Starting phenix.real_space_refine on Mon Nov 13 18:02:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh6_14725/11_2023/7zh6_14725_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh6_14725/11_2023/7zh6_14725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh6_14725/11_2023/7zh6_14725.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh6_14725/11_2023/7zh6_14725.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh6_14725/11_2023/7zh6_14725_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh6_14725/11_2023/7zh6_14725_neut_updated.pdb" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 22 5.16 5 C 2501 2.51 5 N 621 2.21 5 O 627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 70": "OE1" <-> "OE2" Residue "A ARG 73": "NH1" <-> "NH2" Residue "A ARG 87": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 298": "NH1" <-> "NH2" Residue "A GLU 519": "OE1" <-> "OE2" Residue "A GLU 533": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 3771 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3771 Unusual residues: {'C0R': 1} Classifications: {'peptide': 478, 'undetermined': 1} Link IDs: {'PTRANS': 23, 'TRANS': 454, None: 1} Not linked: pdbres="LYS A 534 " pdbres="C0R A 601 " Chain breaks: 4 Time building chain proxies: 2.69, per 1000 atoms: 0.71 Number of scatterers: 3771 At special positions: 0 Unit cell: (101.64, 63.36, 79.2, 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 22 16.00 O 627 8.00 N 621 7.00 C 2501 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 127 " distance=2.03 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 148 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 827.9 milliseconds 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 870 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 1 sheets defined 71.3% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 4 through 10 removed outlier: 3.691A pdb=" N LEU A 8 " --> pdb=" O PHE A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 42 removed outlier: 4.419A pdb=" N VAL A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL A 40 " --> pdb=" O PHE A 36 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE A 41 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 62 removed outlier: 3.789A pdb=" N ARG A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 140 through 144 Processing helix chain 'A' and resid 148 through 178 removed outlier: 3.835A pdb=" N ALA A 151 " --> pdb=" O CYS A 148 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N TRP A 152 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR A 157 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 167 " --> pdb=" O GLY A 164 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR A 171 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY A 173 " --> pdb=" O PHE A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 200 Processing helix chain 'A' and resid 205 through 233 Processing helix chain 'A' and resid 239 through 262 Proline residue: A 258 - end of helix removed outlier: 3.506A pdb=" N TYR A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 283 Proline residue: A 277 - end of helix removed outlier: 3.644A pdb=" N LEU A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 295 No H-bonds generated for 'chain 'A' and resid 292 through 295' Processing helix chain 'A' and resid 302 through 310 Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 345 through 371 Processing helix chain 'A' and resid 381 through 400 removed outlier: 3.749A pdb=" N GLU A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 406 through 425 removed outlier: 3.921A pdb=" N PHE A 410 " --> pdb=" O ARG A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 460 removed outlier: 3.658A pdb=" N LEU A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 494 Proline residue: A 485 - end of helix removed outlier: 3.946A pdb=" N VAL A 494 " --> pdb=" O ARG A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 516 removed outlier: 3.982A pdb=" N MET A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 531 removed outlier: 3.659A pdb=" N ASP A 531 " --> pdb=" O THR A 528 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 528 through 531' Processing sheet with id= A, first strand: chain 'A' and resid 92 through 94 233 hydrogen bonds defined for protein. 630 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.00 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 621 1.33 - 1.45: 1028 1.45 - 1.57: 2188 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 3867 Sorted by residual: bond pdb=" N THR A 297 " pdb=" CA THR A 297 " ideal model delta sigma weight residual 1.458 1.489 -0.032 1.00e-02 1.00e+04 9.98e+00 bond pdb=" N ASN A 335 " pdb=" CA ASN A 335 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.04e-02 9.25e+03 9.62e+00 bond pdb=" N ILE A 311 " pdb=" CA ILE A 311 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.10e+00 bond pdb=" N ILE A 264 " pdb=" CA ILE A 264 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.23e-02 6.61e+03 8.97e+00 bond pdb=" N VAL A 40 " pdb=" CA VAL A 40 " ideal model delta sigma weight residual 1.462 1.497 -0.035 1.18e-02 7.18e+03 8.83e+00 ... (remaining 3862 not shown) Histogram of bond angle deviations from ideal: 98.85 - 105.87: 93 105.87 - 112.90: 2048 112.90 - 119.92: 1382 119.92 - 126.95: 1694 126.95 - 133.97: 52 Bond angle restraints: 5269 Sorted by residual: angle pdb=" N ARG A 128 " pdb=" CA ARG A 128 " pdb=" C ARG A 128 " ideal model delta sigma weight residual 114.62 108.91 5.71 1.14e+00 7.69e-01 2.51e+01 angle pdb=" N PRO A 76 " pdb=" CA PRO A 76 " pdb=" C PRO A 76 " ideal model delta sigma weight residual 114.92 108.98 5.94 1.19e+00 7.06e-01 2.50e+01 angle pdb=" O GLU A 533 " pdb=" C GLU A 533 " pdb=" N LYS A 534 " ideal model delta sigma weight residual 122.03 126.35 -4.32 1.08e+00 8.57e-01 1.60e+01 angle pdb=" C GLU A 533 " pdb=" N LYS A 534 " pdb=" CA LYS A 534 " ideal model delta sigma weight residual 121.70 128.65 -6.95 1.80e+00 3.09e-01 1.49e+01 angle pdb=" N MET A 448 " pdb=" CA MET A 448 " pdb=" C MET A 448 " ideal model delta sigma weight residual 111.71 107.31 4.40 1.15e+00 7.56e-01 1.46e+01 ... (remaining 5264 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.07: 1961 18.07 - 36.14: 208 36.14 - 54.21: 47 54.21 - 72.28: 9 72.28 - 90.35: 7 Dihedral angle restraints: 2232 sinusoidal: 875 harmonic: 1357 Sorted by residual: dihedral pdb=" CB CYS A 90 " pdb=" SG CYS A 90 " pdb=" SG CYS A 148 " pdb=" CB CYS A 148 " ideal model delta sinusoidal sigma weight residual -86.00 -155.72 69.72 1 1.00e+01 1.00e-02 6.27e+01 dihedral pdb=" C ARG A 298 " pdb=" N ARG A 298 " pdb=" CA ARG A 298 " pdb=" CB ARG A 298 " ideal model delta harmonic sigma weight residual -122.60 -131.28 8.68 0 2.50e+00 1.60e-01 1.21e+01 dihedral pdb=" CB GLU A 519 " pdb=" CG GLU A 519 " pdb=" CD GLU A 519 " pdb=" OE1 GLU A 519 " ideal model delta sinusoidal sigma weight residual 0.00 -90.35 90.35 1 3.00e+01 1.11e-03 1.07e+01 ... (remaining 2229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 429 0.046 - 0.092: 108 0.092 - 0.138: 57 0.138 - 0.184: 17 0.184 - 0.230: 6 Chirality restraints: 617 Sorted by residual: chirality pdb=" CA ARG A 298 " pdb=" N ARG A 298 " pdb=" C ARG A 298 " pdb=" CB ARG A 298 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA VAL A 333 " pdb=" N VAL A 333 " pdb=" C VAL A 333 " pdb=" CB VAL A 333 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA LEU A 186 " pdb=" N LEU A 186 " pdb=" C LEU A 186 " pdb=" CB LEU A 186 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.68e-01 ... (remaining 614 not shown) Planarity restraints: 647 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 C0R A 601 " -0.017 2.00e-02 2.50e+03 8.14e-02 8.29e+01 pdb=" C3 C0R A 601 " 0.100 2.00e-02 2.50e+03 pdb=" C4 C0R A 601 " -0.129 2.00e-02 2.50e+03 pdb=" C5 C0R A 601 " -0.027 2.00e-02 2.50e+03 pdb=" C6 C0R A 601 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 183 " -0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C VAL A 183 " 0.065 2.00e-02 2.50e+03 pdb=" O VAL A 183 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE A 184 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 262 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C TYR A 262 " -0.042 2.00e-02 2.50e+03 pdb=" O TYR A 262 " 0.016 2.00e-02 2.50e+03 pdb=" N PHE A 263 " 0.014 2.00e-02 2.50e+03 ... (remaining 644 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 8 2.27 - 2.92: 1687 2.92 - 3.58: 6092 3.58 - 4.24: 8151 4.24 - 4.90: 13820 Nonbonded interactions: 29758 Sorted by model distance: nonbonded pdb=" CD1 ILE A 523 " pdb=" OE1 GLU A 533 " model vdw 1.607 3.460 nonbonded pdb=" OG1 THR A 28 " pdb=" OH TYR A 185 " model vdw 2.143 2.440 nonbonded pdb=" CE2 PHE A 4 " pdb=" NE ARG A 293 " model vdw 2.154 3.420 nonbonded pdb=" O PHE A 468 " pdb=" OG SER A 471 " model vdw 2.230 2.440 nonbonded pdb=" OE2 GLU A 232 " pdb=" NH1 ARG A 466 " model vdw 2.235 2.520 ... (remaining 29753 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 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: 8.490 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.840 Find NCS groups from input model: 0.100 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 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 : 0.006 0.062 3867 Z= 0.370 Angle : 0.900 9.731 5269 Z= 0.586 Chirality : 0.057 0.230 617 Planarity : 0.005 0.081 647 Dihedral : 16.132 90.348 1356 Min Nonbonded Distance : 1.607 Molprobity Statistics. All-atom Clashscore : 26.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.26 % Allowed : 28.46 % Favored : 70.28 % 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: 0.99 (0.40), residues: 468 helix: 1.81 (0.28), residues: 353 sheet: None (None), residues: 0 loop : -3.22 (0.46), residues: 115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 0.453 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 105 average time/residue: 0.1400 time to fit residues: 18.6936 Evaluate side-chains 89 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.435 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 0.3980 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.0670 chunk 36 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 18 GLN A 150 ASN A 414 ASN ** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3867 Z= 0.193 Angle : 0.643 8.409 5269 Z= 0.314 Chirality : 0.041 0.186 617 Planarity : 0.005 0.053 647 Dihedral : 4.458 33.494 525 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 5.29 % Allowed : 25.44 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.40), residues: 468 helix: 1.95 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -3.23 (0.46), residues: 111 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 98 time to evaluate : 0.460 Fit side-chains outliers start: 21 outliers final: 12 residues processed: 109 average time/residue: 0.1159 time to fit residues: 16.7455 Evaluate side-chains 102 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.466 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0391 time to fit residues: 1.4309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 0.1980 chunk 38 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN ** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3867 Z= 0.200 Angle : 0.633 8.313 5269 Z= 0.308 Chirality : 0.040 0.163 617 Planarity : 0.004 0.034 647 Dihedral : 4.346 28.086 525 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.02 % Allowed : 26.95 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.40), residues: 468 helix: 2.03 (0.28), residues: 356 sheet: None (None), residues: 0 loop : -3.33 (0.46), residues: 112 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.436 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 104 average time/residue: 0.1169 time to fit residues: 16.0367 Evaluate side-chains 98 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.423 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0429 time to fit residues: 1.1478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 40 optimal weight: 0.0060 chunk 12 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3867 Z= 0.200 Angle : 0.624 8.957 5269 Z= 0.302 Chirality : 0.039 0.161 617 Planarity : 0.004 0.039 647 Dihedral : 4.398 30.240 525 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.03 % Allowed : 27.46 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.40), residues: 468 helix: 2.00 (0.28), residues: 356 sheet: None (None), residues: 0 loop : -3.47 (0.46), residues: 112 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 0.422 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 103 average time/residue: 0.1144 time to fit residues: 15.5522 Evaluate side-chains 104 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 93 time to evaluate : 0.416 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0378 time to fit residues: 1.3057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 0.2980 chunk 18 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 11 optimal weight: 0.0670 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 0.0370 chunk 26 optimal weight: 0.1980 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3867 Z= 0.171 Angle : 0.588 9.211 5269 Z= 0.286 Chirality : 0.039 0.160 617 Planarity : 0.004 0.039 647 Dihedral : 4.357 31.059 525 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.76 % Allowed : 30.48 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.40), residues: 468 helix: 1.96 (0.28), residues: 355 sheet: None (None), residues: 0 loop : -3.31 (0.47), residues: 113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 0.455 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 103 average time/residue: 0.1358 time to fit residues: 17.8981 Evaluate side-chains 92 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 88 time to evaluate : 0.463 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0469 time to fit residues: 0.9215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 0.0980 chunk 45 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 0.0370 chunk 33 optimal weight: 0.8980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN A 335 ASN A 414 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3867 Z= 0.190 Angle : 0.614 9.187 5269 Z= 0.298 Chirality : 0.039 0.165 617 Planarity : 0.004 0.038 647 Dihedral : 4.343 30.002 525 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.03 % Allowed : 30.98 % Favored : 64.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.40), residues: 468 helix: 1.93 (0.28), residues: 358 sheet: None (None), residues: 0 loop : -3.26 (0.49), residues: 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 0.429 Fit side-chains outliers start: 16 outliers final: 14 residues processed: 98 average time/residue: 0.1274 time to fit residues: 16.1677 Evaluate side-chains 102 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 0.427 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0471 time to fit residues: 1.6741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 0.3980 chunk 38 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 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: 0.7365 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3867 Z= 0.197 Angle : 0.628 9.385 5269 Z= 0.305 Chirality : 0.039 0.166 617 Planarity : 0.004 0.044 647 Dihedral : 4.408 30.758 525 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.50 % Allowed : 32.75 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.40), residues: 468 helix: 1.86 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -3.18 (0.50), residues: 111 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 0.432 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 94 average time/residue: 0.1112 time to fit residues: 14.0866 Evaluate side-chains 87 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 0.432 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0533 time to fit residues: 0.6518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 0.0030 chunk 18 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3867 Z= 0.198 Angle : 0.639 9.407 5269 Z= 0.308 Chirality : 0.040 0.162 617 Planarity : 0.004 0.044 647 Dihedral : 4.381 30.634 525 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.02 % Allowed : 33.00 % Favored : 64.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.40), residues: 468 helix: 1.83 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -3.03 (0.52), residues: 111 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.447 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 93 average time/residue: 0.1156 time to fit residues: 14.4570 Evaluate side-chains 95 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.456 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0466 time to fit residues: 1.1439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 27 optimal weight: 0.0060 chunk 44 optimal weight: 0.9980 chunk 21 optimal weight: 0.0770 chunk 31 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 37 optimal weight: 0.0670 chunk 3 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 overall best weight: 0.2492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 3867 Z= 0.179 Angle : 0.646 9.783 5269 Z= 0.310 Chirality : 0.040 0.169 617 Planarity : 0.004 0.053 647 Dihedral : 4.382 31.388 525 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.25 % Allowed : 34.01 % Favored : 65.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.40), residues: 468 helix: 1.77 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -3.00 (0.51), residues: 111 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 0.442 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.1289 time to fit residues: 16.1250 Evaluate side-chains 91 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.430 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 37 optimal weight: 0.0970 chunk 15 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS A 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 3867 Z= 0.207 Angle : 0.637 7.860 5269 Z= 0.315 Chirality : 0.041 0.167 617 Planarity : 0.004 0.046 647 Dihedral : 4.324 30.112 525 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.76 % Allowed : 35.01 % Favored : 64.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.40), residues: 468 helix: 1.78 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -3.09 (0.51), residues: 111 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 0.419 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 93 average time/residue: 0.1162 time to fit residues: 14.5159 Evaluate side-chains 92 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 0.413 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0388 time to fit residues: 0.6998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 3.9990 chunk 32 optimal weight: 0.0270 chunk 2 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 = 0.4092 r_free = 0.4092 target = 0.164866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.144714 restraints weight = 7057.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.149182 restraints weight = 3680.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.152204 restraints weight = 2275.206| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 3867 Z= 0.205 Angle : 0.670 10.086 5269 Z= 0.322 Chirality : 0.040 0.166 617 Planarity : 0.004 0.048 647 Dihedral : 4.404 30.696 525 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.25 % Allowed : 33.25 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.40), residues: 468 helix: 1.70 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -3.13 (0.51), residues: 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1215.13 seconds wall clock time: 22 minutes 43.19 seconds (1363.19 seconds total)