Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:39:26 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdd_13334/11_2022/7pdd_13334.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdd_13334/11_2022/7pdd_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_13334/11_2022/7pdd_13334.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdd_13334/11_2022/7pdd_13334.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdd_13334/11_2022/7pdd_13334.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdd_13334/11_2022/7pdd_13334.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 Convert atoms to be neutral 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 4516 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3550 Classifications: {'peptide': 449} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 439} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 966 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Time building chain proxies: 3.06, per 1000 atoms: 0.68 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 663.3 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: 0.29 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: 1.33 Time building geometry restraints manager: 2.13 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 2847 2.51 5 N 772 2.21 5 O 864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.480 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.040 Process input model: 17.500 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 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 : 21.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 *********************** 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 : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1914 time to fit residues: 31.7779 Evaluate side-chains 101 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.458 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6806 ------------------------------------------------------------------------------- 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: 0.0470 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: 0.5878 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 4595 Z= 0.189 Angle : 0.656 7.992 6189 Z= 0.347 Chirality : 0.043 0.151 680 Planarity : 0.004 0.057 803 Dihedral : 5.210 22.461 615 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.31), residues: 567 helix: -0.81 (0.27), residues: 281 sheet: -2.06 (0.42), residues: 105 loop : -2.35 (0.43), residues: 181 *********************** 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 135 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 0.559 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 outliers start: 1 outliers final: 1 residues processed: 135 average time/residue: 0.2009 time to fit residues: 33.9882 Evaluate side-chains 103 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.602 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0904 time to fit residues: 0.9856 ------------------------------------------------------------------------------- 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: 2.9990 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 0.0670 overall best weight: 2.0126 ------------------------------------------------------------------------------- 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** ** B 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2950 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= 0.294 Angle : 0.696 7.238 6189 Z= 0.374 Chirality : 0.043 0.139 680 Planarity : 0.004 0.060 803 Dihedral : 5.452 23.240 615 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 23.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer Outliers : 0.42 % 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: -2.30 (0.32), residues: 567 helix: -0.83 (0.28), residues: 282 sheet: -1.90 (0.44), residues: 103 loop : -2.13 (0.44), residues: 182 *********************** 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 124 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 0.577 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 outliers start: 2 outliers final: 1 residues processed: 124 average time/residue: 0.2027 time to fit residues: 30.6281 Evaluate side-chains 92 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.559 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0471 time to fit residues: 0.8327 ------------------------------------------------------------------------------- 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: 0.9980 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 0.3980 chunk 54 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** B 92 HIS ** B 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.3737 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= 0.192 Angle : 0.648 8.518 6189 Z= 0.344 Chirality : 0.043 0.142 680 Planarity : 0.003 0.054 803 Dihedral : 5.066 21.587 615 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.34), residues: 567 helix: -0.33 (0.29), residues: 282 sheet: -1.37 (0.48), residues: 99 loop : -1.90 (0.45), residues: 186 *********************** 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 130 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1794 time to fit residues: 29.0650 Evaluate side-chains 94 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.535 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7504 ------------------------------------------------------------------------------- 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: 1.9990 chunk 46 optimal weight: 0.8980 chunk 37 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 0.1980 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 4595 Z= 0.234 Angle : 0.705 9.963 6189 Z= 0.371 Chirality : 0.043 0.140 680 Planarity : 0.003 0.053 803 Dihedral : 5.140 23.429 615 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 22.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.34), residues: 567 helix: -0.23 (0.29), residues: 285 sheet: -1.25 (0.49), residues: 99 loop : -1.94 (0.46), residues: 183 *********************** 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 116 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 115 average time/residue: 0.1742 time to fit residues: 25.1111 Evaluate side-chains 94 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.571 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7409 ------------------------------------------------------------------------------- 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: 0.9990 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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: 0.7312 moved from start: 0.4332 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= 0.201 Angle : 0.696 11.370 6189 Z= 0.363 Chirality : 0.043 0.138 680 Planarity : 0.003 0.050 803 Dihedral : 5.045 21.675 615 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.34), residues: 567 helix: -0.18 (0.30), residues: 284 sheet: -1.13 (0.49), residues: 99 loop : -2.00 (0.46), residues: 184 *********************** 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 123 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 123 average time/residue: 0.1716 time to fit residues: 26.4280 Evaluate side-chains 87 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.484 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 0.0570 chunk 45 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 0.0020 chunk 24 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.0030 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 overall best weight: 0.3116 ------------------------------------------------------------------------------- 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: 0.7224 moved from start: 0.4786 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= 0.185 Angle : 0.675 7.070 6189 Z= 0.361 Chirality : 0.044 0.147 680 Planarity : 0.003 0.045 803 Dihedral : 4.941 21.905 615 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.35), residues: 567 helix: -0.15 (0.30), residues: 280 sheet: -1.04 (0.50), residues: 99 loop : -1.77 (0.46), residues: 188 *********************** 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 126 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1738 time to fit residues: 27.4690 Evaluate side-chains 98 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.612 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7424 ------------------------------------------------------------------------------- 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: 1.9990 chunk 5 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 47 optimal weight: 0.0870 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 0.2980 chunk 21 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- 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** ** B 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.5023 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= 0.191 Angle : 0.666 7.486 6189 Z= 0.358 Chirality : 0.043 0.147 680 Planarity : 0.004 0.055 803 Dihedral : 4.826 19.889 615 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.34), residues: 567 helix: -0.29 (0.29), residues: 282 sheet: -0.79 (0.52), residues: 89 loop : -1.77 (0.43), residues: 196 *********************** 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 126 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1693 time to fit residues: 26.8226 Evaluate side-chains 97 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.538 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7322 ------------------------------------------------------------------------------- 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: 3.9990 chunk 47 optimal weight: 0.6980 chunk 50 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 0.0270 chunk 25 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- 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** ** B 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.5210 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= 0.193 Angle : 0.689 9.353 6189 Z= 0.363 Chirality : 0.044 0.162 680 Planarity : 0.004 0.048 803 Dihedral : 4.717 19.006 615 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.33), residues: 567 helix: -0.32 (0.29), residues: 283 sheet: -0.75 (0.52), residues: 89 loop : -1.72 (0.43), residues: 195 *********************** 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 130 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1684 time to fit residues: 27.2933 Evaluate side-chains 96 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.495 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6661 ------------------------------------------------------------------------------- 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: 0.6980 chunk 27 optimal weight: 0.4980 chunk 35 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 13 optimal weight: 0.0870 chunk 40 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 0.1980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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: 0.7213 moved from start: 0.5425 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= 0.188 Angle : 0.689 10.107 6189 Z= 0.369 Chirality : 0.045 0.186 680 Planarity : 0.004 0.078 803 Dihedral : 4.794 23.770 615 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.34), residues: 567 helix: -0.19 (0.29), residues: 282 sheet: -0.81 (0.50), residues: 93 loop : -1.55 (0.45), residues: 192 ********************** 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 126 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1695 time to fit residues: 27.1265 Evaluate side-chains 97 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.515 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 2 optimal weight: 0.4980 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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** ** B 102 HIS ** 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 = 0.3993 r_free = 0.3993 target = 0.098780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.076571 restraints weight = 18062.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.078697 restraints weight = 12578.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.080228 restraints weight = 9627.856| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.5401 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= 0.217 Angle : 0.701 9.404 6189 Z= 0.376 Chirality : 0.045 0.178 680 Planarity : 0.004 0.060 803 Dihedral : 4.867 22.615 615 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.34), residues: 567 helix: -0.30 (0.29), residues: 281 sheet: -0.73 (0.51), residues: 93 loop : -1.57 (0.45), residues: 193 =============================================================================== Job complete usr+sys time: 1424.01 seconds wall clock time: 27 minutes 2.63 seconds (1622.63 seconds total)