Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 07:11:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5j_13200/04_2023/7p5j_13200.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5j_13200/04_2023/7p5j_13200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5j_13200/04_2023/7p5j_13200.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5j_13200/04_2023/7p5j_13200.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5j_13200/04_2023/7p5j_13200.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5j_13200/04_2023/7p5j_13200.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 24 5.16 5 C 4034 2.51 5 N 1036 2.21 5 O 1156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 6250 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3069 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 17, 'TRANS': 381} Chain breaks: 1 Chain: "B" Number of atoms: 3069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3069 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 17, 'TRANS': 381} Chain breaks: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.90, per 1000 atoms: 0.62 Number of scatterers: 6250 At special positions: 0 Unit cell: (88.536, 71.61, 134.106, 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 24 16.00 O 1156 8.00 N 1036 7.00 C 4034 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 385 " distance=2.03 Simple disulfide: pdb=" SG CYS A 303 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 275 " - pdb=" SG CYS B 385 " distance=2.03 Simple disulfide: pdb=" SG CYS B 303 " - pdb=" SG CYS B 370 " 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A 501 " - " ASN A 284 " " NAG A 502 " - " ASN A 355 " " NAG B 501 " - " ASN B 284 " " NAG B 502 " - " ASN B 355 " " NAG C 1 " - " ASN A 130 " " NAG D 1 " - " ASN B 130 " Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.1 seconds 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1496 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 0 sheets defined 86.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 10 through 18 removed outlier: 3.604A pdb=" N HIS A 14 " --> pdb=" O SER A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 70 removed outlier: 3.591A pdb=" N GLN A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 161 Processing helix chain 'A' and resid 167 through 187 Processing helix chain 'A' and resid 198 through 238 removed outlier: 3.636A pdb=" N VAL A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 276 removed outlier: 4.116A pdb=" N VAL A 248 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N MET A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 290 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.755A pdb=" N LEU A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 335 removed outlier: 3.759A pdb=" N ARG A 320 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 340 removed outlier: 3.805A pdb=" N GLN A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 368 removed outlier: 3.565A pdb=" N LYS A 345 " --> pdb=" O PRO A 341 " (cutoff:3.500A) Proline residue: A 346 - end of helix removed outlier: 4.183A pdb=" N SER A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 386 removed outlier: 4.266A pdb=" N LEU A 373 " --> pdb=" O HIS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 418 Proline residue: A 414 - end of helix removed outlier: 4.580A pdb=" N ALA A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 18 Processing helix chain 'B' and resid 37 through 70 removed outlier: 3.620A pdb=" N ALA B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 161 Processing helix chain 'B' and resid 167 through 190 removed outlier: 3.694A pdb=" N ALA B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 238 removed outlier: 3.757A pdb=" N VAL B 202 " --> pdb=" O SER B 198 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN B 205 " --> pdb=" O GLN B 201 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL B 206 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 275 removed outlier: 4.010A pdb=" N VAL B 248 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N MET B 249 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 290 Processing helix chain 'B' and resid 293 through 303 Processing helix chain 'B' and resid 311 through 335 Processing helix chain 'B' and resid 335 through 340 removed outlier: 3.925A pdb=" N GLN B 339 " --> pdb=" O GLU B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 368 Processing helix chain 'B' and resid 369 through 385 removed outlier: 4.120A pdb=" N LEU B 373 " --> pdb=" O HIS B 369 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASP B 376 " --> pdb=" O SER B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 418 Proline residue: B 414 - end of helix removed outlier: 4.576A pdb=" N ALA B 418 " --> pdb=" O PRO B 414 " (cutoff:3.500A) 552 hydrogen bonds defined for protein. 1656 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: 1.86 Time building geometry restraints manager: 2.80 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: 1975 1.34 - 1.46: 1103 1.46 - 1.58: 3270 1.58 - 1.70: 0 1.70 - 1.82: 30 Bond restraints: 6378 Sorted by residual: bond pdb=" N ILE B 244 " pdb=" CA ILE B 244 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.19e-02 7.06e+03 1.03e+01 bond pdb=" CA PRO A 421 " pdb=" C PRO A 421 " ideal model delta sigma weight residual 1.517 1.545 -0.028 9.30e-03 1.16e+04 9.10e+00 bond pdb=" N VAL B 243 " pdb=" CA VAL B 243 " ideal model delta sigma weight residual 1.463 1.495 -0.032 1.14e-02 7.69e+03 8.03e+00 bond pdb=" N ASP B 137 " pdb=" CA ASP B 137 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.79e+00 bond pdb=" N LEU B 242 " pdb=" CA LEU B 242 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.16e-02 7.43e+03 6.65e+00 ... (remaining 6373 not shown) Histogram of bond angle deviations from ideal: 99.17 - 106.19: 165 106.19 - 113.20: 3599 113.20 - 120.22: 2339 120.22 - 127.23: 2526 127.23 - 134.25: 75 Bond angle restraints: 8704 Sorted by residual: angle pdb=" N PRO A 421 " pdb=" CA PRO A 421 " pdb=" C PRO A 421 " ideal model delta sigma weight residual 110.70 116.89 -6.19 1.22e+00 6.72e-01 2.57e+01 angle pdb=" CA PRO B 421 " pdb=" C PRO B 421 " pdb=" N PRO B 422 " ideal model delta sigma weight residual 117.93 123.81 -5.88 1.20e+00 6.94e-01 2.40e+01 angle pdb=" CA PRO A 421 " pdb=" C PRO A 421 " pdb=" N PRO A 422 " ideal model delta sigma weight residual 117.93 123.57 -5.64 1.20e+00 6.94e-01 2.21e+01 angle pdb=" O PRO B 421 " pdb=" C PRO B 421 " pdb=" N PRO B 422 " ideal model delta sigma weight residual 121.46 116.44 5.02 1.18e+00 7.18e-01 1.81e+01 angle pdb=" CA ASP B 137 " pdb=" CB ASP B 137 " pdb=" CG ASP B 137 " ideal model delta sigma weight residual 112.60 116.68 -4.08 1.00e+00 1.00e+00 1.67e+01 ... (remaining 8699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 3306 17.82 - 35.64: 327 35.64 - 53.46: 75 53.46 - 71.27: 16 71.27 - 89.09: 8 Dihedral angle restraints: 3732 sinusoidal: 1422 harmonic: 2310 Sorted by residual: dihedral pdb=" CB CYS B 303 " pdb=" SG CYS B 303 " pdb=" SG CYS B 370 " pdb=" CB CYS B 370 " ideal model delta sinusoidal sigma weight residual 93.00 9.23 83.77 1 1.00e+01 1.00e-02 8.56e+01 dihedral pdb=" CA ASP B 279 " pdb=" C ASP B 279 " pdb=" N PRO B 280 " pdb=" CA PRO B 280 " ideal model delta harmonic sigma weight residual 180.00 161.22 18.78 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CB GLU B 204 " pdb=" CG GLU B 204 " pdb=" CD GLU B 204 " pdb=" OE1 GLU B 204 " ideal model delta sinusoidal sigma weight residual 0.00 89.09 -89.09 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 3729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 930 0.061 - 0.122: 131 0.122 - 0.182: 8 0.182 - 0.243: 2 0.243 - 0.304: 1 Chirality restraints: 1072 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.39e+02 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 130 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 130 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 1069 not shown) Planarity restraints: 1092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.295 2.00e-02 2.50e+03 2.56e-01 8.19e+02 pdb=" C7 NAG D 2 " -0.067 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.158 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.454 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.266 2.00e-02 2.50e+03 2.21e-01 6.13e+02 pdb=" C7 NAG D 1 " 0.073 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.183 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.368 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 130 " -0.025 2.00e-02 2.50e+03 2.36e-02 6.95e+00 pdb=" CG ASN A 130 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A 130 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 130 " 0.018 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.022 2.00e-02 2.50e+03 ... (remaining 1089 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1361 2.79 - 3.32: 6914 3.32 - 3.85: 10669 3.85 - 4.37: 11531 4.37 - 4.90: 19376 Nonbonded interactions: 49851 Sorted by model distance: nonbonded pdb=" O GLU B 154 " pdb=" OG1 THR B 157 " model vdw 2.264 2.440 nonbonded pdb=" O GLU A 154 " pdb=" OG1 THR A 157 " model vdw 2.274 2.440 nonbonded pdb=" O VAL A 90 " pdb=" OG SER A 93 " model vdw 2.286 2.440 nonbonded pdb=" O3 NAG C 1 " pdb=" O7 NAG C 2 " model vdw 2.330 2.440 nonbonded pdb=" OD1 ASN A 205 " pdb=" N VAL A 206 " model vdw 2.344 2.520 ... (remaining 49846 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 0.530 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: 2.910 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 20.290 Find NCS groups from input model: 0.350 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: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 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 0.051 6378 Z= 0.262 Angle : 0.725 7.505 8704 Z= 0.405 Chirality : 0.043 0.304 1072 Planarity : 0.011 0.256 1086 Dihedral : 15.496 89.092 2224 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.31), residues: 790 helix: 2.36 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -1.51 (0.54), residues: 132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 239 time to evaluate : 0.719 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 241 average time/residue: 0.1507 time to fit residues: 49.6803 Evaluate side-chains 203 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 201 time to evaluate : 0.754 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2042 time to fit residues: 1.5114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6378 Z= 0.213 Angle : 0.685 9.574 8704 Z= 0.321 Chirality : 0.043 0.315 1072 Planarity : 0.005 0.074 1086 Dihedral : 3.667 18.473 850 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer Outliers : 2.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.30), residues: 790 helix: 2.65 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -1.59 (0.55), residues: 126 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 213 time to evaluate : 0.672 Fit side-chains outliers start: 16 outliers final: 13 residues processed: 219 average time/residue: 0.1468 time to fit residues: 43.9394 Evaluate side-chains 213 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 200 time to evaluate : 0.716 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0604 time to fit residues: 2.3947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 58 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 HIS B 324 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 6378 Z= 0.241 Angle : 0.680 10.283 8704 Z= 0.316 Chirality : 0.041 0.281 1072 Planarity : 0.005 0.062 1086 Dihedral : 3.709 18.295 850 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 1.36 % 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: 3.16 (0.30), residues: 790 helix: 2.71 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -1.53 (0.55), residues: 126 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 204 time to evaluate : 0.727 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 207 average time/residue: 0.1461 time to fit residues: 41.7134 Evaluate side-chains 201 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 198 time to evaluate : 0.723 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0565 time to fit residues: 1.2296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 6378 Z= 0.240 Angle : 0.695 10.542 8704 Z= 0.320 Chirality : 0.041 0.266 1072 Planarity : 0.005 0.060 1086 Dihedral : 3.732 18.329 850 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer Outliers : 2.87 % 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: 3.15 (0.30), residues: 790 helix: 2.71 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -1.61 (0.54), residues: 126 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 207 time to evaluate : 0.767 Fit side-chains outliers start: 19 outliers final: 16 residues processed: 213 average time/residue: 0.1511 time to fit residues: 43.9017 Evaluate side-chains 217 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 201 time to evaluate : 0.692 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0819 time to fit residues: 3.0447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 6378 Z= 0.251 Angle : 0.719 12.011 8704 Z= 0.331 Chirality : 0.041 0.246 1072 Planarity : 0.005 0.054 1086 Dihedral : 3.744 18.390 850 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer Outliers : 1.36 % 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: 3.15 (0.30), residues: 790 helix: 2.70 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -1.57 (0.55), residues: 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 206 time to evaluate : 0.726 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 211 average time/residue: 0.1514 time to fit residues: 43.5668 Evaluate side-chains 205 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 200 time to evaluate : 0.720 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0613 time to fit residues: 1.5366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 6378 Z= 0.248 Angle : 0.735 13.065 8704 Z= 0.338 Chirality : 0.042 0.234 1072 Planarity : 0.005 0.052 1086 Dihedral : 3.821 18.478 850 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 1.66 % 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: 3.09 (0.30), residues: 790 helix: 2.64 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -1.48 (0.56), residues: 126 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 204 time to evaluate : 0.759 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 207 average time/residue: 0.1483 time to fit residues: 42.3286 Evaluate side-chains 205 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 198 time to evaluate : 0.697 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1443 time to fit residues: 2.3543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 6378 Z= 0.220 Angle : 0.738 13.459 8704 Z= 0.335 Chirality : 0.042 0.247 1072 Planarity : 0.005 0.049 1086 Dihedral : 3.811 18.212 850 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer Outliers : 1.51 % 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: 3.08 (0.30), residues: 790 helix: 2.64 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -1.55 (0.56), residues: 124 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 207 time to evaluate : 0.739 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 209 average time/residue: 0.1576 time to fit residues: 44.5587 Evaluate side-chains 202 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 199 time to evaluate : 0.696 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0608 time to fit residues: 1.2898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 0.0970 chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 360 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 6378 Z= 0.232 Angle : 0.753 12.570 8704 Z= 0.342 Chirality : 0.043 0.236 1072 Planarity : 0.005 0.050 1086 Dihedral : 3.784 18.029 850 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.30), residues: 790 helix: 2.62 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -1.44 (0.57), residues: 124 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 204 time to evaluate : 0.737 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 206 average time/residue: 0.1491 time to fit residues: 42.1926 Evaluate side-chains 209 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 200 time to evaluate : 0.712 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0978 time to fit residues: 2.3274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.4980 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.085 6378 Z= 0.242 Angle : 0.761 14.225 8704 Z= 0.346 Chirality : 0.042 0.254 1072 Planarity : 0.005 0.050 1086 Dihedral : 3.799 18.050 850 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 0.60 % 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: 3.05 (0.30), residues: 790 helix: 2.60 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -1.43 (0.58), residues: 124 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 201 time to evaluate : 0.706 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 202 average time/residue: 0.1554 time to fit residues: 43.0732 Evaluate side-chains 200 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 197 time to evaluate : 0.735 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0685 time to fit residues: 1.3164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.085 6378 Z= 0.238 Angle : 0.790 14.333 8704 Z= 0.357 Chirality : 0.044 0.272 1072 Planarity : 0.005 0.051 1086 Dihedral : 3.835 18.084 850 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 0.15 % 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: 3.01 (0.30), residues: 790 helix: 2.55 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -1.38 (0.59), residues: 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 202 time to evaluate : 0.654 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 202 average time/residue: 0.1438 time to fit residues: 39.9497 Evaluate side-chains 200 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 199 time to evaluate : 0.746 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0638 time to fit residues: 1.1050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.0870 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 54 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 0.0370 chunk 41 optimal weight: 0.0050 overall best weight: 0.2850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 326 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.158152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.138338 restraints weight = 9907.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.140954 restraints weight = 6325.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.144896 restraints weight = 4424.829| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.085 6378 Z= 0.205 Angle : 0.772 14.792 8704 Z= 0.347 Chirality : 0.044 0.283 1072 Planarity : 0.004 0.055 1086 Dihedral : 3.844 17.533 850 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 0.15 % 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: 3.11 (0.30), residues: 790 helix: 2.62 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -1.36 (0.59), residues: 122 =============================================================================== Job complete usr+sys time: 1452.45 seconds wall clock time: 27 minutes 5.02 seconds (1625.02 seconds total)