Starting phenix.real_space_refine on Tue Feb 13 19:08:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bys_16332/02_2024/8bys_16332.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bys_16332/02_2024/8bys_16332.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bys_16332/02_2024/8bys_16332.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bys_16332/02_2024/8bys_16332.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bys_16332/02_2024/8bys_16332.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bys_16332/02_2024/8bys_16332.pdb" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 9 5.16 5 C 4579 2.51 5 N 1325 2.21 5 O 1493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7406 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2470 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 2, 'TRANS': 320} Chain: "B" Number of atoms: 2466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2466 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 2, 'TRANS': 319} Chain: "C" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2470 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 2, 'TRANS': 320} Time building chain proxies: 4.14, per 1000 atoms: 0.56 Number of scatterers: 7406 At special positions: 0 Unit cell: (84.952, 94.136, 95.284, 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 9 16.00 O 1493 8.00 N 1325 7.00 C 4579 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: 2.61 Conformation dependent library (CDL) restraints added in 1.1 seconds 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1680 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 6 sheets defined 5.3% alpha, 56.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 100 through 113 Processing helix chain 'B' and resid 101 through 113 removed outlier: 3.581A pdb=" N ARG B 113 " --> pdb=" O ARG B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 244 removed outlier: 4.038A pdb=" N ALA B 243 " --> pdb=" O ASP B 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 114 removed outlier: 3.543A pdb=" N ASP C 112 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG C 113 " --> pdb=" O ARG C 109 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 244 removed outlier: 4.020A pdb=" N ALA C 243 " --> pdb=" O ASP C 240 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 130 removed outlier: 6.866A pdb=" N THR A 160 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG A 185 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LYS A 167 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ILE A 183 " --> pdb=" O LYS A 167 " (cutoff:3.500A) removed outlier: 24.083A pdb=" N THR A 182 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 18.720A pdb=" N THR A 206 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 12.803A pdb=" N ASP A 184 " --> pdb=" O GLN A 204 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLN A 204 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL A 196 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR A 213 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER A 267 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LYS A 376 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER A 400 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL A 390 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 279 through 283 Processing sheet with id=AA3, first strand: chain 'B' and resid 118 through 130 removed outlier: 6.575A pdb=" N THR B 160 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG B 185 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LYS B 167 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ILE B 183 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ASN B 169 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ALA B 181 " --> pdb=" O ASN B 169 " (cutoff:3.500A) removed outlier: 23.957A pdb=" N THR B 182 " --> pdb=" O THR B 206 " (cutoff:3.500A) removed outlier: 18.730A pdb=" N THR B 206 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 12.867A pdb=" N ASP B 184 " --> pdb=" O GLN B 204 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLN B 204 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS B 376 " --> pdb=" O SER B 400 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER B 400 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 279 through 283 Processing sheet with id=AA5, first strand: chain 'C' and resid 118 through 130 removed outlier: 6.752A pdb=" N THR C 160 " --> pdb=" O VAL C 156 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG C 185 " --> pdb=" O ARG C 165 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS C 167 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ILE C 183 " --> pdb=" O LYS C 167 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ASN C 169 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA C 181 " --> pdb=" O ASN C 169 " (cutoff:3.500A) removed outlier: 23.941A pdb=" N THR C 182 " --> pdb=" O THR C 206 " (cutoff:3.500A) removed outlier: 18.576A pdb=" N THR C 206 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 12.761A pdb=" N ASP C 184 " --> pdb=" O GLN C 204 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLN C 204 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS C 376 " --> pdb=" O SER C 400 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER C 400 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL C 390 " --> pdb=" O VAL C 386 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 279 through 283 465 hydrogen bonds defined for protein. 1311 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: 2.43 Time building geometry restraints manager: 2.86 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: 2540 1.34 - 1.45: 1259 1.45 - 1.57: 3724 1.57 - 1.69: 0 1.69 - 1.80: 18 Bond restraints: 7541 Sorted by residual: bond pdb=" CG ASP C 218 " pdb=" OD1 ASP C 218 " ideal model delta sigma weight residual 1.249 1.230 0.019 1.90e-02 2.77e+03 1.03e+00 bond pdb=" CB ILE C 239 " pdb=" CG1 ILE C 239 " ideal model delta sigma weight residual 1.530 1.511 0.019 2.00e-02 2.50e+03 9.31e-01 bond pdb=" CA ASP C 214 " pdb=" C ASP C 214 " ideal model delta sigma weight residual 1.530 1.522 0.009 1.08e-02 8.57e+03 6.73e-01 bond pdb=" CB ASP C 218 " pdb=" CG ASP C 218 " ideal model delta sigma weight residual 1.516 1.496 0.020 2.50e-02 1.60e+03 6.43e-01 bond pdb=" N GLY A 261 " pdb=" CA GLY A 261 " ideal model delta sigma weight residual 1.456 1.447 0.009 1.16e-02 7.43e+03 5.70e-01 ... (remaining 7536 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.89: 72 106.89 - 113.67: 3919 113.67 - 120.46: 2828 120.46 - 127.25: 3304 127.25 - 134.04: 42 Bond angle restraints: 10165 Sorted by residual: angle pdb=" N ASP B 215 " pdb=" CA ASP B 215 " pdb=" C ASP B 215 " ideal model delta sigma weight residual 107.73 113.36 -5.63 1.34e+00 5.57e-01 1.77e+01 angle pdb=" C ASP C 215 " pdb=" N THR C 216 " pdb=" CA THR C 216 " ideal model delta sigma weight residual 120.90 125.84 -4.94 1.41e+00 5.03e-01 1.23e+01 angle pdb=" CA PHE B 203 " pdb=" C PHE B 203 " pdb=" N GLN B 204 " ideal model delta sigma weight residual 115.54 120.09 -4.55 1.52e+00 4.33e-01 8.95e+00 angle pdb=" CA PHE B 203 " pdb=" C PHE B 203 " pdb=" O PHE B 203 " ideal model delta sigma weight residual 121.60 118.32 3.28 1.21e+00 6.83e-01 7.36e+00 angle pdb=" C ALA C 138 " pdb=" N ASN C 139 " pdb=" CA ASN C 139 " ideal model delta sigma weight residual 121.54 126.50 -4.96 1.91e+00 2.74e-01 6.75e+00 ... (remaining 10160 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4015 17.98 - 35.96: 284 35.96 - 53.94: 45 53.94 - 71.92: 16 71.92 - 89.90: 7 Dihedral angle restraints: 4367 sinusoidal: 1662 harmonic: 2705 Sorted by residual: dihedral pdb=" CA ASP C 214 " pdb=" CB ASP C 214 " pdb=" CG ASP C 214 " pdb=" OD1 ASP C 214 " ideal model delta sinusoidal sigma weight residual -30.00 -87.63 57.63 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ASP A 367 " pdb=" C ASP A 367 " pdb=" N LEU A 368 " pdb=" CA LEU A 368 " ideal model delta harmonic sigma weight residual 180.00 163.63 16.37 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA TYR A 213 " pdb=" C TYR A 213 " pdb=" N ASP A 214 " pdb=" CA ASP A 214 " ideal model delta harmonic sigma weight residual 180.00 163.94 16.06 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 4364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 444 0.026 - 0.052: 371 0.052 - 0.077: 139 0.077 - 0.103: 38 0.103 - 0.129: 40 Chirality restraints: 1032 Sorted by residual: chirality pdb=" CA VAL B 224 " pdb=" N VAL B 224 " pdb=" C VAL B 224 " pdb=" CB VAL B 224 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA ASN B 321 " pdb=" N ASN B 321 " pdb=" C ASN B 321 " pdb=" CB ASN B 321 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA VAL C 163 " pdb=" N VAL C 163 " pdb=" C VAL C 163 " pdb=" CB VAL C 163 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 1029 not shown) Planarity restraints: 1367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 214 " 0.006 2.00e-02 2.50e+03 1.19e-02 1.41e+00 pdb=" C ASP C 214 " -0.021 2.00e-02 2.50e+03 pdb=" O ASP C 214 " 0.008 2.00e-02 2.50e+03 pdb=" N ASP C 215 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 139 " 0.005 2.00e-02 2.50e+03 1.03e-02 1.07e+00 pdb=" C ASN C 139 " -0.018 2.00e-02 2.50e+03 pdb=" O ASN C 139 " 0.007 2.00e-02 2.50e+03 pdb=" N SER C 140 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 420 " -0.004 2.00e-02 2.50e+03 7.28e-03 9.27e-01 pdb=" CG PHE A 420 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE A 420 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 420 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 420 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 420 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 420 " 0.001 2.00e-02 2.50e+03 ... (remaining 1364 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 524 2.74 - 3.28: 6826 3.28 - 3.82: 11482 3.82 - 4.36: 14516 4.36 - 4.90: 27290 Nonbonded interactions: 60638 Sorted by model distance: nonbonded pdb=" OD2 ASP B 215 " pdb=" OG SER B 359 " model vdw 2.195 2.440 nonbonded pdb=" OG1 THR C 206 " pdb=" OD2 ASP C 214 " model vdw 2.200 2.440 nonbonded pdb=" O VAL A 263 " pdb=" OG SER A 267 " model vdw 2.204 2.440 nonbonded pdb=" OG1 THR A 206 " pdb=" OD2 ASP A 214 " model vdw 2.204 2.440 nonbonded pdb=" OG1 THR B 206 " pdb=" OD1 ASP B 214 " model vdw 2.235 2.440 ... (remaining 60633 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 100 through 421) selection = chain 'B' selection = (chain 'C' and resid 100 through 421) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.920 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 22.350 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 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 0.023 7541 Z= 0.243 Angle : 0.563 7.741 10165 Z= 0.325 Chirality : 0.044 0.129 1032 Planarity : 0.002 0.032 1367 Dihedral : 13.509 89.900 2687 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.29), residues: 962 helix: 1.49 (0.97), residues: 41 sheet: -0.36 (0.22), residues: 588 loop : -1.11 (0.36), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 325 HIS 0.004 0.002 HIS C 283 PHE 0.016 0.002 PHE A 420 TYR 0.013 0.002 TYR B 235 ARG 0.004 0.000 ARG C 303 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.749 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1790 time to fit residues: 12.7689 Evaluate side-chains 35 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 205 GLN A 221 GLN A 223 ASN A 232 GLN A 246 ASN A 299 ASN A 305 ASN B 180 GLN B 232 GLN ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.0554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 7541 Z= 0.307 Angle : 0.562 8.181 10165 Z= 0.319 Chirality : 0.045 0.131 1032 Planarity : 0.003 0.033 1367 Dihedral : 4.573 16.292 1064 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.66 % Allowed : 5.77 % Favored : 93.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.29), residues: 962 helix: 1.59 (0.95), residues: 41 sheet: -0.37 (0.22), residues: 588 loop : -1.19 (0.36), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 325 HIS 0.006 0.002 HIS B 190 PHE 0.018 0.002 PHE A 217 TYR 0.013 0.002 TYR B 235 ARG 0.003 0.000 ARG C 106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 0.856 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 44 average time/residue: 0.1746 time to fit residues: 11.7141 Evaluate side-chains 38 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain C residue 116 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 29 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 7541 Z= 0.331 Angle : 0.566 8.687 10165 Z= 0.321 Chirality : 0.045 0.134 1032 Planarity : 0.003 0.030 1367 Dihedral : 4.624 16.341 1064 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.57 % Allowed : 8.66 % Favored : 89.76 % 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: -1.03 (0.29), residues: 962 helix: 1.66 (0.94), residues: 41 sheet: -0.43 (0.22), residues: 592 loop : -1.26 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 325 HIS 0.005 0.002 HIS A 190 PHE 0.018 0.002 PHE A 217 TYR 0.014 0.002 TYR A 348 ARG 0.002 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 41 time to evaluate : 0.589 Fit side-chains REVERT: A 420 PHE cc_start: 0.7544 (OUTLIER) cc_final: 0.6671 (m-10) outliers start: 12 outliers final: 9 residues processed: 47 average time/residue: 0.1657 time to fit residues: 11.5280 Evaluate side-chains 46 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 36 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain C residue 116 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 169 ASN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 364 GLN C 406 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 7541 Z= 0.330 Angle : 0.561 8.960 10165 Z= 0.319 Chirality : 0.045 0.132 1032 Planarity : 0.003 0.026 1367 Dihedral : 4.640 16.489 1064 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.23 % Allowed : 9.45 % Favored : 88.32 % 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 (0.29), residues: 962 helix: 1.74 (0.94), residues: 41 sheet: -0.51 (0.22), residues: 585 loop : -1.28 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 325 HIS 0.005 0.002 HIS A 190 PHE 0.017 0.002 PHE C 217 TYR 0.013 0.002 TYR A 348 ARG 0.002 0.000 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 43 time to evaluate : 0.966 Fit side-chains REVERT: A 420 PHE cc_start: 0.7450 (OUTLIER) cc_final: 0.6562 (m-10) outliers start: 17 outliers final: 13 residues processed: 53 average time/residue: 0.1733 time to fit residues: 13.6062 Evaluate side-chains 55 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 41 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 364 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 3.9990 chunk 1 optimal weight: 0.0770 chunk 69 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 0 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 364 GLN C 406 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 7541 Z= 0.252 Angle : 0.528 9.083 10165 Z= 0.301 Chirality : 0.044 0.130 1032 Planarity : 0.002 0.019 1367 Dihedral : 4.507 16.279 1064 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.84 % Allowed : 11.94 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.29), residues: 962 helix: 1.76 (0.94), residues: 41 sheet: -0.48 (0.22), residues: 584 loop : -1.23 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 325 HIS 0.004 0.002 HIS A 190 PHE 0.017 0.002 PHE C 217 TYR 0.011 0.001 TYR A 348 ARG 0.002 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 45 time to evaluate : 0.766 Fit side-chains REVERT: C 215 ASP cc_start: 0.8894 (OUTLIER) cc_final: 0.8683 (t0) outliers start: 14 outliers final: 11 residues processed: 53 average time/residue: 0.1654 time to fit residues: 13.0478 Evaluate side-chains 51 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 39 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 364 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 299 ASN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 7541 Z= 0.227 Angle : 0.515 9.156 10165 Z= 0.294 Chirality : 0.044 0.129 1032 Planarity : 0.002 0.017 1367 Dihedral : 4.419 16.544 1064 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.36 % Allowed : 12.99 % Favored : 84.65 % 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: -1.03 (0.29), residues: 962 helix: 1.77 (0.93), residues: 41 sheet: -0.44 (0.22), residues: 584 loop : -1.21 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 325 HIS 0.004 0.002 HIS A 190 PHE 0.016 0.002 PHE C 217 TYR 0.010 0.001 TYR A 348 ARG 0.002 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 44 time to evaluate : 0.737 Fit side-chains REVERT: A 420 PHE cc_start: 0.7411 (OUTLIER) cc_final: 0.6612 (m-10) REVERT: C 215 ASP cc_start: 0.8871 (OUTLIER) cc_final: 0.8646 (t0) outliers start: 18 outliers final: 12 residues processed: 58 average time/residue: 0.1608 time to fit residues: 14.1206 Evaluate side-chains 56 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 42 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 215 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 299 ASN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7541 Z= 0.221 Angle : 0.511 9.277 10165 Z= 0.290 Chirality : 0.044 0.132 1032 Planarity : 0.002 0.020 1367 Dihedral : 4.357 16.323 1064 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.23 % Allowed : 14.04 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.29), residues: 962 helix: 1.79 (0.93), residues: 41 sheet: -0.37 (0.22), residues: 576 loop : -1.22 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 325 HIS 0.004 0.002 HIS A 190 PHE 0.015 0.002 PHE C 217 TYR 0.010 0.001 TYR A 348 ARG 0.002 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 42 time to evaluate : 0.830 Fit side-chains REVERT: A 299 ASN cc_start: 0.8358 (OUTLIER) cc_final: 0.8115 (p0) REVERT: A 420 PHE cc_start: 0.7411 (OUTLIER) cc_final: 0.6590 (m-10) outliers start: 17 outliers final: 12 residues processed: 55 average time/residue: 0.1983 time to fit residues: 16.6948 Evaluate side-chains 55 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 41 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 326 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 ASN B 403 GLN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 7541 Z= 0.386 Angle : 0.588 9.266 10165 Z= 0.333 Chirality : 0.046 0.140 1032 Planarity : 0.003 0.026 1367 Dihedral : 4.698 17.656 1064 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 3.15 % Allowed : 13.78 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.28), residues: 962 helix: 1.88 (0.94), residues: 41 sheet: -0.52 (0.22), residues: 585 loop : -1.30 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 325 HIS 0.005 0.002 HIS A 190 PHE 0.020 0.002 PHE C 217 TYR 0.015 0.002 TYR A 348 ARG 0.003 0.000 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 41 time to evaluate : 0.717 Fit side-chains REVERT: A 420 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.6811 (m-10) outliers start: 24 outliers final: 22 residues processed: 62 average time/residue: 0.2000 time to fit residues: 17.2751 Evaluate side-chains 63 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 40 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 326 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 ASN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 7541 Z= 0.295 Angle : 0.552 9.393 10165 Z= 0.313 Chirality : 0.045 0.140 1032 Planarity : 0.003 0.051 1367 Dihedral : 4.607 16.712 1064 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.15 % Allowed : 14.17 % Favored : 82.68 % 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: -1.10 (0.28), residues: 962 helix: 1.92 (0.94), residues: 41 sheet: -0.49 (0.22), residues: 584 loop : -1.30 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 325 HIS 0.004 0.002 HIS A 190 PHE 0.016 0.002 PHE C 217 TYR 0.012 0.002 TYR C 187 ARG 0.012 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 39 time to evaluate : 0.933 Fit side-chains REVERT: A 420 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.6679 (m-10) outliers start: 24 outliers final: 21 residues processed: 59 average time/residue: 0.1505 time to fit residues: 13.6809 Evaluate side-chains 61 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 39 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 326 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.0570 chunk 63 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7541 Z= 0.212 Angle : 0.513 9.416 10165 Z= 0.291 Chirality : 0.044 0.139 1032 Planarity : 0.002 0.046 1367 Dihedral : 4.408 16.200 1064 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.89 % Allowed : 14.44 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.29), residues: 962 helix: 1.89 (0.95), residues: 41 sheet: -0.38 (0.22), residues: 579 loop : -1.29 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 325 HIS 0.004 0.002 HIS A 190 PHE 0.014 0.002 PHE C 217 TYR 0.010 0.001 TYR C 187 ARG 0.011 0.000 ARG A 303 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 44 time to evaluate : 0.713 Fit side-chains REVERT: A 420 PHE cc_start: 0.7464 (OUTLIER) cc_final: 0.6719 (m-10) outliers start: 22 outliers final: 21 residues processed: 62 average time/residue: 0.1529 time to fit residues: 14.3179 Evaluate side-chains 65 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 43 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 326 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.0770 chunk 70 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 0.0370 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.129827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.104816 restraints weight = 8458.379| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.33 r_work: 0.3159 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 7541 Z= 0.330 Angle : 0.562 9.409 10165 Z= 0.318 Chirality : 0.045 0.136 1032 Planarity : 0.003 0.045 1367 Dihedral : 4.570 17.077 1064 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.15 % Allowed : 14.30 % Favored : 82.55 % 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: -1.09 (0.29), residues: 962 helix: 1.84 (0.94), residues: 41 sheet: -0.47 (0.22), residues: 584 loop : -1.29 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 325 HIS 0.005 0.002 HIS A 190 PHE 0.018 0.002 PHE C 217 TYR 0.013 0.002 TYR A 348 ARG 0.010 0.000 ARG A 303 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1740.05 seconds wall clock time: 33 minutes 2.73 seconds (1982.73 seconds total)