Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 3 19:24:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zha_14728/07_2023/7zha_14728_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zha_14728/07_2023/7zha_14728.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zha_14728/07_2023/7zha_14728_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zha_14728/07_2023/7zha_14728_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zha_14728/07_2023/7zha_14728_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zha_14728/07_2023/7zha_14728.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zha_14728/07_2023/7zha_14728.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zha_14728/07_2023/7zha_14728_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zha_14728/07_2023/7zha_14728_updated.pdb" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 2543 2.51 5 N 632 2.21 5 O 639 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-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 3836 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3836 Unusual residues: {'JDW': 1} Classifications: {'peptide': 487, 'undetermined': 1} Link IDs: {'PTRANS': 23, 'TRANS': 463, None: 1} Not linked: pdbres="LEU A 535 " pdbres="JDW A 601 " Chain breaks: 3 Time building chain proxies: 2.37, per 1000 atoms: 0.62 Number of scatterers: 3836 At special positions: 0 Unit cell: (98.34, 64.02, 81.84, 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 639 8.00 N 632 7.00 C 2543 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: 1.56 Conformation dependent library (CDL) restraints added in 684.3 milliseconds 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 882 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 22 helices and 1 sheets defined 71.5% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 4 through 10 Processing helix chain 'A' and resid 16 through 41 removed outlier: 4.722A pdb=" N VAL A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N VAL A 40 " --> pdb=" O PHE A 36 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHE A 41 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 67 through 74 Processing helix chain 'A' and resid 140 through 144 Processing helix chain 'A' and resid 148 through 178 removed outlier: 3.508A pdb=" N THR A 167 " --> pdb=" O GLY A 164 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 171 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 172 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 4.199A 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 removed outlier: 3.976A pdb=" N PHE A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 263 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 267 through 282 Proline residue: A 277 - end of helix removed outlier: 3.932A pdb=" N LEU A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 287 No H-bonds generated for 'chain 'A' and resid 285 through 287' 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 312 Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 345 through 372 removed outlier: 3.942A pdb=" N MET A 370 " --> pdb=" O GLN A 366 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 403 removed outlier: 3.842A 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 407 through 426 Processing helix chain 'A' and resid 432 through 435 No H-bonds generated for 'chain 'A' and resid 432 through 435' Processing helix chain 'A' and resid 440 through 460 Processing helix chain 'A' and resid 469 through 494 Proline residue: A 485 - end of helix removed outlier: 3.914A pdb=" N VAL A 494 " --> pdb=" O ARG A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 516 removed outlier: 4.005A pdb=" N MET A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LEU A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 534 removed outlier: 3.582A pdb=" N LYS A 534 " --> pdb=" O ASP A 531 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 49 through 51 237 hydrogen bonds defined for protein. 636 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: 1.01 Time building geometry restraints manager: 1.65 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: 1174 1.34 - 1.46: 782 1.46 - 1.58: 1947 1.58 - 1.70: 0 1.70 - 1.81: 30 Bond restraints: 3933 Sorted by residual: bond pdb=" C11 JDW A 601 " pdb=" N1 JDW A 601 " ideal model delta sigma weight residual 1.360 1.435 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C3 JDW A 601 " pdb=" N1 JDW A 601 " ideal model delta sigma weight residual 1.383 1.451 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C7 JDW A 601 " pdb=" C8 JDW A 601 " ideal model delta sigma weight residual 1.413 1.359 0.054 2.00e-02 2.50e+03 7.24e+00 bond pdb=" C13 JDW A 601 " pdb=" N2 JDW A 601 " ideal model delta sigma weight residual 1.362 1.415 -0.053 2.00e-02 2.50e+03 7.00e+00 bond pdb=" N ASP A 5 " pdb=" CA ASP A 5 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.16e-02 7.43e+03 6.76e+00 ... (remaining 3928 not shown) Histogram of bond angle deviations from ideal: 98.28 - 105.42: 84 105.42 - 112.57: 2023 112.57 - 119.71: 1272 119.71 - 126.85: 1913 126.85 - 134.00: 61 Bond angle restraints: 5353 Sorted by residual: angle pdb=" C10 JDW A 601 " pdb=" C11 JDW A 601 " pdb=" C12 JDW A 601 " ideal model delta sigma weight residual 101.83 123.33 -21.50 3.00e+00 1.11e-01 5.14e+01 angle pdb=" C12 JDW A 601 " pdb=" C11 JDW A 601 " pdb=" N1 JDW A 601 " ideal model delta sigma weight residual 137.49 120.48 17.01 3.00e+00 1.11e-01 3.22e+01 angle pdb=" CA MET A 248 " pdb=" CB MET A 248 " pdb=" CG MET A 248 " ideal model delta sigma weight residual 114.10 120.74 -6.64 2.00e+00 2.50e-01 1.10e+01 angle pdb=" CA ASP A 5 " pdb=" C ASP A 5 " pdb=" O ASP A 5 " ideal model delta sigma weight residual 121.07 118.19 2.88 1.10e+00 8.26e-01 6.84e+00 angle pdb=" C TRP A 152 " pdb=" N MET A 153 " pdb=" CA MET A 153 " ideal model delta sigma weight residual 121.18 116.03 5.15 1.98e+00 2.55e-01 6.77e+00 ... (remaining 5348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.84: 1992 15.84 - 31.69: 202 31.69 - 47.53: 57 47.53 - 63.37: 11 63.37 - 79.22: 5 Dihedral angle restraints: 2267 sinusoidal: 888 harmonic: 1379 Sorted by residual: dihedral pdb=" CB CYS A 51 " pdb=" SG CYS A 51 " pdb=" SG CYS A 127 " pdb=" CB CYS A 127 " ideal model delta sinusoidal sigma weight residual 93.00 43.38 49.62 1 1.00e+01 1.00e-02 3.38e+01 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 -125.09 39.09 1 1.00e+01 1.00e-02 2.15e+01 dihedral pdb=" CA ASN A 467 " pdb=" C ASN A 467 " pdb=" N PHE A 468 " pdb=" CA PHE A 468 " ideal model delta harmonic sigma weight residual -180.00 -161.97 -18.03 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 2264 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 534 0.060 - 0.119: 75 0.119 - 0.179: 9 0.179 - 0.239: 0 0.239 - 0.299: 1 Chirality restraints: 619 Sorted by residual: chirality pdb=" CG LEU A 124 " pdb=" CB LEU A 124 " pdb=" CD1 LEU A 124 " pdb=" CD2 LEU A 124 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA MET A 153 " pdb=" N MET A 153 " pdb=" C MET A 153 " pdb=" CB MET A 153 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.06e-01 chirality pdb=" CB THR A 528 " pdb=" CA THR A 528 " pdb=" OG1 THR A 528 " pdb=" CG2 THR A 528 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.35e-01 ... (remaining 616 not shown) Planarity restraints: 660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 291 " -0.050 5.00e-02 4.00e+02 7.57e-02 9.16e+00 pdb=" N PRO A 292 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 292 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 292 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 284 " 0.008 2.00e-02 2.50e+03 1.37e-02 3.77e+00 pdb=" CG TYR A 284 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 284 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR A 284 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 284 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 284 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 284 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 284 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 34 " -0.010 2.00e-02 2.50e+03 1.19e-02 2.47e+00 pdb=" CG PHE A 34 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 34 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 34 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 34 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 34 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 34 " -0.000 2.00e-02 2.50e+03 ... (remaining 657 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1352 2.86 - 3.37: 4281 3.37 - 3.88: 6382 3.88 - 4.39: 6978 4.39 - 4.90: 11474 Nonbonded interactions: 30467 Sorted by model distance: nonbonded pdb=" O ARG A 343 " pdb=" OG1 THR A 344 " model vdw 2.352 2.440 nonbonded pdb=" NH1 ARG A 407 " pdb=" O LEU A 517 " model vdw 2.362 2.520 nonbonded pdb=" O LEU A 154 " pdb=" OG1 THR A 157 " model vdw 2.370 2.440 nonbonded pdb=" OG1 THR A 28 " pdb=" OH TYR A 185 " model vdw 2.380 2.440 nonbonded pdb=" NE2 GLN A 18 " pdb=" O ILE A 233 " model vdw 2.395 2.520 ... (remaining 30462 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: 2.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.650 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.640 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 3933 Z= 0.306 Angle : 0.830 21.498 5353 Z= 0.399 Chirality : 0.044 0.299 619 Planarity : 0.005 0.076 660 Dihedral : 14.231 79.215 1379 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 0.50 % 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: 1.39 (0.39), residues: 479 helix: 1.52 (0.28), residues: 348 sheet: None (None), residues: 0 loop : -0.62 (0.56), residues: 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 0.425 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 95 average time/residue: 0.1319 time to fit residues: 16.3102 Evaluate side-chains 74 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.438 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 0.0270 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 0.0000 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 ASN A 335 ASN ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 3933 Z= 0.187 Angle : 0.649 8.726 5353 Z= 0.324 Chirality : 0.041 0.179 619 Planarity : 0.005 0.053 660 Dihedral : 5.130 54.278 532 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 3.72 % 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: 1.53 (0.39), residues: 479 helix: 1.62 (0.28), residues: 350 sheet: None (None), residues: 0 loop : -0.59 (0.57), residues: 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 74 time to evaluate : 0.492 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 78 average time/residue: 0.1148 time to fit residues: 11.9887 Evaluate side-chains 74 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.373 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0394 time to fit residues: 1.1324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 47 optimal weight: 0.0040 chunk 38 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3933 Z= 0.216 Angle : 0.645 8.106 5353 Z= 0.322 Chirality : 0.040 0.181 619 Planarity : 0.005 0.043 660 Dihedral : 5.109 52.965 532 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.39), residues: 479 helix: 1.61 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -0.75 (0.57), residues: 130 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 0.454 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 79 average time/residue: 0.1202 time to fit residues: 12.7479 Evaluate side-chains 67 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.448 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0477 time to fit residues: 0.9055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 GLN A 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 3933 Z= 0.278 Angle : 0.687 11.041 5353 Z= 0.343 Chirality : 0.040 0.173 619 Planarity : 0.005 0.037 660 Dihedral : 5.342 54.675 532 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.39), residues: 479 helix: 1.52 (0.28), residues: 345 sheet: None (None), residues: 0 loop : -0.87 (0.57), residues: 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 0.431 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 76 average time/residue: 0.1441 time to fit residues: 14.1203 Evaluate side-chains 67 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.429 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0389 time to fit residues: 0.9968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 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 48 HIS ** 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: 0.7347 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 3933 Z= 0.223 Angle : 0.664 12.803 5353 Z= 0.332 Chirality : 0.039 0.123 619 Planarity : 0.004 0.039 660 Dihedral : 5.301 52.398 532 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.59 % Favored : 95.20 % Rotamer Outliers : 1.99 % 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: 1.36 (0.39), residues: 479 helix: 1.58 (0.28), residues: 343 sheet: None (None), residues: 0 loop : -0.79 (0.56), residues: 136 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.455 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 78 average time/residue: 0.1388 time to fit residues: 14.1874 Evaluate side-chains 69 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.437 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0553 time to fit residues: 0.8186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 0.0870 chunk 33 optimal weight: 0.8980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN A 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 3933 Z= 0.214 Angle : 0.656 12.473 5353 Z= 0.324 Chirality : 0.039 0.146 619 Planarity : 0.004 0.039 660 Dihedral : 5.244 52.036 532 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.01 % Favored : 94.78 % Rotamer Outliers : 2.98 % 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: 1.42 (0.40), residues: 479 helix: 1.62 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -0.75 (0.56), residues: 138 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 0.394 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 77 average time/residue: 0.1229 time to fit residues: 12.4378 Evaluate side-chains 71 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.346 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0377 time to fit residues: 1.0983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** 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: 0.7321 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 3933 Z= 0.206 Angle : 0.657 13.780 5353 Z= 0.324 Chirality : 0.039 0.132 619 Planarity : 0.004 0.041 660 Dihedral : 5.213 51.260 532 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.80 % Favored : 94.78 % Rotamer Outliers : 2.23 % 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: 1.33 (0.39), residues: 479 helix: 1.56 (0.28), residues: 342 sheet: None (None), residues: 0 loop : -0.79 (0.56), residues: 137 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.404 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 81 average time/residue: 0.1493 time to fit residues: 15.2220 Evaluate side-chains 71 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.453 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0439 time to fit residues: 0.9606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 42 optimal weight: 0.4980 chunk 44 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 43 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** 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: 0.7313 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 3933 Z= 0.204 Angle : 0.673 14.038 5353 Z= 0.332 Chirality : 0.039 0.126 619 Planarity : 0.004 0.040 660 Dihedral : 5.187 51.813 532 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.59 % Favored : 94.99 % Rotamer Outliers : 1.74 % 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: 1.29 (0.39), residues: 479 helix: 1.56 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -0.88 (0.55), residues: 138 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 0.473 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 73 average time/residue: 0.1227 time to fit residues: 12.0697 Evaluate side-chains 69 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.427 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0471 time to fit residues: 0.9724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 0.0010 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 0.0870 chunk 31 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 overall best weight: 0.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS A 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 3933 Z= 0.191 Angle : 0.666 14.682 5353 Z= 0.329 Chirality : 0.039 0.126 619 Planarity : 0.004 0.040 660 Dihedral : 5.154 52.620 532 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.59 % Favored : 94.99 % Rotamer Outliers : 0.99 % 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: 1.25 (0.40), residues: 479 helix: 1.53 (0.29), residues: 342 sheet: None (None), residues: 0 loop : -0.91 (0.55), residues: 137 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 0.437 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 72 average time/residue: 0.1375 time to fit residues: 12.9608 Evaluate side-chains 68 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 0.433 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0430 time to fit residues: 0.8127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 0.0000 chunk 3 optimal weight: 0.7980 chunk 29 optimal weight: 0.0270 chunk 23 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 overall best weight: 0.4042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** 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: 0.7271 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 3933 Z= 0.192 Angle : 0.666 14.446 5353 Z= 0.327 Chirality : 0.038 0.126 619 Planarity : 0.004 0.040 660 Dihedral : 5.109 53.517 532 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.22 % Favored : 94.57 % Rotamer Outliers : 0.50 % 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: 1.29 (0.40), residues: 479 helix: 1.57 (0.29), residues: 341 sheet: None (None), residues: 0 loop : -0.93 (0.55), residues: 138 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 0.414 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 72 average time/residue: 0.1268 time to fit residues: 12.1110 Evaluate side-chains 67 residues out of total 403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 0.389 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0410 time to fit residues: 0.6198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 0.1980 chunk 15 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 27 optimal weight: 0.0170 chunk 43 optimal weight: 0.2980 chunk 25 optimal weight: 0.0030 chunk 32 optimal weight: 0.5980 overall best weight: 0.2228 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.172491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.152282 restraints weight = 6436.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.156672 restraints weight = 3060.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.159416 restraints weight = 1778.197| |-----------------------------------------------------------------------------| r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 3933 Z= 0.182 Angle : 0.671 14.929 5353 Z= 0.329 Chirality : 0.039 0.147 619 Planarity : 0.004 0.040 660 Dihedral : 5.080 54.021 532 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.01 % Favored : 94.78 % Rotamer Outliers : 0.50 % 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: 1.36 (0.40), residues: 479 helix: 1.60 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -0.79 (0.55), residues: 140 =============================================================================== Job complete usr+sys time: 1238.92 seconds wall clock time: 23 minutes 21.52 seconds (1401.52 seconds total)