Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 19 23:58:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx7_26156/04_2023/7tx7_26156_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx7_26156/04_2023/7tx7_26156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx7_26156/04_2023/7tx7_26156.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx7_26156/04_2023/7tx7_26156.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx7_26156/04_2023/7tx7_26156_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx7_26156/04_2023/7tx7_26156_updated.pdb" } resolution = 3.8 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 7 5.16 5 C 2158 2.51 5 N 487 2.21 5 O 551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None 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: 3203 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3203 Unusual residues: {'AJP': 4} Classifications: {'peptide': 397, 'undetermined': 4} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 13, 'TRANS': 383, None: 4} Not linked: pdbres="GLN A 459 " pdbres="AJP A 701 " Not linked: pdbres="AJP A 701 " pdbres="AJP A 702 " Not linked: pdbres="AJP A 702 " pdbres="AJP A 703 " Not linked: pdbres="AJP A 703 " pdbres="AJP A 704 " Chain breaks: 1 Unresolved non-hydrogen bonds: 338 Unresolved non-hydrogen angles: 466 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 86 Time building chain proxies: 2.40, per 1000 atoms: 0.75 Number of scatterers: 3203 At special positions: 0 Unit cell: (73.44, 65.88, 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 7 16.00 O 551 8.00 N 487 7.00 C 2158 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 474.4 milliseconds 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 750 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 15 helices and 0 sheets defined 82.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 24 through 39 removed outlier: 3.768A pdb=" N LEU A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N CYS A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 removed outlier: 4.918A pdb=" N THR A 49 " --> pdb=" O SER A 46 " (cutoff:3.500A) Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 61 through 89 removed outlier: 5.052A pdb=" N THR A 69 " --> pdb=" O THR A 65 " (cutoff:3.500A) Proline residue: A 70 - end of helix removed outlier: 4.890A pdb=" N VAL A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix Processing helix chain 'A' and resid 92 through 112 Processing helix chain 'A' and resid 116 through 131 removed outlier: 3.621A pdb=" N VAL A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 143 removed outlier: 3.553A pdb=" N TYR A 136 " --> pdb=" O ARG A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 178 removed outlier: 3.793A pdb=" N SER A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 169 " --> pdb=" O PHE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 202 removed outlier: 4.104A pdb=" N PHE A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 263 removed outlier: 3.644A pdb=" N ARG A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 295 removed outlier: 4.015A pdb=" N LEU A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TRP A 270 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N HIS A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 327 removed outlier: 3.672A pdb=" N GLY A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 355 Processing helix chain 'A' and resid 359 through 390 removed outlier: 3.804A pdb=" N ILE A 362 " --> pdb=" O PRO A 359 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N TRP A 363 " --> pdb=" O SER A 360 " (cutoff:3.500A) Proline residue: A 381 - end of helix removed outlier: 3.782A pdb=" N SER A 389 " --> pdb=" O GLN A 386 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER A 390 " --> pdb=" O ILE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 418 removed outlier: 4.016A pdb=" N ALA A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LEU A 398 " --> pdb=" O GLU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 458 removed outlier: 3.515A pdb=" N VAL A 437 " --> pdb=" O GLN A 433 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) 229 hydrogen bonds defined for protein. 597 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: 0.86 Time building geometry restraints manager: 1.59 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: 909 1.34 - 1.46: 569 1.46 - 1.57: 1817 1.57 - 1.69: 4 1.69 - 1.81: 11 Bond restraints: 3310 Sorted by residual: bond pdb=" C23 AJP A 703 " pdb=" C24 AJP A 703 " ideal model delta sigma weight residual 1.522 1.613 -0.091 2.00e-02 2.50e+03 2.09e+01 bond pdb=" C05 AJP A 704 " pdb=" C06 AJP A 704 " ideal model delta sigma weight residual 1.534 1.445 0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" C23 AJP A 704 " pdb=" C24 AJP A 704 " ideal model delta sigma weight residual 1.522 1.609 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C23 AJP A 701 " pdb=" C24 AJP A 701 " ideal model delta sigma weight residual 1.522 1.609 -0.087 2.00e-02 2.50e+03 1.87e+01 bond pdb=" C23 AJP A 702 " pdb=" C24 AJP A 702 " ideal model delta sigma weight residual 1.522 1.606 -0.084 2.00e-02 2.50e+03 1.77e+01 ... (remaining 3305 not shown) Histogram of bond angle deviations from ideal: 98.82 - 105.86: 82 105.86 - 112.89: 1953 112.89 - 119.93: 1062 119.93 - 126.97: 1447 126.97 - 134.00: 39 Bond angle restraints: 4583 Sorted by residual: angle pdb=" N ALA A 131 " pdb=" CA ALA A 131 " pdb=" C ALA A 131 " ideal model delta sigma weight residual 111.28 116.70 -5.42 1.09e+00 8.42e-01 2.47e+01 angle pdb=" N ALA A 132 " pdb=" CA ALA A 132 " pdb=" C ALA A 132 " ideal model delta sigma weight residual 113.02 117.20 -4.18 1.20e+00 6.94e-01 1.21e+01 angle pdb=" C07 AJP A 701 " pdb=" C06 AJP A 701 " pdb=" C83 AJP A 701 " ideal model delta sigma weight residual 114.76 106.59 8.17 3.00e+00 1.11e-01 7.41e+00 angle pdb=" C07 AJP A 703 " pdb=" C06 AJP A 703 " pdb=" C83 AJP A 703 " ideal model delta sigma weight residual 114.76 107.70 7.06 3.00e+00 1.11e-01 5.53e+00 angle pdb=" C07 AJP A 702 " pdb=" C06 AJP A 702 " pdb=" C83 AJP A 702 " ideal model delta sigma weight residual 114.76 108.24 6.52 3.00e+00 1.11e-01 4.72e+00 ... (remaining 4578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.78: 1738 24.78 - 49.56: 46 49.56 - 74.35: 3 74.35 - 99.13: 0 99.13 - 123.91: 4 Dihedral angle restraints: 1791 sinusoidal: 623 harmonic: 1168 Sorted by residual: dihedral pdb=" C02 AJP A 703 " pdb=" C85 AJP A 703 " pdb=" O84 AJP A 703 " pdb=" C05 AJP A 703 " ideal model delta sinusoidal sigma weight residual -57.60 66.31 -123.91 1 3.00e+01 1.11e-03 1.66e+01 dihedral pdb=" C02 AJP A 704 " pdb=" C85 AJP A 704 " pdb=" O84 AJP A 704 " pdb=" C05 AJP A 704 " ideal model delta sinusoidal sigma weight residual -57.60 66.29 -123.89 1 3.00e+01 1.11e-03 1.66e+01 dihedral pdb=" C02 AJP A 701 " pdb=" C85 AJP A 701 " pdb=" O84 AJP A 701 " pdb=" C05 AJP A 701 " ideal model delta sinusoidal sigma weight residual -57.60 63.25 -120.85 1 3.00e+01 1.11e-03 1.61e+01 ... (remaining 1788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 499 0.064 - 0.128: 50 0.128 - 0.192: 8 0.192 - 0.256: 13 0.256 - 0.320: 15 Chirality restraints: 585 Sorted by residual: chirality pdb=" C19 AJP A 702 " pdb=" C18 AJP A 702 " pdb=" C20 AJP A 702 " pdb=" C24 AJP A 702 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" C11 AJP A 702 " pdb=" C10 AJP A 702 " pdb=" C12 AJP A 702 " pdb=" C16 AJP A 702 " both_signs ideal model delta sigma weight residual False 2.20 2.52 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" C11 AJP A 704 " pdb=" C10 AJP A 704 " pdb=" C12 AJP A 704 " pdb=" C16 AJP A 704 " both_signs ideal model delta sigma weight residual False 2.20 2.51 -0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 582 not shown) Planarity restraints: 518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 93 " 0.040 5.00e-02 4.00e+02 6.14e-02 6.03e+00 pdb=" N PRO A 94 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 94 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 94 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 42 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO A 43 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 205 " 0.022 5.00e-02 4.00e+02 3.34e-02 1.79e+00 pdb=" N PRO A 206 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 206 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 206 " 0.019 5.00e-02 4.00e+02 ... (remaining 515 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 29 2.64 - 3.20: 3285 3.20 - 3.77: 4940 3.77 - 4.33: 6169 4.33 - 4.90: 10235 Nonbonded interactions: 24658 Sorted by model distance: nonbonded pdb=" O33 AJP A 701 " pdb=" O77 AJP A 701 " model vdw 2.072 2.440 nonbonded pdb=" O GLN A 433 " pdb=" OG SER A 436 " model vdw 2.270 2.440 nonbonded pdb=" O LEU A 124 " pdb=" OG SER A 127 " model vdw 2.279 2.440 nonbonded pdb=" ND1 HIS A 289 " pdb=" OD1 ASN A 306 " model vdw 2.410 2.520 nonbonded pdb=" O TYR A 126 " pdb=" OG1 THR A 129 " model vdw 2.421 2.440 ... (remaining 24653 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 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: 1.860 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.740 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 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 0.091 3310 Z= 0.481 Angle : 0.760 8.165 4583 Z= 0.336 Chirality : 0.068 0.320 585 Planarity : 0.005 0.061 518 Dihedral : 12.936 123.910 1041 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.77 (0.42), residues: 393 helix: 3.08 (0.27), residues: 317 sheet: None (None), residues: 0 loop : -0.26 (0.80), residues: 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.368 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1672 time to fit residues: 25.8780 Evaluate side-chains 104 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.366 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4447 ------------------------------------------------------------------------------- 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: 5.9990 chunk 30 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.0770 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 0.0870 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 0.0030 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 0.4980 overall best weight: 0.2726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN A 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 3310 Z= 0.175 Angle : 0.674 7.657 4583 Z= 0.311 Chirality : 0.036 0.122 585 Planarity : 0.005 0.051 518 Dihedral : 9.540 108.896 449 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer Outliers : 1.63 % 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: 3.25 (0.42), residues: 393 helix: 2.57 (0.28), residues: 328 sheet: None (None), residues: 0 loop : -0.13 (0.83), residues: 65 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 114 time to evaluate : 0.377 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 117 average time/residue: 0.1334 time to fit residues: 19.3969 Evaluate side-chains 101 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 0.333 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0350 time to fit residues: 0.6314 ------------------------------------------------------------------------------- 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: 0.6980 chunk 24 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.0030 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 3310 Z= 0.179 Angle : 0.637 6.889 4583 Z= 0.301 Chirality : 0.037 0.132 585 Planarity : 0.005 0.048 518 Dihedral : 9.713 111.818 449 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer Outliers : 2.28 % 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: 2.76 (0.43), residues: 393 helix: 2.37 (0.29), residues: 315 sheet: None (None), residues: 0 loop : -0.47 (0.72), residues: 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 0.362 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 109 average time/residue: 0.1270 time to fit residues: 17.2417 Evaluate side-chains 101 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 0.357 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0350 time to fit residues: 0.8417 ------------------------------------------------------------------------------- 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: 0.2980 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 32 optimal weight: 0.0010 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- 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: 0.7470 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 3310 Z= 0.161 Angle : 0.638 9.002 4583 Z= 0.295 Chirality : 0.035 0.128 585 Planarity : 0.005 0.043 518 Dihedral : 9.580 109.553 449 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer Outliers : 2.28 % 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: 2.58 (0.43), residues: 393 helix: 2.20 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -0.58 (0.73), residues: 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 106 time to evaluate : 0.387 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 108 average time/residue: 0.1258 time to fit residues: 17.1124 Evaluate side-chains 100 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 0.375 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0437 time to fit residues: 0.7689 ------------------------------------------------------------------------------- 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: 0.8980 chunk 15 optimal weight: 0.0170 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 3310 Z= 0.175 Angle : 0.638 8.003 4583 Z= 0.295 Chirality : 0.035 0.130 585 Planarity : 0.004 0.042 518 Dihedral : 9.618 110.538 449 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer Outliers : 1.95 % 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: 2.54 (0.43), residues: 393 helix: 2.20 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -0.74 (0.71), residues: 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 0.360 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 105 average time/residue: 0.1267 time to fit residues: 16.6697 Evaluate side-chains 94 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 0.364 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0355 time to fit residues: 0.6268 ------------------------------------------------------------------------------- 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: 0.8980 chunk 38 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7510 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 3310 Z= 0.173 Angle : 0.660 9.664 4583 Z= 0.298 Chirality : 0.036 0.132 585 Planarity : 0.004 0.040 518 Dihedral : 9.582 109.794 449 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 1.63 % 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: 2.41 (0.43), residues: 393 helix: 2.16 (0.29), residues: 322 sheet: None (None), residues: 0 loop : -1.08 (0.66), residues: 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 97 time to evaluate : 0.329 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 99 average time/residue: 0.1285 time to fit residues: 15.9836 Evaluate side-chains 93 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.374 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0431 time to fit residues: 0.7046 ------------------------------------------------------------------------------- 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: 2.9990 chunk 32 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 15 optimal weight: 0.0570 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3310 Z= 0.184 Angle : 0.697 9.805 4583 Z= 0.308 Chirality : 0.037 0.222 585 Planarity : 0.004 0.041 518 Dihedral : 9.573 109.433 449 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.43), residues: 393 helix: 2.07 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -1.06 (0.70), residues: 70 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 0.366 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 93 average time/residue: 0.1354 time to fit residues: 15.5121 Evaluate side-chains 90 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 0.315 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0319 time to fit residues: 0.5311 ------------------------------------------------------------------------------- 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: 0.0980 chunk 35 optimal weight: 0.0970 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 32 optimal weight: 0.0060 chunk 23 optimal weight: 0.9980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 3310 Z= 0.171 Angle : 0.698 9.645 4583 Z= 0.309 Chirality : 0.036 0.132 585 Planarity : 0.004 0.041 518 Dihedral : 9.477 108.692 449 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.43), residues: 393 helix: 2.05 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -0.98 (0.73), residues: 70 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 0.348 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 92 average time/residue: 0.1393 time to fit residues: 15.9056 Evaluate side-chains 87 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 0.426 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0383 time to fit residues: 0.5647 ------------------------------------------------------------------------------- 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: 0.8980 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.0010 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 0.2980 chunk 3 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 3310 Z= 0.183 Angle : 0.711 10.324 4583 Z= 0.315 Chirality : 0.036 0.132 585 Planarity : 0.004 0.040 518 Dihedral : 9.457 109.138 449 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.43), residues: 393 helix: 2.01 (0.29), residues: 322 sheet: None (None), residues: 0 loop : -1.12 (0.71), residues: 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.362 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1251 time to fit residues: 13.8456 Evaluate side-chains 86 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.360 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4673 ------------------------------------------------------------------------------- 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: 0.0050 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 3310 Z= 0.176 Angle : 0.719 9.202 4583 Z= 0.314 Chirality : 0.036 0.145 585 Planarity : 0.004 0.039 518 Dihedral : 9.394 109.041 449 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 0.33 % 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: 2.21 (0.43), residues: 393 helix: 2.02 (0.29), residues: 322 sheet: None (None), residues: 0 loop : -1.18 (0.70), residues: 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.357 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 94 average time/residue: 0.1232 time to fit residues: 14.5936 Evaluate side-chains 89 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 0.375 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0288 time to fit residues: 0.4318 ------------------------------------------------------------------------------- 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: 0.6980 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.139450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.126104 restraints weight = 6068.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.129817 restraints weight = 3253.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.132172 restraints weight = 1979.466| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 3310 Z= 0.196 Angle : 0.725 10.128 4583 Z= 0.321 Chirality : 0.036 0.144 585 Planarity : 0.004 0.039 518 Dihedral : 9.402 109.531 449 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 0.33 % 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: 2.15 (0.43), residues: 393 helix: 2.00 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -1.26 (0.69), residues: 72 =============================================================================== Job complete usr+sys time: 1067.39 seconds wall clock time: 19 minutes 53.10 seconds (1193.10 seconds total)