Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 19 23:56:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx6_26155/04_2023/7tx6_26155_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx6_26155/04_2023/7tx6_26155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx6_26155/04_2023/7tx6_26155.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx6_26155/04_2023/7tx6_26155.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx6_26155/04_2023/7tx6_26155_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx6_26155/04_2023/7tx6_26155_updated.pdb" } resolution = 3.3 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= 0.002 sd= 0.033 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 10 5.16 5 C 2122 2.51 5 N 503 2.21 5 O 534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 67": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 3169 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3169 Unusual residues: {'AJP': 1, 'MTX': 1} Classifications: {'peptide': 398, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 13, 'TRANS': 384, None: 2} Not linked: pdbres="GLN A 459 " pdbres="MTX A2644 " Not linked: pdbres="MTX A2644 " pdbres="AJP A2501 " Chain breaks: 1 Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'MTX:plan-3': 1, 'ARG:plan': 10, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 65 Time building chain proxies: 2.43, per 1000 atoms: 0.77 Number of scatterers: 3169 At special positions: 0 Unit cell: (72.36, 61.56, 79.92, 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 10 16.00 O 534 8.00 N 503 7.00 C 2122 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 617.0 milliseconds 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 754 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 17 helices and 0 sheets defined 81.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 24 through 39 removed outlier: 3.894A pdb=" N LEU A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 68 through 89 removed outlier: 3.835A pdb=" N LEU A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 3.986A pdb=" N ASP A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 112 Processing helix chain 'A' and resid 116 through 131 Processing helix chain 'A' and resid 133 through 143 removed outlier: 3.580A pdb=" N TYR A 136 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 137 " --> pdb=" O ILE A 134 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 143 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 176 removed outlier: 5.402A pdb=" N GLN A 150 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG A 151 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER A 168 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 174 " --> pdb=" O GLY A 171 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR A 176 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 201 removed outlier: 3.616A pdb=" N PHE A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 201 " --> pdb=" O VAL A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 263 removed outlier: 3.936A pdb=" N ARG A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 295 removed outlier: 3.573A pdb=" N SER A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N HIS A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 327 removed outlier: 4.015A pdb=" N PHE A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 333 removed outlier: 4.097A pdb=" N ARG A 333 " --> pdb=" O ARG A 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 330 through 333' Processing helix chain 'A' and resid 336 through 355 Processing helix chain 'A' and resid 359 through 390 removed outlier: 5.284A pdb=" N TRP A 363 " --> pdb=" O SER A 360 " (cutoff:3.500A) Proline residue: A 381 - end of helix removed outlier: 4.095A pdb=" N SER A 389 " --> pdb=" O GLN A 386 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 390 " --> pdb=" O ILE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 418 removed outlier: 3.726A pdb=" N ALA A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU A 398 " --> pdb=" O GLU A 394 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 458 224 hydrogen bonds defined for protein. 519 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: 0.83 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 446 1.31 - 1.43: 993 1.43 - 1.56: 1806 1.56 - 1.68: 5 1.68 - 1.81: 15 Bond restraints: 3265 Sorted by residual: bond pdb=" C VAL A 410 " pdb=" N LYS A 411 " ideal model delta sigma weight residual 1.335 1.449 -0.114 1.31e-02 5.83e+03 7.53e+01 bond pdb=" C4 MTX A2644 " pdb=" NA4 MTX A2644 " ideal model delta sigma weight residual 1.328 1.449 -0.121 2.00e-02 2.50e+03 3.68e+01 bond pdb=" N MTX A2644 " pdb=" C MTX A2644 " ideal model delta sigma weight residual 1.339 1.455 -0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" C2 MTX A2644 " pdb=" NA2 MTX A2644 " ideal model delta sigma weight residual 1.341 1.451 -0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C14 MTX A2644 " pdb=" N10 MTX A2644 " ideal model delta sigma weight residual 1.368 1.453 -0.085 2.00e-02 2.50e+03 1.82e+01 ... (remaining 3260 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.41: 78 106.41 - 113.31: 1823 113.31 - 120.21: 1248 120.21 - 127.12: 1294 127.12 - 134.02: 37 Bond angle restraints: 4480 Sorted by residual: angle pdb=" C VAL A 410 " pdb=" N LYS A 411 " pdb=" CA LYS A 411 " ideal model delta sigma weight residual 120.28 114.07 6.21 1.34e+00 5.57e-01 2.15e+01 angle pdb=" CA ILE A 48 " pdb=" C ILE A 48 " pdb=" O ILE A 48 " ideal model delta sigma weight residual 121.17 116.45 4.72 1.06e+00 8.90e-01 1.98e+01 angle pdb=" CA ILE A 417 " pdb=" C ILE A 417 " pdb=" O ILE A 417 " ideal model delta sigma weight residual 120.85 116.34 4.51 1.06e+00 8.90e-01 1.81e+01 angle pdb=" CA VAL A 71 " pdb=" C VAL A 71 " pdb=" O VAL A 71 " ideal model delta sigma weight residual 120.57 116.30 4.27 1.07e+00 8.73e-01 1.59e+01 angle pdb=" N PHE A 416 " pdb=" CA PHE A 416 " pdb=" C PHE A 416 " ideal model delta sigma weight residual 111.28 106.94 4.34 1.09e+00 8.42e-01 1.58e+01 ... (remaining 4475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.23: 1744 24.23 - 48.46: 66 48.46 - 72.69: 5 72.69 - 96.92: 0 96.92 - 121.14: 2 Dihedral angle restraints: 1817 sinusoidal: 644 harmonic: 1173 Sorted by residual: dihedral pdb=" N MTX A2644 " pdb=" C MTX A2644 " pdb=" CA MTX A2644 " pdb=" CB MTX A2644 " ideal model delta harmonic sigma weight residual 122.80 10.81 111.99 0 2.50e+00 1.60e-01 2.01e+03 dihedral pdb=" C MTX A2644 " pdb=" N MTX A2644 " pdb=" CA MTX A2644 " pdb=" CB MTX A2644 " ideal model delta harmonic sigma weight residual -122.60 -172.60 50.00 0 2.50e+00 1.60e-01 4.00e+02 dihedral pdb=" C02 AJP A2501 " pdb=" C85 AJP A2501 " pdb=" O84 AJP A2501 " pdb=" C05 AJP A2501 " ideal model delta sinusoidal sigma weight residual -57.60 63.54 -121.14 1 3.00e+01 1.11e-03 1.62e+01 ... (remaining 1814 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 469 0.070 - 0.141: 50 0.141 - 0.211: 12 0.211 - 0.281: 6 0.281 - 0.352: 1 Chirality restraints: 538 Sorted by residual: chirality pdb=" C11 AJP A2501 " pdb=" C10 AJP A2501 " pdb=" C12 AJP A2501 " pdb=" C16 AJP A2501 " both_signs ideal model delta sigma weight residual False 2.20 2.56 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C15 AJP A2501 " pdb=" C14 AJP A2501 " pdb=" C16 AJP A2501 " pdb=" C20 AJP A2501 " both_signs ideal model delta sigma weight residual False -2.42 -2.70 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C23 AJP A2501 " pdb=" C22 AJP A2501 " pdb=" C24 AJP A2501 " pdb=" O25 AJP A2501 " both_signs ideal model delta sigma weight residual False -2.50 -2.78 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 535 not shown) Planarity restraints: 529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 62 " -0.016 2.00e-02 2.50e+03 3.07e-02 9.41e+00 pdb=" C GLU A 62 " 0.053 2.00e-02 2.50e+03 pdb=" O GLU A 62 " -0.020 2.00e-02 2.50e+03 pdb=" N GLN A 63 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 93 " -0.047 5.00e-02 4.00e+02 7.08e-02 8.03e+00 pdb=" N PRO A 94 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 94 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 94 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 68 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.50e+00 pdb=" C ILE A 68 " -0.032 2.00e-02 2.50e+03 pdb=" O ILE A 68 " 0.012 2.00e-02 2.50e+03 pdb=" N THR A 69 " 0.011 2.00e-02 2.50e+03 ... (remaining 526 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 1094 2.84 - 3.36: 3440 3.36 - 3.87: 5073 3.87 - 4.39: 5561 4.39 - 4.90: 9416 Nonbonded interactions: 24584 Sorted by model distance: nonbonded pdb=" OD1 ASN A 300 " pdb=" N SER A 301 " model vdw 2.327 2.520 nonbonded pdb=" OD1 ASP A 56 " pdb=" N LYS A 57 " model vdw 2.386 2.520 nonbonded pdb=" O SER A 102 " pdb=" OG SER A 105 " model vdw 2.421 2.440 nonbonded pdb=" O LEU A 440 " pdb=" OG SER A 443 " model vdw 2.482 2.440 nonbonded pdb=" O THR A 87 " pdb=" O LEU A 90 " model vdw 2.484 3.040 ... (remaining 24579 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.900 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.370 Find NCS groups from input model: 0.090 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 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 : 0.008 0.121 3265 Z= 0.500 Angle : 0.902 7.786 4480 Z= 0.564 Chirality : 0.055 0.352 538 Planarity : 0.005 0.071 529 Dihedral : 12.435 121.145 1063 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.27 % 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: 2.51 (0.42), residues: 394 helix: 2.27 (0.28), residues: 313 sheet: None (None), residues: 0 loop : -0.83 (0.73), residues: 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 0.353 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 104 average time/residue: 0.1523 time to fit residues: 19.0655 Evaluate side-chains 93 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.348 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 3265 Z= 0.197 Angle : 0.703 16.964 4480 Z= 0.334 Chirality : 0.047 0.679 538 Planarity : 0.006 0.064 529 Dihedral : 7.328 104.275 444 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.27 % 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: 2.14 (0.42), residues: 394 helix: 1.94 (0.28), residues: 316 sheet: None (None), residues: 0 loop : -0.73 (0.74), residues: 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 91 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 91 average time/residue: 0.1455 time to fit residues: 16.1485 Evaluate side-chains 86 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 0.347 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0324 time to fit residues: 0.5891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 3265 Z= 0.192 Angle : 0.656 16.192 4480 Z= 0.310 Chirality : 0.046 0.654 538 Planarity : 0.006 0.059 529 Dihedral : 7.185 108.061 444 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.42), residues: 394 helix: 1.70 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -0.90 (0.70), residues: 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 86 average time/residue: 0.1383 time to fit residues: 14.7647 Evaluate side-chains 81 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 0.351 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0338 time to fit residues: 0.5375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 3265 Z= 0.209 Angle : 0.634 17.443 4480 Z= 0.304 Chirality : 0.047 0.704 538 Planarity : 0.005 0.057 529 Dihedral : 7.144 108.311 444 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.42), residues: 394 helix: 1.54 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -0.94 (0.70), residues: 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 80 average time/residue: 0.1439 time to fit residues: 14.2408 Evaluate side-chains 83 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 81 time to evaluate : 0.364 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0343 time to fit residues: 0.6156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 0.1980 chunk 32 optimal weight: 0.0070 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 overall best weight: 0.5200 ------------------------------------------------------------------------------- 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: 0.7491 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 3265 Z= 0.162 Angle : 0.611 17.218 4480 Z= 0.287 Chirality : 0.046 0.689 538 Planarity : 0.005 0.056 529 Dihedral : 7.052 107.341 444 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.43), residues: 394 helix: 1.66 (0.29), residues: 317 sheet: None (None), residues: 0 loop : -1.12 (0.71), residues: 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 0.345 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 83 average time/residue: 0.1332 time to fit residues: 13.8128 Evaluate side-chains 79 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.340 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0346 time to fit residues: 0.5890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.0670 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- 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: 0.7518 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 3265 Z= 0.195 Angle : 0.648 16.987 4480 Z= 0.301 Chirality : 0.047 0.691 538 Planarity : 0.005 0.055 529 Dihedral : 7.015 108.233 444 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.42), residues: 394 helix: 1.59 (0.29), residues: 316 sheet: None (None), residues: 0 loop : -1.04 (0.71), residues: 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 85 average time/residue: 0.1398 time to fit residues: 14.7398 Evaluate side-chains 86 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 0.349 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0342 time to fit residues: 0.6624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 3265 Z= 0.203 Angle : 0.660 17.028 4480 Z= 0.309 Chirality : 0.047 0.703 538 Planarity : 0.005 0.054 529 Dihedral : 6.820 108.312 444 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.42), residues: 394 helix: 1.56 (0.29), residues: 316 sheet: None (None), residues: 0 loop : -1.04 (0.71), residues: 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 84 average time/residue: 0.1415 time to fit residues: 14.7661 Evaluate side-chains 84 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.348 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0347 time to fit residues: 0.5981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.7531 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 3265 Z= 0.213 Angle : 0.678 16.905 4480 Z= 0.315 Chirality : 0.046 0.669 538 Planarity : 0.005 0.054 529 Dihedral : 6.817 108.524 444 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.42), residues: 394 helix: 1.49 (0.29), residues: 317 sheet: None (None), residues: 0 loop : -1.06 (0.73), residues: 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 81 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 83 average time/residue: 0.1408 time to fit residues: 14.4419 Evaluate side-chains 82 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.350 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.7526 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 3265 Z= 0.200 Angle : 0.675 17.471 4480 Z= 0.311 Chirality : 0.047 0.718 538 Planarity : 0.005 0.053 529 Dihedral : 6.852 108.184 444 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.42), residues: 394 helix: 1.54 (0.29), residues: 317 sheet: None (None), residues: 0 loop : -1.18 (0.72), residues: 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 85 average time/residue: 0.1379 time to fit residues: 14.5541 Evaluate side-chains 83 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 0.351 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0343 time to fit residues: 0.5443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 3.9990 chunk 9 optimal weight: 0.2980 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 0.1980 chunk 8 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7498 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 3265 Z= 0.176 Angle : 0.667 17.495 4480 Z= 0.304 Chirality : 0.047 0.734 538 Planarity : 0.005 0.053 529 Dihedral : 6.792 107.350 444 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.43), residues: 394 helix: 1.63 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -1.13 (0.73), residues: 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.352 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 83 average time/residue: 0.1336 time to fit residues: 13.8660 Evaluate side-chains 83 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 81 time to evaluate : 0.351 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0406 time to fit residues: 0.6444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 0.0770 chunk 1 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.0050 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 overall best weight: 0.4552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.143999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.133202 restraints weight = 5250.021| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.36 r_work: 0.3536 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 3265 Z= 0.169 Angle : 0.670 16.467 4480 Z= 0.306 Chirality : 0.046 0.697 538 Planarity : 0.005 0.053 529 Dihedral : 6.621 106.832 444 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.44), residues: 394 helix: 1.58 (0.29), residues: 324 sheet: None (None), residues: 0 loop : -1.18 (0.78), residues: 70 =============================================================================== Job complete usr+sys time: 1059.06 seconds wall clock time: 19 minutes 35.39 seconds (1175.39 seconds total)