Starting phenix.real_space_refine (version: dev) on Fri Feb 17 10:25:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdd_13334/02_2023/7pdd_13334.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdd_13334/02_2023/7pdd_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_2023/7pdd_13334.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdd_13334/02_2023/7pdd_13334.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdd_13334/02_2023/7pdd_13334.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdd_13334/02_2023/7pdd_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 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-4877/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: 2.89, per 1000 atoms: 0.64 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: 2.00 Conformation dependent library (CDL) restraints added in 695.7 milliseconds 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1058 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 4 sheets defined 50.1% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 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: 1.32 Time building geometry restraints manager: 2.16 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: 1.260 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: 6.220 Check model and map are aligned: 0.060 Process input model: 16.410 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.000 ------------------------------------------------------------------------------- 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 : 20.92 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 : 0.563 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: 0.2106 time to fit residues: 34.8394 Evaluate side-chains 101 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.571 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7545 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.2556 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= 0.192 Angle : 0.656 8.010 6189 Z= 0.348 Chirality : 0.043 0.150 680 Planarity : 0.004 0.056 803 Dihedral : 5.221 22.459 615 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 18.23 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: -2.47 (0.31), residues: 567 helix: -0.85 (0.27), residues: 281 sheet: -2.07 (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 134 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 0.582 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: 1 outliers final: 1 residues processed: 134 average time/residue: 0.1815 time to fit residues: 30.1735 Evaluate side-chains 103 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.540 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0767 time to fit residues: 0.8804 ------------------------------------------------------------------------------- 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: 0.9980 chunk 15 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7324 moved from start: 0.3173 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= 0.185 Angle : 0.618 7.513 6189 Z= 0.328 Chirality : 0.041 0.147 680 Planarity : 0.003 0.055 803 Dihedral : 5.018 22.283 615 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % 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: -2.02 (0.33), residues: 567 helix: -0.55 (0.28), residues: 282 sheet: -1.84 (0.44), residues: 105 loop : -2.05 (0.45), residues: 180 *********************** 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: 2 poor density : 127 time to evaluate : 0.570 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: 2 outliers final: 1 residues processed: 129 average time/residue: 0.2006 time to fit residues: 31.7668 Evaluate side-chains 96 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.579 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0470 time to fit residues: 0.8281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 54 optimal weight: 0.0370 chunk 48 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 30 optimal weight: 0.0770 chunk 0 optimal weight: 4.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 ASN A1131 HIS ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.3867 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= 0.170 Angle : 0.629 8.849 6189 Z= 0.331 Chirality : 0.042 0.150 680 Planarity : 0.003 0.049 803 Dihedral : 4.885 21.399 615 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % 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: -1.49 (0.34), residues: 567 helix: -0.21 (0.29), residues: 282 sheet: -1.23 (0.48), residues: 99 loop : -1.88 (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 135 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 133 time to evaluate : 0.513 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: 134 average time/residue: 0.1970 time to fit residues: 32.4614 Evaluate side-chains 105 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 0.519 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0857 time to fit residues: 0.9042 ------------------------------------------------------------------------------- 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: 0.1980 chunk 22 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 8.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 389 GLN ** 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: 0.7467 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 4595 Z= 0.341 Angle : 0.771 8.464 6189 Z= 0.410 Chirality : 0.045 0.128 680 Planarity : 0.004 0.055 803 Dihedral : 5.551 22.725 615 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 25.84 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: -1.81 (0.33), residues: 567 helix: -0.50 (0.29), residues: 283 sheet: -1.29 (0.48), residues: 99 loop : -2.04 (0.44), residues: 185 *********************** 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 114 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1915 time to fit residues: 26.9602 Evaluate side-chains 92 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.484 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6703 ------------------------------------------------------------------------------- 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: 2.9990 chunk 54 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** 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: 0.7348 moved from start: 0.4287 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= 0.208 Angle : 0.691 9.097 6189 Z= 0.366 Chirality : 0.043 0.142 680 Planarity : 0.004 0.053 803 Dihedral : 5.246 21.498 615 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 21.70 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: -1.62 (0.34), residues: 567 helix: -0.35 (0.29), residues: 282 sheet: -1.06 (0.49), residues: 101 loop : -2.03 (0.45), 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 119 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1991 time to fit residues: 29.2951 Evaluate side-chains 94 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.490 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6752 ------------------------------------------------------------------------------- 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: 0.8980 chunk 45 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.0970 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7276 moved from start: 0.4657 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= 0.181 Angle : 0.667 9.273 6189 Z= 0.348 Chirality : 0.043 0.144 680 Planarity : 0.003 0.048 803 Dihedral : 4.895 20.923 615 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % 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: -1.27 (0.34), residues: 567 helix: -0.06 (0.30), residues: 284 sheet: -0.91 (0.49), residues: 101 loop : -1.88 (0.45), residues: 182 *********************** 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 122 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1993 time to fit residues: 30.0264 Evaluate side-chains 91 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.544 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6465 ------------------------------------------------------------------------------- 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: 0.0270 chunk 5 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 47 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.7285 moved from start: 0.4812 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= 0.194 Angle : 0.689 9.414 6189 Z= 0.364 Chirality : 0.044 0.169 680 Planarity : 0.003 0.046 803 Dihedral : 4.898 20.015 615 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 19.35 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: -1.27 (0.34), residues: 567 helix: -0.08 (0.30), residues: 281 sheet: -0.90 (0.49), residues: 99 loop : -1.81 (0.45), residues: 187 *********************** 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 128 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2009 time to fit residues: 31.3820 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6773 ------------------------------------------------------------------------------- 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: 2.9990 chunk 47 optimal weight: 0.7980 chunk 50 optimal weight: 0.0370 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 32 optimal weight: 0.1980 chunk 25 optimal weight: 0.0050 chunk 36 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 51 optimal weight: 0.0570 chunk 44 optimal weight: 0.9990 overall best weight: 0.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7194 moved from start: 0.5248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 4595 Z= 0.187 Angle : 0.699 9.888 6189 Z= 0.361 Chirality : 0.044 0.203 680 Planarity : 0.004 0.044 803 Dihedral : 4.713 18.794 615 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 18.34 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: -1.12 (0.35), residues: 567 helix: -0.05 (0.30), residues: 280 sheet: -0.81 (0.49), residues: 99 loop : -1.57 (0.45), residues: 188 *********************** 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 134 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.2057 time to fit residues: 33.6631 Evaluate side-chains 101 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.490 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7304 ------------------------------------------------------------------------------- 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: 8.9990 chunk 34 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7273 moved from start: 0.5298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 4595 Z= 0.212 Angle : 0.740 9.688 6189 Z= 0.386 Chirality : 0.046 0.286 680 Planarity : 0.004 0.050 803 Dihedral : 4.863 18.842 615 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 20.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % 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: -1.34 (0.34), residues: 567 helix: -0.22 (0.30), residues: 282 sheet: -1.00 (0.48), residues: 101 loop : -1.67 (0.47), residues: 184 ********************** 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 : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1983 time to fit residues: 30.7049 Evaluate side-chains 96 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.533 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7457 ------------------------------------------------------------------------------- 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: 8.9990 chunk 8 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 32 optimal weight: 0.0870 chunk 50 optimal weight: 0.0070 chunk 29 optimal weight: 0.0010 chunk 38 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4051 r_free = 0.4051 target = 0.101096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.079789 restraints weight = 17761.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.081701 restraints weight = 13025.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.083116 restraints weight = 10267.274| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.5574 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= 0.179 Angle : 0.730 9.732 6189 Z= 0.377 Chirality : 0.046 0.234 680 Planarity : 0.004 0.044 803 Dihedral : 4.796 18.631 615 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 17.90 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: -1.20 (0.35), residues: 567 helix: -0.16 (0.30), residues: 282 sheet: -0.99 (0.48), residues: 101 loop : -1.44 (0.47), residues: 184 =============================================================================== Job complete usr+sys time: 1468.68 seconds wall clock time: 27 minutes 23.12 seconds (1643.12 seconds total)