Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 13:06:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c03_16354/08_2023/8c03_16354_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c03_16354/08_2023/8c03_16354.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c03_16354/08_2023/8c03_16354_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c03_16354/08_2023/8c03_16354_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c03_16354/08_2023/8c03_16354_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c03_16354/08_2023/8c03_16354.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c03_16354/08_2023/8c03_16354.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c03_16354/08_2023/8c03_16354_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c03_16354/08_2023/8c03_16354_updated.pdb" } resolution = 3.89 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= 0.001 sd= 0.028 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: 5 Type Number sf(0) Gaussians S 26 5.16 5 C 2187 2.51 5 N 542 2.21 5 O 574 1.98 5 F 1 1.80 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-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 3330 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3330 Unusual residues: {'SZU': 1} Classifications: {'peptide': 429, 'undetermined': 1} Link IDs: {'PTRANS': 9, 'TRANS': 419, None: 1} Not linked: pdbres="LYS A 549 " pdbres="SZU A 601 " Chain breaks: 2 Time building chain proxies: 2.25, per 1000 atoms: 0.68 Number of scatterers: 3330 At special positions: 0 Unit cell: (78.12, 67.704, 84.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 F 1 9.00 O 574 8.00 N 542 7.00 C 2187 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 649.9 milliseconds 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 788 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 0 sheets defined 85.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 19 through 22 No H-bonds generated for 'chain 'A' and resid 19 through 22' Processing helix chain 'A' and resid 24 through 53 removed outlier: 3.767A pdb=" N GLY A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 85 removed outlier: 3.634A pdb=" N GLY A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP A 84 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 115 removed outlier: 3.782A pdb=" N ALA A 92 " --> pdb=" O ARG A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 120 No H-bonds generated for 'chain 'A' and resid 117 through 120' Processing helix chain 'A' and resid 126 through 155 Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 167 through 198 Proline residue: A 189 - end of helix Processing helix chain 'A' and resid 201 through 229 removed outlier: 3.742A pdb=" N GLY A 206 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 209 " --> pdb=" O CYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 289 through 304 Processing helix chain 'A' and resid 308 through 318 Processing helix chain 'A' and resid 326 through 335 Processing helix chain 'A' and resid 339 through 366 Processing helix chain 'A' and resid 370 through 392 Processing helix chain 'A' and resid 452 through 482 Processing helix chain 'A' and resid 486 through 513 removed outlier: 3.690A pdb=" N ARG A 489 " --> pdb=" O GLU A 486 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLY A 490 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE A 491 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE A 492 " --> pdb=" O ARG A 489 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN A 493 " --> pdb=" O GLY A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 545 279 hydrogen bonds defined for protein. 777 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.98 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1028 1.34 - 1.46: 824 1.46 - 1.58: 1505 1.58 - 1.70: 0 1.70 - 1.82: 44 Bond restraints: 3401 Sorted by residual: bond pdb=" C1 SZU A 601 " pdb=" C8 SZU A 601 " ideal model delta sigma weight residual 1.547 1.325 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C2 SZU A 601 " pdb=" C3 SZU A 601 " ideal model delta sigma weight residual 1.558 1.377 0.181 2.00e-02 2.50e+03 8.22e+01 bond pdb=" C1 SZU A 601 " pdb=" N1 SZU A 601 " ideal model delta sigma weight residual 1.455 1.329 0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" C16 SZU A 601 " pdb=" C17 SZU A 601 " ideal model delta sigma weight residual 1.417 1.329 0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C9 SZU A 601 " pdb=" O2 SZU A 601 " ideal model delta sigma weight residual 1.333 1.405 -0.072 2.00e-02 2.50e+03 1.29e+01 ... (remaining 3396 not shown) Histogram of bond angle deviations from ideal: 99.70 - 106.55: 75 106.55 - 113.40: 1952 113.40 - 120.25: 1289 120.25 - 127.10: 1271 127.10 - 133.95: 40 Bond angle restraints: 4627 Sorted by residual: angle pdb=" C14 SZU A 601 " pdb=" C15 SZU A 601 " pdb=" N4 SZU A 601 " ideal model delta sigma weight residual 144.40 125.60 18.80 3.00e+00 1.11e-01 3.93e+01 angle pdb=" C14 SZU A 601 " pdb=" C15 SZU A 601 " pdb=" N5 SZU A 601 " ideal model delta sigma weight residual 105.58 124.12 -18.54 3.00e+00 1.11e-01 3.82e+01 angle pdb=" C11 SZU A 601 " pdb=" C10 SZU A 601 " pdb=" N6 SZU A 601 " ideal model delta sigma weight residual 139.27 123.98 15.29 3.00e+00 1.11e-01 2.60e+01 angle pdb=" C11 SZU A 601 " pdb=" C10 SZU A 601 " pdb=" O2 SZU A 601 " ideal model delta sigma weight residual 110.79 125.74 -14.95 3.00e+00 1.11e-01 2.48e+01 angle pdb=" N GLN A 496 " pdb=" CA GLN A 496 " pdb=" C GLN A 496 " ideal model delta sigma weight residual 111.36 106.91 4.45 1.09e+00 8.42e-01 1.67e+01 ... (remaining 4622 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.29: 1807 16.29 - 32.58: 109 32.58 - 48.87: 31 48.87 - 65.16: 11 65.16 - 81.45: 2 Dihedral angle restraints: 1960 sinusoidal: 731 harmonic: 1229 Sorted by residual: dihedral pdb=" N GLU A 518 " pdb=" CA GLU A 518 " pdb=" CB GLU A 518 " pdb=" CG GLU A 518 " ideal model delta sinusoidal sigma weight residual -60.00 -119.88 59.88 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ILE A 186 " pdb=" CB ILE A 186 " pdb=" CG1 ILE A 186 " pdb=" CD1 ILE A 186 " ideal model delta sinusoidal sigma weight residual 180.00 123.89 56.11 3 1.50e+01 4.44e-03 9.38e+00 dihedral pdb=" N ILE A 78 " pdb=" CA ILE A 78 " pdb=" CB ILE A 78 " pdb=" CG1 ILE A 78 " ideal model delta sinusoidal sigma weight residual -60.00 -114.35 54.35 3 1.50e+01 4.44e-03 9.28e+00 ... (remaining 1957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 473 0.052 - 0.104: 74 0.104 - 0.156: 9 0.156 - 0.208: 3 0.208 - 0.260: 1 Chirality restraints: 560 Sorted by residual: chirality pdb=" CA LEU A 59 " pdb=" N LEU A 59 " pdb=" C LEU A 59 " pdb=" CB LEU A 59 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA TYR A 333 " pdb=" N TYR A 333 " pdb=" C TYR A 333 " pdb=" CB TYR A 333 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA PHE A 324 " pdb=" N PHE A 324 " pdb=" C PHE A 324 " pdb=" CB PHE A 324 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.98e-01 ... (remaining 557 not shown) Planarity restraints: 556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 53 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.86e+00 pdb=" C LEU A 53 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU A 53 " -0.011 2.00e-02 2.50e+03 pdb=" N TYR A 54 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 324 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C PHE A 324 " -0.029 2.00e-02 2.50e+03 pdb=" O PHE A 324 " 0.011 2.00e-02 2.50e+03 pdb=" N ASP A 325 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 SZU A 601 " -0.004 2.00e-02 2.50e+03 1.42e-02 2.53e+00 pdb=" C2 SZU A 601 " 0.016 2.00e-02 2.50e+03 pdb=" C8 SZU A 601 " 0.013 2.00e-02 2.50e+03 pdb=" N1 SZU A 601 " -0.023 2.00e-02 2.50e+03 pdb=" O1 SZU A 601 " -0.002 2.00e-02 2.50e+03 ... (remaining 553 not shown) Histogram of nonbonded interaction distances: 1.23 - 1.97: 1 1.97 - 2.70: 83 2.70 - 3.43: 5442 3.43 - 4.17: 7372 4.17 - 4.90: 13869 Nonbonded interactions: 26767 Sorted by model distance: nonbonded pdb=" OH TYR A 302 " pdb=" OE1 GLN A 496 " model vdw 1.232 2.440 nonbonded pdb=" CD1 LEU A 469 " pdb=" F1 SZU A 601 " model vdw 2.141 3.410 nonbonded pdb=" O TYR A 20 " pdb=" OG SER A 23 " model vdw 2.205 2.440 nonbonded pdb=" O ASN A 86 " pdb=" NZ LYS A 236 " model vdw 2.209 2.520 nonbonded pdb=" O LEU A 369 " pdb=" OG1 THR A 372 " model vdw 2.260 2.440 ... (remaining 26762 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.520 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.180 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 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 : 0.007 0.222 3401 Z= 0.448 Angle : 0.858 18.796 4627 Z= 0.441 Chirality : 0.040 0.260 560 Planarity : 0.003 0.017 556 Dihedral : 12.868 81.455 1172 Min Nonbonded Distance : 1.232 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer Outliers : 3.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.41), residues: 423 helix: 2.29 (0.26), residues: 357 sheet: None (None), residues: 0 loop : -0.88 (0.85), residues: 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 132 time to evaluate : 0.378 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 138 average time/residue: 0.1393 time to fit residues: 23.6291 Evaluate side-chains 104 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 0.356 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0384 time to fit residues: 0.6882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 0.0970 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 39 optimal weight: 0.0770 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS A 194 GLN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 3401 Z= 0.193 Angle : 0.570 8.511 4627 Z= 0.289 Chirality : 0.037 0.126 560 Planarity : 0.004 0.025 556 Dihedral : 5.694 52.748 464 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 3.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.40), residues: 423 helix: 2.24 (0.26), residues: 366 sheet: None (None), residues: 0 loop : -0.27 (0.98), residues: 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 0.374 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 111 average time/residue: 0.1211 time to fit residues: 17.0706 Evaluate side-chains 105 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 0.331 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0364 time to fit residues: 0.8011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 3401 Z= 0.251 Angle : 0.607 8.161 4627 Z= 0.306 Chirality : 0.038 0.156 560 Planarity : 0.004 0.029 556 Dihedral : 5.722 57.082 464 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 3.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.41), residues: 423 helix: 2.08 (0.26), residues: 362 sheet: None (None), residues: 0 loop : -0.46 (0.94), residues: 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 0.399 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 108 average time/residue: 0.1305 time to fit residues: 17.8681 Evaluate side-chains 107 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 0.361 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0374 time to fit residues: 1.0148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 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 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 3401 Z= 0.218 Angle : 0.592 8.944 4627 Z= 0.296 Chirality : 0.038 0.152 560 Planarity : 0.004 0.029 556 Dihedral : 5.543 60.693 464 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 3.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.41), residues: 423 helix: 2.10 (0.26), residues: 365 sheet: None (None), residues: 0 loop : -0.65 (0.94), residues: 58 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 107 time to evaluate : 0.390 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 112 average time/residue: 0.1297 time to fit residues: 18.2048 Evaluate side-chains 105 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 0.385 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0421 time to fit residues: 0.9469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 30 optimal weight: 0.0370 chunk 17 optimal weight: 4.9990 chunk 35 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 3401 Z= 0.212 Angle : 0.612 10.011 4627 Z= 0.304 Chirality : 0.038 0.195 560 Planarity : 0.003 0.024 556 Dihedral : 5.501 60.610 464 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.41), residues: 423 helix: 2.04 (0.26), residues: 365 sheet: None (None), residues: 0 loop : -0.68 (0.94), residues: 58 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 0.402 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 105 average time/residue: 0.1296 time to fit residues: 17.0973 Evaluate side-chains 97 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 0.375 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0361 time to fit residues: 0.6447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 3401 Z= 0.258 Angle : 0.665 10.659 4627 Z= 0.329 Chirality : 0.039 0.172 560 Planarity : 0.004 0.021 556 Dihedral : 5.471 60.340 464 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.41), residues: 423 helix: 2.00 (0.26), residues: 365 sheet: None (None), residues: 0 loop : -0.61 (0.95), residues: 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 0.370 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 99 average time/residue: 0.1277 time to fit residues: 15.9191 Evaluate side-chains 99 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 0.368 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0352 time to fit residues: 0.6229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.0670 chunk 23 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 3401 Z= 0.234 Angle : 0.641 11.309 4627 Z= 0.318 Chirality : 0.038 0.172 560 Planarity : 0.003 0.024 556 Dihedral : 5.441 60.342 464 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.41), residues: 423 helix: 1.99 (0.27), residues: 365 sheet: None (None), residues: 0 loop : -0.57 (0.94), residues: 58 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 0.378 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 98 average time/residue: 0.1306 time to fit residues: 16.1542 Evaluate side-chains 98 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.375 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0391 time to fit residues: 0.7733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 37 optimal weight: 0.3980 chunk 39 optimal weight: 0.0770 chunk 36 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 3401 Z= 0.198 Angle : 0.640 11.576 4627 Z= 0.310 Chirality : 0.038 0.174 560 Planarity : 0.003 0.022 556 Dihedral : 5.393 60.487 464 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.42), residues: 423 helix: 1.99 (0.27), residues: 365 sheet: None (None), residues: 0 loop : -0.65 (0.92), residues: 58 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 0.374 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 99 average time/residue: 0.1278 time to fit residues: 15.9065 Evaluate side-chains 94 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.370 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0357 time to fit residues: 0.5866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 3401 Z= 0.231 Angle : 0.652 12.724 4627 Z= 0.319 Chirality : 0.038 0.169 560 Planarity : 0.004 0.058 556 Dihedral : 5.378 60.071 464 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.42), residues: 423 helix: 1.89 (0.27), residues: 365 sheet: None (None), residues: 0 loop : -0.64 (0.92), residues: 58 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 0.343 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 97 average time/residue: 0.1245 time to fit residues: 15.3234 Evaluate side-chains 92 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 0.310 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0352 time to fit residues: 0.5490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 0.6980 chunk 3 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 36 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 14 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 43 HIS ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 3401 Z= 0.243 Angle : 0.665 10.004 4627 Z= 0.329 Chirality : 0.039 0.170 560 Planarity : 0.004 0.058 556 Dihedral : 5.409 59.029 464 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.42), residues: 423 helix: 1.85 (0.27), residues: 363 sheet: None (None), residues: 0 loop : -0.70 (0.89), residues: 60 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 0.379 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 97 average time/residue: 0.1266 time to fit residues: 15.6795 Evaluate side-chains 95 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 0.377 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0419 time to fit residues: 0.6495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 29 optimal weight: 0.0980 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.164630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.129966 restraints weight = 4907.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.133946 restraints weight = 3153.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.136749 restraints weight = 2422.810| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 3401 Z= 0.249 Angle : 0.659 10.077 4627 Z= 0.329 Chirality : 0.039 0.169 560 Planarity : 0.004 0.052 556 Dihedral : 5.362 58.194 464 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.42), residues: 423 helix: 1.87 (0.27), residues: 362 sheet: None (None), residues: 0 loop : -0.70 (0.90), residues: 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1036.14 seconds wall clock time: 19 minutes 28.57 seconds (1168.57 seconds total)