.34), residues: 567 helix: 0.10 (0.30), residues: 280 sheet: -0.46 (0.52), residues: 84 loop : -1.72 (0.41), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 56 HIS 0.004 0.001 HIS B 59 PHE 0.009 0.001 PHE A 507 TYR 0.010 0.001 TYR A1115 ARG 0.003 0.000 ARG B 31 *********************** 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 59 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: A 1080 LYS cc_start: 0.7644 (mttp) cc_final: 0.7097 (mtmm) REVERT: A 1147 MET cc_start: 0.8583 (ptt) cc_final: 0.7437 (mtt) REVERT: A 1157 MET cc_start: 0.7877 (tmm) cc_final: 0.7498 (tmm) REVERT: A 1183 LEU cc_start: 0.7973 (mt) cc_final: 0.7438 (mp) REVERT: A 1238 MET cc_start: 0.8786 (tpp) cc_final: 0.8389 (tpp) outliers start: 4 outliers final: 3 residues processed: 57 average time/residue: 0.1617 time to fit residues: 12.1545 Evaluate side-chains 55 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 1173 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 45 optimal weight: 0.0570 chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 overall best weight: 1.5502 ------------------------------------------------------------------------------- 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 26 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4595 Z= 0.237 Angle : 0.645 6.665 6189 Z= 0.341 Chirality : 0.042 0.144 680 Planarity : 0.004 0.058 803 Dihedral : 4.989 22.018 615 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.08 % Allowed : 14.38 % Favored : 83.54 % 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: -0.96 (0.34), residues: 567 helix: 0.15 (0.31), residues: 275 sheet: -0.77 (0.46), residues: 100 loop : -1.57 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 56 HIS 0.004 0.001 HIS A 335 PHE 0.011 0.002 PHE A1062 TYR 0.015 0.002 TYR A1039 ARG 0.004 0.001 ARG B 31 *********************** 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 69 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1080 LYS cc_start: 0.7672 (mttp) cc_final: 0.7443 (mtmm) REVERT: A 1147 MET cc_start: 0.8583 (ptt) cc_final: 0.7336 (ttp) outliers start: 10 outliers final: 9 residues processed: 66 average time/residue: 0.1673 time to fit residues: 14.2494 Evaluate side-chains 61 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 52 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1141 GLU Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1214 TYR Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 107 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 54 optimal weight: 0.0970 chunk 48 optimal weight: 0.0870 chunk 14 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- 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 48 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4595 Z= 0.137 Angle : 0.580 6.613 6189 Z= 0.300 Chirality : 0.041 0.142 680 Planarity : 0.003 0.060 803 Dihedral : 4.545 21.095 615 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.71 % Allowed : 15.62 % Favored : 81.67 % 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: -0.81 (0.34), residues: 567 helix: 0.32 (0.30), residues: 281 sheet: -0.66 (0.50), residues: 90 loop : -1.61 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 56 HIS 0.003 0.001 HIS B 59 PHE 0.009 0.001 PHE A 507 TYR 0.010 0.001 TYR A 543 ARG 0.003 0.000 ARG A1215 *********************** 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 72 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 59 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.8894 (p0) cc_final: 0.8646 (p0) REVERT: A 465 MET cc_start: 0.7960 (mmm) cc_final: 0.7724 (mmm) REVERT: A 1080 LYS cc_start: 0.7643 (mttp) cc_final: 0.7206 (mtmm) REVERT: A 1147 MET cc_start: 0.8644 (ptt) cc_final: 0.7399 (ttp) outliers start: 13 outliers final: 7 residues processed: 70 average time/residue: 0.1468 time to fit residues: 13.6874 Evaluate side-chains 62 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 1141 GLU Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1214 TYR Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 107 ASN 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: 1.9990 chunk 46 optimal weight: 0.9990 chunk 37 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 48 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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: 0.7037 moved from start: 0.2178 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= 0.175 Angle : 0.599 6.710 6189 Z= 0.313 Chirality : 0.041 0.141 680 Planarity : 0.004 0.059 803 Dihedral : 4.642 21.261 615 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.71 % Allowed : 16.25 % Favored : 81.04 % 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: -0.58 (0.35), residues: 567 helix: 0.49 (0.31), residues: 275 sheet: -0.54 (0.49), residues: 92 loop : -1.43 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 56 HIS 0.003 0.001 HIS A 335 PHE 0.010 0.001 PHE A1062 TYR 0.017 0.002 TYR A1072 ARG 0.002 0.000 ARG B 31 *********************** 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 71 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1080 LYS cc_start: 0.7674 (mttp) cc_final: 0.7236 (mtmm) REVERT: A 1147 MET cc_start: 0.8649 (ptt) cc_final: 0.7379 (ttp) REVERT: A 1157 MET cc_start: 0.7319 (tmm) cc_final: 0.7053 (tmm) REVERT: A 1183 LEU cc_start: 0.7927 (mt) cc_final: 0.7468 (mp) outliers start: 13 outliers final: 10 residues processed: 67 average time/residue: 0.1431 time to fit residues: 12.7413 Evaluate side-chains 64 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 1141 GLU Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1214 TYR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 82 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 30 optimal weight: 0.0060 chunk 39 optimal weight: 0.9980 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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: 0.7016 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4595 Z= 0.155 Angle : 0.597 6.981 6189 Z= 0.309 Chirality : 0.041 0.144 680 Planarity : 0.003 0.058 803 Dihedral : 4.556 20.686 615 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.33 % Allowed : 17.29 % Favored : 79.38 % 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: 0.38 (0.31), residues: 281 sheet: -0.40 (0.53), residues: 82 loop : -1.62 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 56 HIS 0.003 0.001 HIS A 335 PHE 0.009 0.001 PHE A 507 TYR 0.018 0.001 TYR A1072 ARG 0.002 0.000 ARG B 31 *********************** 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 73 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 57 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 419 LEU cc_start: 0.8992 (mt) cc_final: 0.8735 (mm) REVERT: A 1080 LYS cc_start: 0.7665 (mttp) cc_final: 0.7234 (mtmm) REVERT: A 1183 LEU cc_start: 0.7845 (mt) cc_final: 0.6887 (mp) outliers start: 16 outliers final: 11 residues processed: 69 average time/residue: 0.1603 time to fit residues: 14.5055 Evaluate side-chains 66 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 1141 GLU Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1214 TYR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 0.0670 chunk 45 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 overall best weight: 1.3120 ------------------------------------------------------------------------------- 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: 0.7072 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4595 Z= 0.220 Angle : 0.646 9.666 6189 Z= 0.338 Chirality : 0.042 0.144 680 Planarity : 0.004 0.059 803 Dihedral : 4.851 21.529 615 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.75 % Allowed : 17.92 % Favored : 78.33 % 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: -0.68 (0.36), residues: 567 helix: 0.35 (0.31), residues: 276 sheet: -0.67 (0.49), residues: 93 loop : -1.34 (0.47), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 56 HIS 0.004 0.001 HIS B 59 PHE 0.012 0.001 PHE A1062 TYR 0.016 0.002 TYR A1072 ARG 0.003 0.000 ARG B 31 *********************** 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 74 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 56 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1080 LYS cc_start: 0.7670 (mttp) cc_final: 0.7242 (mtmm) outliers start: 18 outliers final: 11 residues processed: 69 average time/residue: 0.1523 time to fit residues: 13.9108 Evaluate side-chains 62 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 1141 GLU Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1214 TYR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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: 0.7115 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4595 Z= 0.266 Angle : 0.692 9.068 6189 Z= 0.363 Chirality : 0.043 0.155 680 Planarity : 0.004 0.061 803 Dihedral : 5.134 22.098 615 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 3.33 % Allowed : 19.79 % Favored : 76.88 % 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: 0.28 (0.31), residues: 268 sheet: -0.87 (0.48), residues: 96 loop : -1.47 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 56 HIS 0.004 0.001 HIS A1135 PHE 0.014 0.002 PHE A1062 TYR 0.017 0.002 TYR A1039 ARG 0.004 0.001 ARG B 23 *********************** 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 66 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 50 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1080 LYS cc_start: 0.7686 (mttp) cc_final: 0.7270 (mtmm) REVERT: A 1095 GLU cc_start: 0.6960 (pp20) cc_final: 0.6581 (pp20) outliers start: 16 outliers final: 13 residues processed: 63 average time/residue: 0.1460 time to fit residues: 12.3426 Evaluate side-chains 62 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 49 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 1141 GLU Chi-restraints excluded: chain A residue 1159 TRP Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1214 TYR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 33 optimal weight: 0.0030 chunk 53 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 51 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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: 0.7040 moved from start: 0.2869 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= 0.161 Angle : 0.636 9.017 6189 Z= 0.323 Chirality : 0.042 0.144 680 Planarity : 0.003 0.058 803 Dihedral : 4.698 20.551 615 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.88 % Allowed : 21.67 % Favored : 76.46 % 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: -0.93 (0.35), residues: 567 helix: 0.22 (0.31), residues: 282 sheet: -0.72 (0.52), residues: 85 loop : -1.68 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 56 HIS 0.002 0.001 HIS B 59 PHE 0.009 0.001 PHE A 507 TYR 0.011 0.001 TYR A1115 ARG 0.002 0.000 ARG A1215 *********************** 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 65 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 THR cc_start: 0.8023 (p) cc_final: 0.7808 (p) REVERT: A 465 MET cc_start: 0.8311 (mmm) cc_final: 0.7923 (mmm) REVERT: A 1080 LYS cc_start: 0.7660 (mttp) cc_final: 0.7245 (mtmm) outliers start: 9 outliers final: 8 residues processed: 62 average time/residue: 0.1537 time to fit residues: 12.6946 Evaluate side-chains 61 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 1141 GLU Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1214 TYR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.7064 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4595 Z= 0.184 Angle : 0.663 8.758 6189 Z= 0.334 Chirality : 0.042 0.149 680 Planarity : 0.004 0.058 803 Dihedral : 4.727 21.646 615 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.29 % Allowed : 21.67 % Favored : 76.04 % 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: -0.83 (0.35), residues: 567 helix: 0.25 (0.31), residues: 281 sheet: -0.78 (0.52), residues: 83 loop : -1.46 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 56 HIS 0.003 0.001 HIS B 59 PHE 0.010 0.001 PHE A 507 TYR 0.011 0.001 TYR A 446 ARG 0.002 0.000 ARG B 23 ********************** 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 62 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1080 LYS cc_start: 0.7665 (mttp) cc_final: 0.7253 (mtmm) outliers start: 11 outliers final: 9 residues processed: 58 average time/residue: 0.1411 time to fit residues: 11.0357 Evaluate side-chains 60 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 1141 GLU Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1214 TYR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 32 optimal weight: 0.0770 chunk 50 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 35 optimal weight: 0.0370 overall best weight: 0.4616 ------------------------------------------------------------------------------- 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 = 0.4205 r_free = 0.4205 target = 0.103498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.075003 restraints weight = 16255.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.077228 restraints weight = 11454.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.078638 restraints weight = 8798.168| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4595 Z= 0.154 Angle : 0.647 9.715 6189 Z= 0.321 Chirality : 0.041 0.148 680 Planarity : 0.003 0.056 803 Dihedral : 4.541 20.314 615 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.88 % Allowed : 22.08 % Favored : 76.04 % 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: -0.70 (0.35), residues: 567 helix: 0.33 (0.31), residues: 281 sheet: -0.65 (0.52), residues: 83 loop : -1.40 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 56 HIS 0.003 0.001 HIS B 59 PHE 0.008 0.001 PHE A 507 TYR 0.014 0.001 TYR A 543 ARG 0.002 0.000 ARG A1215 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1325.75 seconds wall clock time: 24 minutes 34.36 seconds (1474.36 seconds total)