Starting phenix.real_space_refine on Tue Feb 13 08:29:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdd_13334/02_2024/7pdd_13334.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdd_13334/02_2024/7pdd_13334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdd_13334/02_2024/7pdd_13334.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdd_13334/02_2024/7pdd_13334.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdd_13334/02_2024/7pdd_13334.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdd_13334/02_2024/7pdd_13334.pdb" } resolution = 4.2 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= 0.001 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 ARG 340": "NH1" <-> "NH2" Residue "A PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A ARG 471": "NH1" <-> "NH2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "A ASP 1027": "OD1" <-> "OD2" Residue "A GLU 1081": "OE1" <-> "OE2" Residue "A TYR 1083": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1094": "OD1" <-> "OD2" Residue "A TYR 1115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1127": "NH1" <-> "NH2" Residue "A PHE 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1148": "NH1" <-> "NH2" Residue "A PHE 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1206": "NH1" <-> "NH2" Residue "A TYR 1222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 28": "OD1" <-> "OD2" Residue "B PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 89": "NH1" <-> "NH2" Residue "B PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 2.65, per 1000 atoms: 0.59 Number of scatterers: 4516 At special positions: 0 Unit cell: (94.77, 77.76, 79.38, 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 734.2 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 50.1% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 321 through 335 Processing helix chain 'A' and resid 339 through 348 removed outlier: 3.552A pdb=" N LYS A 348 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 359 removed outlier: 3.694A pdb=" N GLU A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 3.602A pdb=" N MET A 406 " --> pdb=" O GLY A 402 " (cutoff:3.500A) 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: 3.779A 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 1047 Processing helix chain 'A' and resid 1067 through 1072 removed outlier: 3.699A pdb=" N PHE A1071 " --> pdb=" O ASN A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1097 removed outlier: 3.912A pdb=" N LEU A1097 " --> pdb=" O PHE A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1157 removed outlier: 3.878A pdb=" N GLN A1137 " --> pdb=" O GLN A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1200 removed outlier: 4.280A pdb=" N ASN A1193 " --> pdb=" O GLY A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1219 removed outlier: 3.625A pdb=" N LYS A1219 " --> pdb=" O ARG A1215 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 25 Processing helix chain 'B' and resid 26 through 36 Processing helix chain 'B' and resid 49 through 58 Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 82 through 91 Processing helix chain 'B' and resid 92 through 102 Processing helix chain 'B' and resid 115 through 123 Processing helix chain 'B' and resid 125 through 134 Processing sheet with id=AA1, first strand: chain 'A' and resid 436 through 439 removed outlier: 7.373A pdb=" N TYR A 446 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 394 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLN A 389 " --> pdb=" O CYS A 497 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N CYS A 497 " --> pdb=" O GLN A 389 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLU A 391 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 495 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 439 removed outlier: 7.373A pdb=" N TYR A 446 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 394 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLN A 389 " --> pdb=" O CYS A 497 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N CYS A 497 " --> pdb=" O GLN A 389 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLU A 391 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 495 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER A 532 " --> pdb=" O VAL A 490 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR A 492 " --> pdb=" O SER A 532 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1052 through 1055 Processing sheet with id=AA4, first strand: chain 'A' and resid 1105 through 1109 removed outlier: 7.182A pdb=" N MET A1116 " --> pdb=" O ILE A1108 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N GLN A1208 " --> pdb=" O LEU A1164 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL A1166 " --> pdb=" O GLN A1208 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR A1241 " --> pdb=" O VAL A1209 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A1228 " --> pdb=" O THR A1240 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU A1242 " --> pdb=" O TYR A1226 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N TYR A1226 " --> pdb=" O LEU A1242 " (cutoff:3.500A) 259 hydrogen bonds defined for protein. 756 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: 1.36 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: 1.22 - 1.34: 1515 1.34 - 1.46: 976 1.46 - 1.58: 2050 1.58 - 1.70: 0 1.70 - 1.82: 54 Bond restraints: 4595 Sorted by residual: bond pdb=" N ASP A 541 " pdb=" CA ASP A 541 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.69e+00 bond pdb=" N GLU A 453 " pdb=" CA GLU A 453 " ideal model delta sigma weight residual 1.460 1.446 0.014 1.29e-02 6.01e+03 1.11e+00 bond pdb=" CA ASN A1035 " pdb=" C ASN A1035 " ideal model delta sigma weight residual 1.524 1.513 0.011 1.24e-02 6.50e+03 8.21e-01 bond pdb=" C GLU A 453 " pdb=" O GLU A 453 " ideal model delta sigma weight residual 1.248 1.237 0.011 1.26e-02 6.30e+03 7.75e-01 bond pdb=" CB PRO A 384 " pdb=" CG PRO A 384 " ideal model delta sigma weight residual 1.492 1.536 -0.044 5.00e-02 4.00e+02 7.66e-01 ... (remaining 4590 not shown) Histogram of bond angle deviations from ideal: 99.64 - 106.51: 89 106.51 - 113.38: 2521 113.38 - 120.25: 1697 120.25 - 127.12: 1841 127.12 - 133.99: 41 Bond angle restraints: 6189 Sorted by residual: angle pdb=" N TYR A 446 " pdb=" CA TYR A 446 " pdb=" C TYR A 446 " ideal model delta sigma weight residual 108.79 113.27 -4.48 1.53e+00 4.27e-01 8.58e+00 angle pdb=" C TYR A 445 " pdb=" N TYR A 446 " pdb=" CA TYR A 446 " ideal model delta sigma weight residual 121.62 116.31 5.31 1.83e+00 2.99e-01 8.43e+00 angle pdb=" C LYS A 437 " pdb=" N ILE A 438 " pdb=" CA ILE A 438 " ideal model delta sigma weight residual 121.97 117.45 4.52 1.80e+00 3.09e-01 6.29e+00 angle pdb=" N ASN A 409 " pdb=" CA ASN A 409 " pdb=" C ASN A 409 " ideal model delta sigma weight residual 110.44 113.29 -2.85 1.20e+00 6.94e-01 5.63e+00 angle pdb=" C THR A1181 " pdb=" N LYS A1182 " pdb=" CA LYS A1182 " ideal model delta sigma weight residual 122.39 126.25 -3.86 1.64e+00 3.72e-01 5.54e+00 ... (remaining 6184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 2448 17.24 - 34.48: 248 34.48 - 51.72: 44 51.72 - 68.96: 7 68.96 - 86.20: 5 Dihedral angle restraints: 2752 sinusoidal: 1102 harmonic: 1650 Sorted by residual: 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 -156.99 -23.01 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA TYR A1072 " pdb=" C TYR A1072 " pdb=" N GLU A1073 " pdb=" CA GLU A1073 " ideal model delta harmonic sigma weight residual 180.00 -160.00 -20.00 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA LYS A 321 " pdb=" C LYS A 321 " pdb=" N ASP A 322 " pdb=" CA ASP A 322 " ideal model delta harmonic sigma weight residual 180.00 161.18 18.82 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 2749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 383 0.029 - 0.059: 186 0.059 - 0.088: 78 0.088 - 0.117: 29 0.117 - 0.146: 4 Chirality restraints: 680 Sorted by residual: 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 2.36 0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CA ILE A 395 " pdb=" N ILE A 395 " pdb=" C ILE A 395 " pdb=" CB ILE A 395 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA VAL A 509 " pdb=" N VAL A 509 " pdb=" C VAL A 509 " pdb=" CB VAL A 509 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 677 not shown) Planarity restraints: 803 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1037 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.65e+00 pdb=" N PRO A1038 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A1038 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1038 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A1072 " 0.007 2.00e-02 2.50e+03 1.36e-02 1.84e+00 pdb=" C TYR A1072 " -0.023 2.00e-02 2.50e+03 pdb=" O TYR A1072 " 0.009 2.00e-02 2.50e+03 pdb=" N GLU A1073 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 453 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO A 454 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 454 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 454 " 0.017 5.00e-02 4.00e+02 ... (remaining 800 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 95 2.65 - 3.22: 4861 3.22 - 3.78: 7361 3.78 - 4.34: 9956 4.34 - 4.90: 15254 Nonbonded interactions: 37527 Sorted by model distance: nonbonded pdb=" O SER A 532 " pdb=" OG1 THR A 535 " model vdw 2.092 2.440 nonbonded pdb=" O ALA A 412 " pdb=" OG SER A1052 " model vdw 2.093 2.440 nonbonded pdb=" OH TYR A1226 " pdb=" OG1 THR A1229 " model vdw 2.153 2.440 nonbonded pdb=" O SER A1196 " pdb=" OG1 THR A1200 " model vdw 2.218 2.440 nonbonded pdb=" NH2 ARG A1206 " pdb=" O PRO A1244 " model vdw 2.222 2.520 ... (remaining 37522 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: 1.240 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: 5.470 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.320 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 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 : 0.004 0.044 4595 Z= 0.254 Angle : 0.748 7.879 6189 Z= 0.445 Chirality : 0.042 0.146 680 Planarity : 0.004 0.048 803 Dihedral : 14.377 86.204 1694 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % 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: -4.11 (0.29), residues: 567 helix: -2.34 (0.25), residues: 273 sheet: -2.54 (0.40), residues: 105 loop : -3.08 (0.39), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1031 HIS 0.005 0.002 HIS A1170 PHE 0.010 0.002 PHE A1224 TYR 0.015 0.002 TYR A1241 ARG 0.003 0.000 ARG A1165 *********************** 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 137 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 PHE cc_start: 0.8592 (m-10) cc_final: 0.8227 (m-80) REVERT: A 425 ARG cc_start: 0.8923 (mtt180) cc_final: 0.8453 (mtp180) REVERT: A 429 LEU cc_start: 0.9525 (tp) cc_final: 0.9280 (tt) REVERT: B 56 TRP cc_start: 0.7689 (t60) cc_final: 0.7441 (t-100) REVERT: B 114 LYS cc_start: 0.8616 (mmtt) cc_final: 0.8269 (mmtt) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2091 time to fit residues: 34.5461 Evaluate side-chains 101 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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: 6.9990 chunk 42 optimal weight: 0.8980 chunk 23 optimal weight: 0.2980 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 0.0980 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 HIS A1154 ASN A1237 GLN ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4595 Z= 0.185 Angle : 0.648 7.019 6189 Z= 0.344 Chirality : 0.043 0.150 680 Planarity : 0.004 0.056 803 Dihedral : 5.190 22.506 615 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % 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: -2.45 (0.31), residues: 567 helix: -0.84 (0.27), residues: 281 sheet: -2.05 (0.43), residues: 105 loop : -2.35 (0.43), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A1159 HIS 0.004 0.001 HIS B 92 PHE 0.012 0.002 PHE A1168 TYR 0.018 0.002 TYR A 446 ARG 0.005 0.001 ARG B 23 *********************** 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 136 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 PHE cc_start: 0.8376 (m-10) cc_final: 0.8039 (m-80) REVERT: A 425 ARG cc_start: 0.8840 (mtt180) cc_final: 0.8082 (mtp180) REVERT: A 510 TRP cc_start: 0.7070 (m-90) cc_final: 0.6829 (m-90) REVERT: A 520 MET cc_start: 0.7189 (ttm) cc_final: 0.6925 (mtp) REVERT: A 543 TYR cc_start: 0.7196 (m-80) cc_final: 0.6645 (m-80) REVERT: A 1075 ASN cc_start: 0.7743 (m-40) cc_final: 0.7453 (p0) REVERT: A 1141 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8524 (mm-30) REVERT: A 1146 MET cc_start: 0.8835 (ppp) cc_final: 0.8572 (ppp) REVERT: B 112 PHE cc_start: 0.7299 (m-80) cc_final: 0.7089 (m-80) REVERT: B 114 LYS cc_start: 0.8304 (mmtt) cc_final: 0.7899 (mmtt) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1849 time to fit residues: 30.9347 Evaluate side-chains 108 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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: 2.9990 chunk 15 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 55 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 38 optimal weight: 0.0970 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4595 Z= 0.179 Angle : 0.610 6.888 6189 Z= 0.326 Chirality : 0.041 0.148 680 Planarity : 0.003 0.054 803 Dihedral : 5.015 22.201 615 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.21 % Allowed : 3.96 % Favored : 95.83 % 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: -1.85 (0.33), residues: 567 helix: -0.29 (0.28), residues: 282 sheet: -1.79 (0.45), residues: 106 loop : -2.17 (0.45), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 56 HIS 0.003 0.001 HIS A1170 PHE 0.011 0.001 PHE A1168 TYR 0.012 0.002 TYR A1083 ARG 0.002 0.000 ARG A 471 *********************** 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 129 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 391 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8059 (tp30) REVERT: A 396 LEU cc_start: 0.8659 (tt) cc_final: 0.8381 (tt) REVERT: A 423 PHE cc_start: 0.8375 (m-10) cc_final: 0.8037 (m-80) REVERT: A 425 ARG cc_start: 0.8892 (mtt180) cc_final: 0.8168 (mtp180) REVERT: A 483 MET cc_start: 0.5982 (tpt) cc_final: 0.5694 (tpt) REVERT: A 1084 ARG cc_start: 0.8725 (mtt90) cc_final: 0.8124 (mtt-85) REVERT: A 1141 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8579 (mm-30) REVERT: A 1146 MET cc_start: 0.8811 (ppp) cc_final: 0.8537 (ppp) REVERT: A 1198 MET cc_start: 0.8449 (mtp) cc_final: 0.8162 (tmm) REVERT: B 16 LYS cc_start: 0.8908 (mmmt) cc_final: 0.8590 (mmtm) REVERT: B 112 PHE cc_start: 0.7288 (m-80) cc_final: 0.7025 (m-80) REVERT: B 114 LYS cc_start: 0.8352 (mmtt) cc_final: 0.7969 (mmtt) outliers start: 1 outliers final: 1 residues processed: 129 average time/residue: 0.1896 time to fit residues: 30.1970 Evaluate side-chains 97 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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: 0.2980 chunk 5 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 30 optimal weight: 0.0570 chunk 0 optimal weight: 4.9990 overall best weight: 0.5100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 ASN ** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4595 Z= 0.178 Angle : 0.649 8.597 6189 Z= 0.341 Chirality : 0.043 0.146 680 Planarity : 0.003 0.048 803 Dihedral : 4.825 21.469 615 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.21 % Allowed : 4.58 % Favored : 95.21 % 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: -1.60 (0.33), residues: 567 helix: -0.22 (0.29), residues: 285 sheet: -1.35 (0.47), residues: 106 loop : -2.04 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP B 56 HIS 0.005 0.001 HIS A 530 PHE 0.011 0.001 PHE A1168 TYR 0.012 0.002 TYR A1083 ARG 0.010 0.001 ARG B 23 *********************** 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 131 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 PHE cc_start: 0.8303 (m-10) cc_final: 0.7935 (m-80) REVERT: A 483 MET cc_start: 0.5807 (tpt) cc_final: 0.5495 (tpt) REVERT: A 1134 GLU cc_start: 0.8526 (pp20) cc_final: 0.7691 (pp20) REVERT: A 1141 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8526 (mm-30) REVERT: A 1198 MET cc_start: 0.8404 (mtp) cc_final: 0.8172 (tmm) outliers start: 1 outliers final: 0 residues processed: 130 average time/residue: 0.1923 time to fit residues: 30.5769 Evaluate side-chains 102 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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: 0.8980 chunk 22 optimal weight: 0.8980 chunk 46 optimal weight: 0.4980 chunk 37 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4595 Z= 0.185 Angle : 0.659 9.920 6189 Z= 0.351 Chirality : 0.043 0.149 680 Planarity : 0.004 0.050 803 Dihedral : 4.862 21.069 615 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % 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: -1.38 (0.34), residues: 567 helix: -0.13 (0.29), residues: 284 sheet: -1.12 (0.49), residues: 99 loop : -1.84 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP B 56 HIS 0.005 0.001 HIS B 59 PHE 0.009 0.001 PHE A1168 TYR 0.015 0.002 TYR A1083 ARG 0.005 0.001 ARG A1206 *********************** 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 128 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 PHE cc_start: 0.8353 (m-10) cc_final: 0.7961 (m-80) REVERT: A 483 MET cc_start: 0.5796 (tpt) cc_final: 0.5477 (tpt) REVERT: A 1084 ARG cc_start: 0.8738 (mtt90) cc_final: 0.8284 (mtt-85) REVERT: A 1094 ASP cc_start: 0.7380 (m-30) cc_final: 0.6368 (m-30) REVERT: A 1134 GLU cc_start: 0.8588 (pp20) cc_final: 0.7922 (pp20) REVERT: A 1141 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8569 (mm-30) REVERT: A 1146 MET cc_start: 0.8843 (ppp) cc_final: 0.8627 (ppp) REVERT: A 1190 ASP cc_start: 0.8388 (p0) cc_final: 0.8053 (p0) REVERT: B 23 ARG cc_start: 0.8763 (ptm160) cc_final: 0.8519 (ptm-80) REVERT: B 68 LYS cc_start: 0.8254 (mttt) cc_final: 0.7854 (mmtt) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1896 time to fit residues: 29.8707 Evaluate side-chains 96 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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: 0.8980 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 6 optimal weight: 0.0770 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- 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** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4595 Z= 0.189 Angle : 0.631 6.646 6189 Z= 0.336 Chirality : 0.042 0.140 680 Planarity : 0.003 0.048 803 Dihedral : 4.794 20.364 615 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.21 % Allowed : 1.25 % Favored : 98.54 % 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: -1.38 (0.34), residues: 567 helix: -0.08 (0.29), residues: 282 sheet: -1.13 (0.48), residues: 101 loop : -1.93 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 56 HIS 0.004 0.001 HIS B 59 PHE 0.008 0.001 PHE A1093 TYR 0.011 0.002 TYR A1083 ARG 0.004 0.000 ARG A1206 *********************** 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 125 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 MET cc_start: 0.8522 (mmm) cc_final: 0.7929 (mmm) REVERT: A 423 PHE cc_start: 0.8433 (m-10) cc_final: 0.8032 (m-80) REVERT: A 483 MET cc_start: 0.5771 (tpt) cc_final: 0.5457 (tpt) REVERT: A 520 MET cc_start: 0.6620 (ttt) cc_final: 0.5436 (tmm) REVERT: A 1084 ARG cc_start: 0.8714 (mtt90) cc_final: 0.8322 (mtt-85) REVERT: A 1094 ASP cc_start: 0.7295 (m-30) cc_final: 0.6243 (m-30) REVERT: A 1134 GLU cc_start: 0.8604 (pp20) cc_final: 0.8185 (pp20) REVERT: A 1141 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8568 (mm-30) REVERT: A 1190 ASP cc_start: 0.8369 (p0) cc_final: 0.8004 (p0) REVERT: B 68 LYS cc_start: 0.8225 (mttt) cc_final: 0.8017 (mttp) outliers start: 1 outliers final: 0 residues processed: 125 average time/residue: 0.1856 time to fit residues: 28.5590 Evaluate side-chains 95 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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: 2.9990 chunk 45 optimal weight: 2.9990 chunk 53 optimal weight: 0.0770 chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.7744 ------------------------------------------------------------------------------- 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** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4595 Z= 0.183 Angle : 0.635 6.871 6189 Z= 0.337 Chirality : 0.042 0.142 680 Planarity : 0.003 0.048 803 Dihedral : 4.746 19.882 615 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % 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: -1.21 (0.34), residues: 567 helix: -0.00 (0.29), residues: 283 sheet: -1.03 (0.49), residues: 101 loop : -1.75 (0.46), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 56 HIS 0.004 0.001 HIS A 530 PHE 0.018 0.001 PHE A1168 TYR 0.011 0.001 TYR A1083 ARG 0.003 0.000 ARG A1206 *********************** 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 125 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 MET cc_start: 0.8485 (mmm) cc_final: 0.7973 (mmm) REVERT: A 423 PHE cc_start: 0.8408 (m-10) cc_final: 0.7990 (m-80) REVERT: A 425 ARG cc_start: 0.8766 (ptp-170) cc_final: 0.8525 (ptp-170) REVERT: A 483 MET cc_start: 0.5730 (tpt) cc_final: 0.5425 (tpt) REVERT: A 520 MET cc_start: 0.6736 (ttt) cc_final: 0.5565 (tmm) REVERT: A 569 TYR cc_start: 0.7922 (m-80) cc_final: 0.7470 (m-80) REVERT: A 1084 ARG cc_start: 0.8696 (mtt90) cc_final: 0.8319 (mtt-85) REVERT: A 1094 ASP cc_start: 0.7291 (m-30) cc_final: 0.6364 (m-30) REVERT: A 1134 GLU cc_start: 0.8587 (pp20) cc_final: 0.8216 (pp20) REVERT: A 1141 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8573 (mm-30) REVERT: A 1190 ASP cc_start: 0.8372 (p0) cc_final: 0.8057 (p0) REVERT: A 1198 MET cc_start: 0.8342 (ppp) cc_final: 0.7715 (ppp) REVERT: B 68 LYS cc_start: 0.8376 (mttt) cc_final: 0.8016 (mmtt) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1914 time to fit residues: 29.4448 Evaluate side-chains 96 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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: 0.9990 chunk 5 optimal weight: 0.5980 chunk 42 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 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** A1170 HIS ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4595 Z= 0.190 Angle : 0.645 7.225 6189 Z= 0.345 Chirality : 0.043 0.155 680 Planarity : 0.003 0.047 803 Dihedral : 4.763 19.933 615 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % 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: -1.11 (0.34), residues: 567 helix: -0.04 (0.29), residues: 284 sheet: -0.87 (0.49), residues: 99 loop : -1.56 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A1159 HIS 0.003 0.001 HIS A 530 PHE 0.017 0.002 PHE A1168 TYR 0.012 0.001 TYR A 446 ARG 0.003 0.000 ARG A1206 *********************** 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 122 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 PHE cc_start: 0.8421 (m-10) cc_final: 0.7995 (m-80) REVERT: A 425 ARG cc_start: 0.8762 (ptp-170) cc_final: 0.8515 (ptp-170) REVERT: A 483 MET cc_start: 0.5662 (tpt) cc_final: 0.5392 (tpt) REVERT: A 520 MET cc_start: 0.6733 (ttt) cc_final: 0.5547 (tmm) REVERT: A 1084 ARG cc_start: 0.8694 (mtt90) cc_final: 0.8303 (mtt-85) REVERT: A 1094 ASP cc_start: 0.7058 (m-30) cc_final: 0.6019 (m-30) REVERT: A 1134 GLU cc_start: 0.8594 (pp20) cc_final: 0.8220 (pp20) REVERT: A 1141 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8538 (mm-30) REVERT: A 1190 ASP cc_start: 0.8337 (p0) cc_final: 0.8002 (p0) REVERT: A 1198 MET cc_start: 0.8303 (ppp) cc_final: 0.7609 (ppp) REVERT: B 68 LYS cc_start: 0.8383 (mttt) cc_final: 0.8032 (mmtt) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1842 time to fit residues: 27.7336 Evaluate side-chains 94 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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: 1.9990 chunk 47 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 0.0970 chunk 32 optimal weight: 0.0570 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 overall best weight: 0.8298 ------------------------------------------------------------------------------- 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 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 4595 Z= 0.207 Angle : 0.674 7.467 6189 Z= 0.361 Chirality : 0.044 0.216 680 Planarity : 0.004 0.049 803 Dihedral : 4.853 20.274 615 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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: -1.14 (0.34), residues: 567 helix: -0.08 (0.29), residues: 284 sheet: -0.86 (0.49), residues: 101 loop : -1.57 (0.47), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A1159 HIS 0.004 0.001 HIS A 530 PHE 0.016 0.001 PHE A1168 TYR 0.012 0.001 TYR A1083 ARG 0.003 0.000 ARG A1206 *********************** 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 119 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 MET cc_start: 0.8440 (mmm) cc_final: 0.8001 (mmm) REVERT: A 423 PHE cc_start: 0.8408 (m-10) cc_final: 0.7992 (m-80) REVERT: A 483 MET cc_start: 0.5656 (tpt) cc_final: 0.5406 (tpt) REVERT: A 520 MET cc_start: 0.6642 (ttt) cc_final: 0.5472 (tmm) REVERT: A 1084 ARG cc_start: 0.8705 (mtt90) cc_final: 0.8304 (mtt-85) REVERT: A 1094 ASP cc_start: 0.7025 (m-30) cc_final: 0.6030 (m-30) REVERT: A 1134 GLU cc_start: 0.8599 (pp20) cc_final: 0.8240 (pp20) REVERT: A 1141 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8560 (mm-30) REVERT: A 1190 ASP cc_start: 0.8291 (p0) cc_final: 0.7921 (p0) REVERT: A 1198 MET cc_start: 0.8256 (ppp) cc_final: 0.7530 (ppp) REVERT: B 68 LYS cc_start: 0.8401 (mttt) cc_final: 0.8068 (mmtt) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1749 time to fit residues: 26.0002 Evaluate side-chains 94 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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: 5.9990 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4595 Z= 0.194 Angle : 0.651 7.583 6189 Z= 0.350 Chirality : 0.043 0.167 680 Planarity : 0.003 0.047 803 Dihedral : 4.836 20.220 615 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: -1.13 (0.34), residues: 567 helix: -0.05 (0.29), residues: 282 sheet: -0.84 (0.50), residues: 101 loop : -1.60 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A1159 HIS 0.008 0.001 HIS A 530 PHE 0.016 0.001 PHE A1168 TYR 0.013 0.001 TYR A 446 ARG 0.003 0.000 ARG A1206 ********************** 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 123 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 PHE cc_start: 0.8400 (m-10) cc_final: 0.7980 (m-80) REVERT: A 483 MET cc_start: 0.5583 (tpt) cc_final: 0.5328 (tpt) REVERT: A 520 MET cc_start: 0.6739 (ttt) cc_final: 0.5549 (tmm) REVERT: A 1084 ARG cc_start: 0.8702 (mtt90) cc_final: 0.8299 (mtt-85) REVERT: A 1094 ASP cc_start: 0.7042 (m-30) cc_final: 0.6152 (m-30) REVERT: A 1134 GLU cc_start: 0.8599 (pp20) cc_final: 0.8238 (pp20) REVERT: A 1141 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8540 (mm-30) REVERT: A 1190 ASP cc_start: 0.8310 (p0) cc_final: 0.7933 (p0) REVERT: A 1198 MET cc_start: 0.8235 (ppp) cc_final: 0.7958 (ppp) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1927 time to fit residues: 29.2018 Evaluate side-chains 98 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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: 0.8980 chunk 5 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 32 optimal weight: 0.0040 chunk 50 optimal weight: 30.0000 chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.099535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.077182 restraints weight = 17797.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.079160 restraints weight = 12710.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.080651 restraints weight = 9893.566| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4595 Z= 0.187 Angle : 0.667 7.675 6189 Z= 0.356 Chirality : 0.045 0.222 680 Planarity : 0.004 0.064 803 Dihedral : 4.804 19.083 615 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.17 (0.34), residues: 567 helix: -0.13 (0.29), residues: 283 sheet: -0.85 (0.50), residues: 101 loop : -1.54 (0.47), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A1159 HIS 0.006 0.001 HIS A 530 PHE 0.016 0.001 PHE A1168 TYR 0.012 0.001 TYR A 446 ARG 0.008 0.000 ARG B 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1480.60 seconds wall clock time: 27 minutes 29.37 seconds (1649.37 seconds total)