Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 3 01:26:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr5_34046/10_2023/7yr5_34046.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr5_34046/10_2023/7yr5_34046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr5_34046/10_2023/7yr5_34046.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr5_34046/10_2023/7yr5_34046.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr5_34046/10_2023/7yr5_34046.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr5_34046/10_2023/7yr5_34046.pdb" } resolution = 3.63 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= 0.015 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 35 5.16 5 C 3164 2.51 5 N 775 2.21 5 O 854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 79": "OE1" <-> "OE2" Residue "B GLU 149": "OE1" <-> "OE2" Residue "A GLU 48": "OE1" <-> "OE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 4828 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 1899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1899 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 8, 'TRANS': 228} Chain: "A" Number of atoms: 2929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2929 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 367} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 3.08, per 1000 atoms: 0.64 Number of scatterers: 4828 At special positions: 0 Unit cell: (73.08, 103.32, 123.48, 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 35 16.00 O 854 8.00 N 775 7.00 C 3164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 88 " - pdb=" SG CYS B 142 " distance=2.04 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 237 " distance=2.03 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: 2.05 Conformation dependent library (CDL) restraints added in 729.5 milliseconds 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1126 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 5 sheets defined 61.7% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'B' and resid 257 through 290 removed outlier: 4.103A pdb=" N LYS B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Proline residue: B 263 - end of helix Processing helix chain 'A' and resid 19 through 40 removed outlier: 4.237A pdb=" N PHE A 36 " --> pdb=" O PHE A 32 " (cutoff:3.500A) Proline residue: A 37 - end of helix Processing helix chain 'A' and resid 40 through 51 removed outlier: 4.150A pdb=" N LYS A 45 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 50 " --> pdb=" O GLU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 72 removed outlier: 5.085A pdb=" N ILE A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 83 Processing helix chain 'A' and resid 84 through 104 Processing helix chain 'A' and resid 111 through 139 removed outlier: 3.690A pdb=" N CYS A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Proline residue: A 130 - end of helix Processing helix chain 'A' and resid 142 through 152 Processing helix chain 'A' and resid 152 through 162 removed outlier: 4.313A pdb=" N VAL A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 172 removed outlier: 5.924A pdb=" N PHE A 169 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY A 170 " --> pdb=" O GLN A 166 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 171 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 188 removed outlier: 3.519A pdb=" N ILE A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 194 Processing helix chain 'A' and resid 254 through 259 removed outlier: 3.551A pdb=" N LEU A 257 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 291 removed outlier: 4.491A pdb=" N PHE A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLY A 276 " --> pdb=" O ILE A 272 " (cutoff:3.500A) Proline residue: A 280 - end of helix removed outlier: 5.279A pdb=" N SER A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N SER A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 322 removed outlier: 3.590A pdb=" N LEU A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) Proline residue: A 314 - end of helix Processing helix chain 'A' and resid 323 through 326 Processing helix chain 'A' and resid 328 through 347 removed outlier: 3.607A pdb=" N VAL A 338 " --> pdb=" O ALA A 334 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 339 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN A 340 " --> pdb=" O SER A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 374 removed outlier: 3.859A pdb=" N TRP A 369 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 382 Processing helix chain 'A' and resid 383 through 412 removed outlier: 3.983A pdb=" N SER A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N SER A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY A 392 " --> pdb=" O SER A 388 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N CYS A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) Proline residue: A 401 - end of helix Proline residue: A 406 - end of helix Processing helix chain 'A' and resid 418 through 420 No H-bonds generated for 'chain 'A' and resid 418 through 420' Processing helix chain 'A' and resid 421 through 448 removed outlier: 3.934A pdb=" N ALA A 425 " --> pdb=" O TYR A 421 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS A 426 " --> pdb=" O THR A 422 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 61 through 64 removed outlier: 5.621A pdb=" N ILE B 62 " --> pdb=" O GLN B 89 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N THR B 91 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU B 64 " --> pdb=" O THR B 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 72 through 74 removed outlier: 3.715A pdb=" N GLN B 150 " --> pdb=" O PHE B 144 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TRP B 103 " --> pdb=" O LEU B 110 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 169 through 171 Processing sheet with id=AA4, first strand: chain 'B' and resid 191 through 194 Processing sheet with id=AA5, first strand: chain 'B' and resid 210 through 213 278 hydrogen bonds defined for protein. 798 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: 1.26 Time building geometry restraints manager: 2.21 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: 1472 1.34 - 1.46: 1090 1.46 - 1.58: 2336 1.58 - 1.70: 0 1.70 - 1.81: 51 Bond restraints: 4949 Sorted by residual: bond pdb=" N VAL B 84 " pdb=" CA VAL B 84 " ideal model delta sigma weight residual 1.456 1.493 -0.038 1.11e-02 8.12e+03 1.16e+01 bond pdb=" N ILE B 76 " pdb=" CA ILE B 76 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.19e-02 7.06e+03 9.69e+00 bond pdb=" N VAL B 116 " pdb=" CA VAL B 116 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.22e-02 6.72e+03 8.68e+00 bond pdb=" N VAL B 72 " pdb=" CA VAL B 72 " ideal model delta sigma weight residual 1.459 1.494 -0.036 1.24e-02 6.50e+03 8.36e+00 bond pdb=" N LYS B 104 " pdb=" CA LYS B 104 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.27e-02 6.20e+03 7.61e+00 ... (remaining 4944 not shown) Histogram of bond angle deviations from ideal: 99.03 - 106.08: 110 106.08 - 113.13: 2604 113.13 - 120.18: 1927 120.18 - 127.23: 2022 127.23 - 134.28: 52 Bond angle restraints: 6715 Sorted by residual: angle pdb=" C ARG B 128 " pdb=" N PHE B 129 " pdb=" CA PHE B 129 " ideal model delta sigma weight residual 122.77 117.48 5.29 1.33e+00 5.65e-01 1.58e+01 angle pdb=" CA PHE B 129 " pdb=" CB PHE B 129 " pdb=" CG PHE B 129 " ideal model delta sigma weight residual 113.80 117.77 -3.97 1.00e+00 1.00e+00 1.58e+01 angle pdb=" N PHE B 154 " pdb=" CA PHE B 154 " pdb=" C PHE B 154 " ideal model delta sigma weight residual 109.46 103.18 6.28 1.66e+00 3.63e-01 1.43e+01 angle pdb=" C CYS A 106 " pdb=" N ASN A 107 " pdb=" CA ASN A 107 " ideal model delta sigma weight residual 122.61 128.02 -5.41 1.56e+00 4.11e-01 1.20e+01 angle pdb=" C CYS B 88 " pdb=" N GLN B 89 " pdb=" CA GLN B 89 " ideal model delta sigma weight residual 123.05 118.23 4.82 1.40e+00 5.10e-01 1.18e+01 ... (remaining 6710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.54: 2481 14.54 - 29.07: 292 29.07 - 43.61: 82 43.61 - 58.14: 13 58.14 - 72.68: 7 Dihedral angle restraints: 2875 sinusoidal: 1101 harmonic: 1774 Sorted by residual: dihedral pdb=" CA GLN A 166 " pdb=" C GLN A 166 " pdb=" N VAL A 167 " pdb=" CA VAL A 167 " ideal model delta harmonic sigma weight residual 180.00 153.92 26.08 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA LEU A 164 " pdb=" C LEU A 164 " pdb=" N ASN A 165 " pdb=" CA ASN A 165 " ideal model delta harmonic sigma weight residual 180.00 158.35 21.65 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA GLN A 110 " pdb=" C GLN A 110 " pdb=" N GLN A 111 " pdb=" CA GLN A 111 " ideal model delta harmonic sigma weight residual 180.00 159.98 20.02 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 2872 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 571 0.052 - 0.104: 141 0.104 - 0.156: 34 0.156 - 0.208: 12 0.208 - 0.261: 4 Chirality restraints: 762 Sorted by residual: chirality pdb=" CA PHE B 154 " pdb=" N PHE B 154 " pdb=" C PHE B 154 " pdb=" CB PHE B 154 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA CYS B 88 " pdb=" N CYS B 88 " pdb=" C CYS B 88 " pdb=" CB CYS B 88 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ILE B 62 " pdb=" N ILE B 62 " pdb=" C ILE B 62 " pdb=" CB ILE B 62 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 759 not shown) Planarity restraints: 834 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 253 " 0.021 2.00e-02 2.50e+03 4.20e-02 1.76e+01 pdb=" C VAL B 253 " -0.073 2.00e-02 2.50e+03 pdb=" O VAL B 253 " 0.027 2.00e-02 2.50e+03 pdb=" N VAL B 254 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 99 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" C VAL B 99 " 0.043 2.00e-02 2.50e+03 pdb=" O VAL B 99 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN B 100 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 114 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.42e+00 pdb=" C VAL A 114 " 0.032 2.00e-02 2.50e+03 pdb=" O VAL A 114 " -0.012 2.00e-02 2.50e+03 pdb=" N CYS A 115 " -0.011 2.00e-02 2.50e+03 ... (remaining 831 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1062 2.78 - 3.31: 4795 3.31 - 3.84: 7906 3.84 - 4.37: 9100 4.37 - 4.90: 15390 Nonbonded interactions: 38253 Sorted by model distance: nonbonded pdb=" OG SER A 63 " pdb=" O LEU A 403 " model vdw 2.250 2.440 nonbonded pdb=" OG SER A 29 " pdb=" O ASN A 127 " model vdw 2.276 2.440 nonbonded pdb=" OH TYR A 138 " pdb=" O ARG A 196 " model vdw 2.290 2.440 nonbonded pdb=" OH TYR B 210 " pdb=" OH TYR B 235 " model vdw 2.292 2.440 nonbonded pdb=" OG SER B 134 " pdb=" O GLU B 160 " model vdw 2.318 2.440 ... (remaining 38248 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 6.990 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.360 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 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 : 0.005 0.042 4949 Z= 0.326 Angle : 0.808 6.881 6715 Z= 0.501 Chirality : 0.054 0.261 762 Planarity : 0.005 0.042 834 Dihedral : 13.919 72.678 1743 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: -0.05 (0.34), residues: 616 helix: 0.65 (0.29), residues: 362 sheet: 0.32 (0.53), residues: 102 loop : -1.81 (0.42), residues: 152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.554 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1442 time to fit residues: 21.3816 Evaluate side-chains 84 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.593 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN A 165 ASN A 260 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 4949 Z= 0.402 Angle : 0.733 11.019 6715 Z= 0.387 Chirality : 0.046 0.158 762 Planarity : 0.005 0.048 834 Dihedral : 5.269 26.802 665 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.42 % Allowed : 15.75 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.34), residues: 616 helix: 0.52 (0.28), residues: 365 sheet: 0.09 (0.53), residues: 100 loop : -1.58 (0.44), residues: 151 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 0.571 Fit side-chains outliers start: 18 outliers final: 10 residues processed: 98 average time/residue: 0.1336 time to fit residues: 17.9072 Evaluate side-chains 90 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 0.586 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0491 time to fit residues: 1.6497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 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 89 GLN A 127 ASN A 129 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4949 Z= 0.232 Angle : 0.633 9.067 6715 Z= 0.330 Chirality : 0.043 0.135 762 Planarity : 0.005 0.044 834 Dihedral : 5.023 22.929 665 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.71 % Allowed : 19.35 % Favored : 78.94 % 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: 0.09 (0.34), residues: 616 helix: 0.76 (0.28), residues: 365 sheet: 0.00 (0.54), residues: 104 loop : -1.49 (0.46), residues: 147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 0.521 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 95 average time/residue: 0.1317 time to fit residues: 17.0356 Evaluate side-chains 87 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 0.517 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0510 time to fit residues: 1.0543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 0.0870 chunk 58 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN A 129 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4949 Z= 0.260 Angle : 0.642 8.212 6715 Z= 0.333 Chirality : 0.043 0.144 762 Planarity : 0.005 0.043 834 Dihedral : 5.024 24.195 665 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.90 % Allowed : 22.39 % Favored : 75.71 % 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: 0.18 (0.35), residues: 616 helix: 0.80 (0.28), residues: 365 sheet: 0.24 (0.55), residues: 100 loop : -1.47 (0.46), residues: 151 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.567 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 87 average time/residue: 0.1359 time to fit residues: 16.2426 Evaluate side-chains 89 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 0.577 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0532 time to fit residues: 1.4424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 19 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 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 89 GLN ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN A 129 ASN A 291 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4949 Z= 0.216 Angle : 0.608 7.842 6715 Z= 0.315 Chirality : 0.042 0.134 762 Planarity : 0.005 0.042 834 Dihedral : 4.913 22.927 665 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.33 % Allowed : 24.48 % Favored : 74.19 % 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: 0.26 (0.35), residues: 616 helix: 0.86 (0.29), residues: 365 sheet: 0.18 (0.55), residues: 101 loop : -1.38 (0.46), residues: 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 0.669 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 90 average time/residue: 0.1378 time to fit residues: 17.0089 Evaluate side-chains 84 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 0.545 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0528 time to fit residues: 1.0352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 0.0670 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 20.0000 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN A 129 ASN A 291 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4949 Z= 0.241 Angle : 0.633 8.662 6715 Z= 0.329 Chirality : 0.042 0.137 762 Planarity : 0.005 0.041 834 Dihedral : 4.902 23.323 665 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.52 % Allowed : 26.00 % Favored : 72.49 % 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: 0.24 (0.35), residues: 616 helix: 0.86 (0.29), residues: 365 sheet: 0.16 (0.56), residues: 101 loop : -1.42 (0.46), residues: 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 0.496 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 87 average time/residue: 0.1459 time to fit residues: 17.0641 Evaluate side-chains 82 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 0.559 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0491 time to fit residues: 1.2115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN A 129 ASN A 165 ASN A 166 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4949 Z= 0.248 Angle : 0.632 9.314 6715 Z= 0.331 Chirality : 0.042 0.137 762 Planarity : 0.005 0.042 834 Dihedral : 4.964 24.581 665 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.71 % Allowed : 26.57 % Favored : 71.73 % 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: 0.23 (0.35), residues: 616 helix: 0.87 (0.29), residues: 365 sheet: 0.09 (0.56), residues: 101 loop : -1.40 (0.47), residues: 150 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 0.567 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 87 average time/residue: 0.1359 time to fit residues: 16.1117 Evaluate side-chains 83 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 78 time to evaluate : 0.558 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0542 time to fit residues: 1.2151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 51 optimal weight: 0.0970 chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN A 129 ASN A 165 ASN A 166 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4949 Z= 0.235 Angle : 0.629 9.055 6715 Z= 0.326 Chirality : 0.042 0.137 762 Planarity : 0.005 0.042 834 Dihedral : 4.947 24.482 665 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.57 % Allowed : 27.70 % Favored : 71.73 % 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: 0.22 (0.35), residues: 616 helix: 0.87 (0.29), residues: 365 sheet: 0.07 (0.56), residues: 101 loop : -1.42 (0.46), residues: 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 0.559 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 83 average time/residue: 0.1421 time to fit residues: 15.9770 Evaluate side-chains 81 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 0.555 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0535 time to fit residues: 0.8885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 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 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN A 129 ASN A 165 ASN ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4949 Z= 0.220 Angle : 0.622 8.761 6715 Z= 0.325 Chirality : 0.042 0.137 762 Planarity : 0.005 0.041 834 Dihedral : 4.931 25.564 665 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.57 % Allowed : 28.84 % Favored : 70.59 % 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: 0.22 (0.35), residues: 616 helix: 0.88 (0.29), residues: 365 sheet: 0.06 (0.56), residues: 101 loop : -1.44 (0.45), residues: 150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 0.568 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 84 average time/residue: 0.1366 time to fit residues: 15.8633 Evaluate side-chains 82 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 0.568 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0726 time to fit residues: 0.8997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 5 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN A 129 ASN ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4949 Z= 0.209 Angle : 0.628 9.315 6715 Z= 0.324 Chirality : 0.041 0.135 762 Planarity : 0.005 0.041 834 Dihedral : 4.868 24.528 665 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.57 % Allowed : 28.65 % Favored : 70.78 % 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: 0.20 (0.35), residues: 616 helix: 0.94 (0.29), residues: 362 sheet: 0.05 (0.56), residues: 101 loop : -1.60 (0.44), residues: 153 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 80 time to evaluate : 0.562 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 81 average time/residue: 0.1360 time to fit residues: 15.2235 Evaluate side-chains 80 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 0.565 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0494 time to fit residues: 0.8534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 0.0000 chunk 20 optimal weight: 0.6980 chunk 49 optimal weight: 0.4980 chunk 6 optimal weight: 20.0000 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN A 129 ASN ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.173335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.128142 restraints weight = 7909.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.131905 restraints weight = 3787.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.134241 restraints weight = 2289.706| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4949 Z= 0.186 Angle : 0.614 9.217 6715 Z= 0.315 Chirality : 0.041 0.133 762 Planarity : 0.004 0.042 834 Dihedral : 4.745 24.483 665 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.19 % Allowed : 29.60 % Favored : 70.21 % 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: 0.24 (0.35), residues: 616 helix: 0.95 (0.29), residues: 362 sheet: 0.09 (0.56), residues: 101 loop : -1.57 (0.44), residues: 153 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1224.96 seconds wall clock time: 22 minutes 59.35 seconds (1379.35 seconds total)