Starting phenix.real_space_refine on Sun Mar 10 15:44:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ug0_26482/03_2024/7ug0_26482_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ug0_26482/03_2024/7ug0_26482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ug0_26482/03_2024/7ug0_26482.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ug0_26482/03_2024/7ug0_26482.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ug0_26482/03_2024/7ug0_26482_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ug0_26482/03_2024/7ug0_26482_updated.pdb" } resolution = 2.55 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= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 17 5.16 5 Na 2 4.78 5 C 2050 2.51 5 N 507 2.21 5 O 549 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 48": "OD1" <-> "OD2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 394": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3126 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3126 Unusual residues: {' NA': 2, 'TB1': 1} Classifications: {'peptide': 418, 'undetermined': 3, 'water': 4} Link IDs: {'PTRANS': 18, 'TRANS': 399, None: 7} Not linked: pdbres="THR A 418 " pdbres="TB1 A 501 " Not linked: pdbres="TB1 A 501 " pdbres=" NA A 502 " Not linked: pdbres=" NA A 502 " pdbres=" NA A 503 " Not linked: pdbres=" NA A 503 " pdbres="HOH A 601 " Not linked: pdbres="HOH A 601 " pdbres="HOH A 602 " ... (remaining 2 not shown) Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EFC:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.18, per 1000 atoms: 0.70 Number of scatterers: 3126 At special positions: 0 Unit cell: (67.308, 78.384, 70.716, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 17 16.00 Na 2 11.00 F 1 9.00 O 549 8.00 N 507 7.00 C 2050 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: 1.31 Conformation dependent library (CDL) restraints added in 558.3 milliseconds 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 750 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 17 helices and 0 sheets defined 79.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 removed outlier: 3.637A pdb=" N ILE A 8 " --> pdb=" O TYR A 4 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU A 9 " --> pdb=" O ARG A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 33 removed outlier: 3.625A pdb=" N TYR A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 72 removed outlier: 4.088A pdb=" N LYS A 44 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Proline residue: A 45 - end of helix removed outlier: 3.542A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N MET A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Proline residue: A 60 - end of helix removed outlier: 3.573A pdb=" N LEU A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 106 Processing helix chain 'A' and resid 130 through 137 removed outlier: 3.853A pdb=" N ILE A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 151 through 170 removed outlier: 3.715A pdb=" N ASN A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 219 removed outlier: 3.514A pdb=" N GLN A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix Processing helix chain 'A' and resid 225 through 245 Processing helix chain 'A' and resid 247 through 254 Processing helix chain 'A' and resid 258 through 275 removed outlier: 5.198A pdb=" N ASP A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ALA A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 296 through 309 removed outlier: 4.448A pdb=" N PHE A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) Proline residue: A 304 - end of helix removed outlier: 3.993A pdb=" N THR A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 329 removed outlier: 3.581A pdb=" N PHE A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 removed outlier: 3.516A pdb=" N SER A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 370 Processing helix chain 'A' and resid 377 through 417 removed outlier: 4.108A pdb=" N ILE A 389 " --> pdb=" O EFC A 385 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP A 390 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ILE A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) 226 hydrogen bonds defined for protein. 678 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.86 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 987 1.37 - 1.55: 2162 1.55 - 1.73: 0 1.73 - 1.92: 32 1.92 - 2.10: 1 Bond restraints: 3182 Sorted by residual: bond pdb=" C EFC A 385 " pdb=" O EFC A 385 " ideal model delta sigma weight residual 1.231 1.184 0.047 2.00e-02 2.50e+03 5.59e+00 bond pdb=" SG EFC A 385 " pdb=" SD EFC A 385 " ideal model delta sigma weight residual 2.054 2.101 -0.047 2.00e-02 2.50e+03 5.52e+00 bond pdb=" C1 TB1 A 501 " pdb=" C4 TB1 A 501 " ideal model delta sigma weight residual 1.503 1.529 -0.026 2.00e-02 2.50e+03 1.67e+00 bond pdb=" C2 EFC A 385 " pdb=" F2 EFC A 385 " ideal model delta sigma weight residual 1.388 1.365 0.023 2.00e-02 2.50e+03 1.38e+00 bond pdb=" C10 TB1 A 501 " pdb=" C7 TB1 A 501 " ideal model delta sigma weight residual 1.548 1.526 0.022 2.00e-02 2.50e+03 1.20e+00 ... (remaining 3177 not shown) Histogram of bond angle deviations from ideal: 100.68 - 106.80: 97 106.80 - 112.91: 1795 112.91 - 119.02: 775 119.02 - 125.13: 1640 125.13 - 131.25: 30 Bond angle restraints: 4337 Sorted by residual: angle pdb=" CB EFC A 385 " pdb=" SG EFC A 385 " pdb=" SD EFC A 385 " ideal model delta sigma weight residual 101.65 108.90 -7.25 3.00e+00 1.11e-01 5.83e+00 angle pdb=" O1 TB1 A 501 " pdb=" C9 TB1 A 501 " pdb=" O5 TB1 A 501 " ideal model delta sigma weight residual 126.71 119.70 7.01 3.00e+00 1.11e-01 5.47e+00 angle pdb=" O3 TB1 A 501 " pdb=" C10 TB1 A 501 " pdb=" O4 TB1 A 501 " ideal model delta sigma weight residual 126.45 120.01 6.44 3.00e+00 1.11e-01 4.61e+00 angle pdb=" SG EFC A 385 " pdb=" SD EFC A 385 " pdb=" C1 EFC A 385 " ideal model delta sigma weight residual 103.98 109.54 -5.56 3.00e+00 1.11e-01 3.44e+00 angle pdb=" C11 TB1 A 501 " pdb=" C9 TB1 A 501 " pdb=" O5 TB1 A 501 " ideal model delta sigma weight residual 115.01 120.10 -5.09 3.00e+00 1.11e-01 2.88e+00 ... (remaining 4332 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.74: 1682 12.74 - 25.49: 131 25.49 - 38.23: 39 38.23 - 50.98: 9 50.98 - 63.72: 9 Dihedral angle restraints: 1870 sinusoidal: 686 harmonic: 1184 Sorted by residual: dihedral pdb=" CB MET A 194 " pdb=" CG MET A 194 " pdb=" SD MET A 194 " pdb=" CE MET A 194 " ideal model delta sinusoidal sigma weight residual 180.00 122.68 57.32 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CB MET A 292 " pdb=" CG MET A 292 " pdb=" SD MET A 292 " pdb=" CE MET A 292 " ideal model delta sinusoidal sigma weight residual -60.00 -113.78 53.78 3 1.50e+01 4.44e-03 9.23e+00 dihedral pdb=" CG ARG A 80 " pdb=" CD ARG A 80 " pdb=" NE ARG A 80 " pdb=" CZ ARG A 80 " ideal model delta sinusoidal sigma weight residual -90.00 -129.22 39.22 2 1.50e+01 4.44e-03 8.53e+00 ... (remaining 1867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 387 0.033 - 0.066: 120 0.066 - 0.098: 26 0.098 - 0.131: 8 0.131 - 0.164: 1 Chirality restraints: 542 Sorted by residual: chirality pdb=" C7 TB1 A 501 " pdb=" N TB1 A 501 " pdb=" C10 TB1 A 501 " pdb=" C11 TB1 A 501 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" CA VAL A 355 " pdb=" N VAL A 355 " pdb=" C VAL A 355 " pdb=" CB VAL A 355 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.09e-01 chirality pdb=" CA MET A 59 " pdb=" N MET A 59 " pdb=" C MET A 59 " pdb=" CB MET A 59 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.96e-01 ... (remaining 539 not shown) Planarity restraints: 534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 44 " 0.021 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO A 45 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 152 " -0.015 5.00e-02 4.00e+02 2.27e-02 8.26e-01 pdb=" N PRO A 153 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 153 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 153 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 376 " 0.014 5.00e-02 4.00e+02 2.16e-02 7.48e-01 pdb=" N PRO A 377 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO A 377 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 377 " 0.012 5.00e-02 4.00e+02 ... (remaining 531 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 852 2.81 - 3.33: 3196 3.33 - 3.85: 4836 3.85 - 4.38: 5671 4.38 - 4.90: 9872 Nonbonded interactions: 24427 Sorted by model distance: nonbonded pdb=" OG SER A 278 " pdb=" O3 TB1 A 501 " model vdw 2.287 2.440 nonbonded pdb=" O HOH A 601 " pdb=" O HOH A 604 " model vdw 2.310 2.440 nonbonded pdb=" OH TYR A 247 " pdb=" OD2 ASP A 312 " model vdw 2.341 2.440 nonbonded pdb=" OD2 ASP A 405 " pdb=" O HOH A 601 " model vdw 2.359 2.440 nonbonded pdb=" N TB1 A 501 " pdb=" O1 TB1 A 501 " model vdw 2.361 2.520 ... (remaining 24422 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.540 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: 11.570 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.750 Find NCS groups from input model: 0.080 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:10.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 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 : 0.002 0.047 3182 Z= 0.165 Angle : 0.451 7.246 4337 Z= 0.208 Chirality : 0.036 0.164 542 Planarity : 0.003 0.031 534 Dihedral : 11.574 63.720 1120 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.39), residues: 413 helix: 1.50 (0.26), residues: 336 sheet: None (None), residues: 0 loop : 0.91 (0.78), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 40 PHE 0.005 0.001 PHE A 210 TYR 0.013 0.001 TYR A 299 ARG 0.001 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.397 Fit side-chains REVERT: A 174 GLU cc_start: 0.7990 (tp30) cc_final: 0.7645 (tp30) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 1.5158 time to fit residues: 62.2068 Evaluate side-chains 37 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3182 Z= 0.237 Angle : 0.476 4.638 4337 Z= 0.259 Chirality : 0.038 0.113 542 Planarity : 0.004 0.029 534 Dihedral : 7.494 58.210 461 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.23 % Allowed : 3.70 % Favored : 95.06 % 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: 3.31 (0.40), residues: 413 helix: 2.52 (0.27), residues: 341 sheet: None (None), residues: 0 loop : 0.61 (0.67), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 219 PHE 0.008 0.001 PHE A 323 TYR 0.020 0.001 TYR A 299 ARG 0.002 0.000 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 0.360 Fit side-chains REVERT: A 227 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7740 (mm-30) REVERT: A 296 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7773 (tm-30) REVERT: A 311 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8281 (mtp) REVERT: A 390 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7905 (m-30) outliers start: 4 outliers final: 0 residues processed: 36 average time/residue: 1.5594 time to fit residues: 57.6227 Evaluate side-chains 35 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 390 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 37 optimal weight: 0.0040 chunk 13 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3182 Z= 0.173 Angle : 0.424 4.670 4337 Z= 0.225 Chirality : 0.036 0.111 542 Planarity : 0.004 0.030 534 Dihedral : 6.483 54.135 461 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.54 % Allowed : 5.86 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.69 (0.41), residues: 413 helix: 2.81 (0.28), residues: 342 sheet: None (None), residues: 0 loop : 0.50 (0.69), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 219 PHE 0.008 0.001 PHE A 156 TYR 0.019 0.001 TYR A 299 ARG 0.001 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 32 time to evaluate : 0.326 Fit side-chains REVERT: A 296 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7557 (tm-30) REVERT: A 311 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8203 (mtp) outliers start: 5 outliers final: 0 residues processed: 35 average time/residue: 1.5152 time to fit residues: 54.4492 Evaluate side-chains 33 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3182 Z= 0.190 Angle : 0.438 4.630 4337 Z= 0.232 Chirality : 0.036 0.111 542 Planarity : 0.003 0.030 534 Dihedral : 5.948 48.470 461 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.54 % Allowed : 6.79 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.76 (0.41), residues: 413 helix: 2.87 (0.28), residues: 342 sheet: None (None), residues: 0 loop : 0.48 (0.69), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 219 PHE 0.008 0.001 PHE A 156 TYR 0.019 0.001 TYR A 299 ARG 0.001 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.364 Fit side-chains REVERT: A 296 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7528 (tm-30) REVERT: A 311 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8187 (mtp) outliers start: 5 outliers final: 3 residues processed: 34 average time/residue: 1.5111 time to fit residues: 52.7799 Evaluate side-chains 37 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 311 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 28 optimal weight: 0.0670 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 0.0870 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3182 Z= 0.143 Angle : 0.406 4.612 4337 Z= 0.213 Chirality : 0.035 0.112 542 Planarity : 0.003 0.031 534 Dihedral : 5.271 40.752 461 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.93 % Allowed : 7.41 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.96 (0.42), residues: 413 helix: 2.99 (0.28), residues: 342 sheet: None (None), residues: 0 loop : 0.64 (0.70), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 219 PHE 0.007 0.001 PHE A 156 TYR 0.017 0.001 TYR A 299 ARG 0.001 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.354 Fit side-chains REVERT: A 296 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7428 (tm-30) REVERT: A 311 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8123 (mtp) outliers start: 3 outliers final: 0 residues processed: 35 average time/residue: 1.4044 time to fit residues: 50.5776 Evaluate side-chains 33 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 0.0030 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3182 Z= 0.176 Angle : 0.427 4.637 4337 Z= 0.224 Chirality : 0.036 0.116 542 Planarity : 0.003 0.030 534 Dihedral : 5.055 39.288 461 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.93 % Allowed : 8.95 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.89 (0.42), residues: 413 helix: 2.95 (0.28), residues: 342 sheet: None (None), residues: 0 loop : 0.62 (0.71), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 219 PHE 0.008 0.001 PHE A 156 TYR 0.018 0.001 TYR A 299 ARG 0.002 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.365 Fit side-chains REVERT: A 296 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7473 (tm-30) REVERT: A 311 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8155 (mtp) outliers start: 3 outliers final: 2 residues processed: 34 average time/residue: 1.5646 time to fit residues: 54.5912 Evaluate side-chains 37 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 311 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.3980 chunk 34 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 0.0670 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3182 Z= 0.152 Angle : 0.416 4.595 4337 Z= 0.218 Chirality : 0.035 0.115 542 Planarity : 0.003 0.031 534 Dihedral : 4.787 35.538 461 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.93 % Allowed : 9.26 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.99 (0.42), residues: 413 helix: 3.01 (0.28), residues: 342 sheet: None (None), residues: 0 loop : 0.65 (0.71), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 219 PHE 0.007 0.001 PHE A 156 TYR 0.017 0.001 TYR A 299 ARG 0.001 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.356 Fit side-chains REVERT: A 5 ARG cc_start: 0.8180 (tpp-160) cc_final: 0.7972 (tpp-160) REVERT: A 296 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7446 (tm-30) REVERT: A 311 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8117 (mtp) outliers start: 3 outliers final: 0 residues processed: 33 average time/residue: 1.5754 time to fit residues: 53.3684 Evaluate side-chains 33 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 22 optimal weight: 0.2980 chunk 16 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 0.0070 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3182 Z= 0.150 Angle : 0.417 4.735 4337 Z= 0.217 Chirality : 0.035 0.116 542 Planarity : 0.003 0.031 534 Dihedral : 4.536 32.597 461 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.31 % Allowed : 10.49 % Favored : 89.20 % 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: 4.03 (0.42), residues: 413 helix: 3.03 (0.28), residues: 342 sheet: None (None), residues: 0 loop : 0.72 (0.72), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS A 219 PHE 0.007 0.001 PHE A 156 TYR 0.017 0.001 TYR A 299 ARG 0.001 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.379 Fit side-chains REVERT: A 5 ARG cc_start: 0.8200 (tpp-160) cc_final: 0.7975 (tpp-160) REVERT: A 296 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7436 (tm-30) REVERT: A 311 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8081 (mtp) outliers start: 1 outliers final: 0 residues processed: 32 average time/residue: 1.5250 time to fit residues: 50.1521 Evaluate side-chains 33 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3182 Z= 0.200 Angle : 0.446 4.641 4337 Z= 0.233 Chirality : 0.036 0.114 542 Planarity : 0.003 0.031 534 Dihedral : 4.622 34.383 461 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.31 % Allowed : 10.19 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.87 (0.42), residues: 413 helix: 2.93 (0.28), residues: 342 sheet: None (None), residues: 0 loop : 0.62 (0.71), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 219 PHE 0.008 0.001 PHE A 156 TYR 0.019 0.001 TYR A 299 ARG 0.001 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.360 Fit side-chains REVERT: A 5 ARG cc_start: 0.8202 (tpp-160) cc_final: 0.7566 (tpp-160) REVERT: A 9 GLU cc_start: 0.7975 (mp0) cc_final: 0.7745 (mp0) REVERT: A 296 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7502 (tm-30) REVERT: A 311 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8121 (mtp) outliers start: 1 outliers final: 0 residues processed: 33 average time/residue: 1.6298 time to fit residues: 55.1266 Evaluate side-chains 34 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 0.3980 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3182 Z= 0.170 Angle : 0.429 4.621 4337 Z= 0.225 Chirality : 0.036 0.115 542 Planarity : 0.003 0.031 534 Dihedral : 4.489 32.318 461 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.62 % Allowed : 9.88 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.93 (0.42), residues: 413 helix: 2.97 (0.28), residues: 342 sheet: None (None), residues: 0 loop : 0.63 (0.71), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 219 PHE 0.008 0.001 PHE A 156 TYR 0.018 0.001 TYR A 299 ARG 0.001 0.000 ARG A 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.361 Fit side-chains REVERT: A 5 ARG cc_start: 0.8194 (tpp-160) cc_final: 0.7538 (tpp-160) REVERT: A 9 GLU cc_start: 0.7963 (mp0) cc_final: 0.7726 (mp0) REVERT: A 296 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7461 (tm-30) REVERT: A 311 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8101 (mtp) outliers start: 2 outliers final: 0 residues processed: 33 average time/residue: 1.6512 time to fit residues: 55.8707 Evaluate side-chains 34 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 28 optimal weight: 0.0670 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.095267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.072361 restraints weight = 5507.610| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.39 r_work: 0.2819 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3182 Z= 0.162 Angle : 0.425 4.620 4337 Z= 0.222 Chirality : 0.036 0.115 542 Planarity : 0.003 0.031 534 Dihedral : 4.301 29.665 461 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.62 % Allowed : 9.57 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.98 (0.42), residues: 413 helix: 3.01 (0.28), residues: 342 sheet: None (None), residues: 0 loop : 0.62 (0.72), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 219 PHE 0.007 0.001 PHE A 156 TYR 0.017 0.001 TYR A 299 ARG 0.001 0.000 ARG A 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1672.73 seconds wall clock time: 30 minutes 12.42 seconds (1812.42 seconds total)