Starting phenix.real_space_refine on Thu Dec 7 18:01:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f62_31470/12_2023/7f62_31470.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f62_31470/12_2023/7f62_31470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f62_31470/12_2023/7f62_31470.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f62_31470/12_2023/7f62_31470.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f62_31470/12_2023/7f62_31470.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f62_31470/12_2023/7f62_31470.pdb" } resolution = 3.6 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= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 2104 2.51 5 N 552 2.21 5 O 647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3321 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1579 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 11, 'TRANS': 187} Chain breaks: 1 Chain: "H" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 914 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 828 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Time building chain proxies: 2.24, per 1000 atoms: 0.67 Number of scatterers: 3321 At special positions: 0 Unit cell: (77, 53.9, 102.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 647 8.00 N 552 7.00 C 2104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 577.6 milliseconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 784 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 10 sheets defined 9.8% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.007A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.936A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.197A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.625A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'H' and resid 61 through 65 removed outlier: 4.075A pdb=" N ALA H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 65' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.998A pdb=" N ALA L 84 " --> pdb=" O ALA L 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.561A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL A 395 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER A 514 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA A 397 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL A 512 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SER A 399 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL A 510 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL A 401 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N TYR A 508 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 19 through 21 Processing sheet with id=AA5, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.919A pdb=" N ASN H 59 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU H 50 " --> pdb=" O ASN H 59 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 5 through 6 removed outlier: 4.072A pdb=" N SER L 71 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER L 68 " --> pdb=" O SER L 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 12 through 14 removed outlier: 6.133A pdb=" N GLU L 106 " --> pdb=" O VAL L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'L' and resid 35 through 36 removed outlier: 4.195A pdb=" N ILE L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 86 through 87 removed outlier: 3.725A pdb=" N TYR L 87 " --> pdb=" O THR L 103 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 90 through 91 removed outlier: 3.741A pdb=" N GLN L 91 " --> pdb=" O THR L 98 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 68 hydrogen bonds defined for protein. 153 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: 0.80 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1046 1.34 - 1.46: 748 1.46 - 1.58: 1588 1.58 - 1.70: 0 1.70 - 1.82: 24 Bond restraints: 3406 Sorted by residual: bond pdb=" N TYR A 449 " pdb=" CA TYR A 449 " ideal model delta sigma weight residual 1.457 1.425 0.032 1.29e-02 6.01e+03 6.35e+00 bond pdb=" C ASN A 448 " pdb=" N TYR A 449 " ideal model delta sigma weight residual 1.332 1.301 0.031 1.40e-02 5.10e+03 5.04e+00 bond pdb=" C TYR A 449 " pdb=" O TYR A 449 " ideal model delta sigma weight residual 1.235 1.218 0.018 1.26e-02 6.30e+03 1.99e+00 bond pdb=" CE2 TYR A 449 " pdb=" CZ TYR A 449 " ideal model delta sigma weight residual 1.378 1.345 0.033 2.40e-02 1.74e+03 1.92e+00 bond pdb=" C SER L 95 " pdb=" O SER L 95 " ideal model delta sigma weight residual 1.241 1.231 0.011 9.80e-03 1.04e+04 1.19e+00 ... (remaining 3401 not shown) Histogram of bond angle deviations from ideal: 99.51 - 106.40: 93 106.40 - 113.29: 1753 113.29 - 120.18: 1159 120.18 - 127.07: 1584 127.07 - 133.96: 35 Bond angle restraints: 4624 Sorted by residual: angle pdb=" CA SER L 95 " pdb=" C SER L 95 " pdb=" N PRO L 96 " ideal model delta sigma weight residual 120.79 116.56 4.23 9.70e-01 1.06e+00 1.91e+01 angle pdb=" C SER L 95 " pdb=" N PRO L 96 " pdb=" CA PRO L 96 " ideal model delta sigma weight residual 119.99 124.05 -4.06 1.08e+00 8.57e-01 1.41e+01 angle pdb=" CA TYR A 449 " pdb=" CB TYR A 449 " pdb=" CG TYR A 449 " ideal model delta sigma weight residual 113.90 119.63 -5.73 1.80e+00 3.09e-01 1.01e+01 angle pdb=" N LEU A 452 " pdb=" CA LEU A 452 " pdb=" C LEU A 452 " ideal model delta sigma weight residual 109.41 113.80 -4.39 1.52e+00 4.33e-01 8.32e+00 angle pdb=" C PRO A 330 " pdb=" N ASN A 331 " pdb=" CA ASN A 331 " ideal model delta sigma weight residual 120.65 124.21 -3.56 1.32e+00 5.74e-01 7.27e+00 ... (remaining 4619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.33: 1770 15.33 - 30.66: 174 30.66 - 45.99: 49 45.99 - 61.32: 12 61.32 - 76.65: 4 Dihedral angle restraints: 2009 sinusoidal: 771 harmonic: 1238 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 26.90 66.10 1 1.00e+01 1.00e-02 5.71e+01 dihedral pdb=" CA GLN H 3 " pdb=" C GLN H 3 " pdb=" N LEU H 4 " pdb=" CA LEU H 4 " ideal model delta harmonic sigma weight residual 180.00 151.87 28.13 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -132.09 46.09 1 1.00e+01 1.00e-02 2.94e+01 ... (remaining 2006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 308 0.032 - 0.063: 120 0.063 - 0.095: 41 0.095 - 0.127: 22 0.127 - 0.159: 4 Chirality restraints: 495 Sorted by residual: chirality pdb=" CB ILE L 49 " pdb=" CA ILE L 49 " pdb=" CG1 ILE L 49 " pdb=" CG2 ILE L 49 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.29e-01 chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA VAL A 401 " pdb=" N VAL A 401 " pdb=" C VAL A 401 " pdb=" CB VAL A 401 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 492 not shown) Planarity restraints: 593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 448 " 0.010 2.00e-02 2.50e+03 2.00e-02 4.02e+00 pdb=" C ASN A 448 " -0.035 2.00e-02 2.50e+03 pdb=" O ASN A 448 " 0.013 2.00e-02 2.50e+03 pdb=" N TYR A 449 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO A 521 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 13 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO H 14 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " -0.020 5.00e-02 4.00e+02 ... (remaining 590 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 44 2.52 - 3.11: 2497 3.11 - 3.71: 5200 3.71 - 4.30: 7066 4.30 - 4.90: 11389 Nonbonded interactions: 26196 Sorted by model distance: nonbonded pdb=" O VAL L 29 " pdb=" ND1 HIS L 93 " model vdw 1.925 2.520 nonbonded pdb=" CE2 TYR L 33 " pdb=" CD2 HIS L 93 " model vdw 1.951 3.560 nonbonded pdb=" CD2 TYR L 33 " pdb=" CD2 HIS L 93 " model vdw 1.983 3.560 nonbonded pdb=" OH TYR H 60 " pdb=" O THR H 65 " model vdw 2.177 2.440 nonbonded pdb=" OG1 THR H 33 " pdb=" O PHE H 99 " model vdw 2.207 2.440 ... (remaining 26191 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 11.460 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.470 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 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 : 0.003 0.033 3406 Z= 0.166 Angle : 0.649 6.271 4624 Z= 0.369 Chirality : 0.043 0.159 495 Planarity : 0.004 0.047 593 Dihedral : 13.209 76.650 1207 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.11 % Favored : 91.65 % Rotamer: Outliers : 1.38 % Allowed : 1.65 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.39), residues: 419 helix: -4.04 (0.68), residues: 30 sheet: -0.91 (0.48), residues: 123 loop : -2.11 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 48 HIS 0.002 0.001 HIS L 35 PHE 0.011 0.001 PHE H 27 TYR 0.013 0.001 TYR H 95 ARG 0.001 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 98 average time/residue: 0.2456 time to fit residues: 27.3207 Evaluate side-chains 50 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.391 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2844 time to fit residues: 1.1595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.6980 chunk 30 optimal weight: 0.0370 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.0020 chunk 23 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.3470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN H 74 ASN L 93 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3406 Z= 0.229 Angle : 0.632 6.171 4624 Z= 0.327 Chirality : 0.045 0.141 495 Planarity : 0.004 0.046 593 Dihedral : 4.867 25.105 472 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 3.86 % Allowed : 11.57 % Favored : 84.57 % 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 (0.39), residues: 419 helix: -3.72 (0.78), residues: 30 sheet: -0.91 (0.48), residues: 125 loop : -1.81 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 48 HIS 0.003 0.001 HIS L 35 PHE 0.017 0.002 PHE L 63 TYR 0.018 0.002 TYR H 95 ARG 0.005 0.001 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 51 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 60 average time/residue: 0.1547 time to fit residues: 11.4528 Evaluate side-chains 53 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.354 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0344 time to fit residues: 1.0712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.0040 chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 0.0010 chunk 27 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6424 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3406 Z= 0.145 Angle : 0.570 6.386 4624 Z= 0.291 Chirality : 0.044 0.137 495 Planarity : 0.004 0.045 593 Dihedral : 4.530 20.946 472 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.65 % Allowed : 15.98 % Favored : 82.37 % 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: -2.30 (0.39), residues: 419 helix: -3.92 (0.67), residues: 30 sheet: -0.41 (0.50), residues: 117 loop : -1.85 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 48 HIS 0.002 0.001 HIS L 93 PHE 0.014 0.001 PHE L 63 TYR 0.009 0.001 TYR L 87 ARG 0.004 0.001 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 58 average time/residue: 0.2012 time to fit residues: 13.8238 Evaluate side-chains 48 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.349 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0463 time to fit residues: 0.6473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 0.2980 chunk 10 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 74 ASN L 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3406 Z= 0.291 Angle : 0.650 5.448 4624 Z= 0.340 Chirality : 0.046 0.147 495 Planarity : 0.005 0.046 593 Dihedral : 5.201 18.735 472 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.69 % Favored : 88.31 % Rotamer: Outliers : 3.86 % Allowed : 21.21 % Favored : 74.93 % 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: -2.28 (0.39), residues: 419 helix: -3.92 (0.70), residues: 24 sheet: -0.31 (0.52), residues: 105 loop : -1.88 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 48 HIS 0.006 0.002 HIS L 90 PHE 0.016 0.002 PHE H 29 TYR 0.012 0.002 TYR H 102 ARG 0.009 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 44 time to evaluate : 0.353 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 52 average time/residue: 0.1443 time to fit residues: 9.5827 Evaluate side-chains 50 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 39 time to evaluate : 0.395 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0369 time to fit residues: 1.2333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.0770 chunk 15 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- 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: 0.6484 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3406 Z= 0.160 Angle : 0.555 4.860 4624 Z= 0.286 Chirality : 0.044 0.145 495 Planarity : 0.004 0.044 593 Dihedral : 4.715 17.671 472 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 1.38 % Allowed : 20.66 % Favored : 77.96 % 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: -2.16 (0.39), residues: 419 helix: -3.94 (0.68), residues: 24 sheet: -0.13 (0.54), residues: 105 loop : -1.83 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 48 HIS 0.002 0.001 HIS L 90 PHE 0.016 0.001 PHE H 68 TYR 0.017 0.001 TYR H 95 ARG 0.006 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 49 average time/residue: 0.1663 time to fit residues: 10.0794 Evaluate side-chains 40 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.425 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0423 time to fit residues: 0.5700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.0970 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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: 0.6504 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3406 Z= 0.207 Angle : 0.578 5.701 4624 Z= 0.299 Chirality : 0.044 0.148 495 Planarity : 0.004 0.046 593 Dihedral : 4.778 17.932 472 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 2.20 % Allowed : 23.42 % Favored : 74.38 % 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: -2.16 (0.39), residues: 419 helix: -3.75 (0.76), residues: 24 sheet: -0.06 (0.56), residues: 103 loop : -1.87 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 36 HIS 0.003 0.001 HIS L 90 PHE 0.017 0.001 PHE H 68 TYR 0.017 0.001 TYR H 95 ARG 0.006 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 46 average time/residue: 0.1855 time to fit residues: 10.3979 Evaluate side-chains 45 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.372 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1102 time to fit residues: 1.3194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.5437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3406 Z= 0.196 Angle : 0.556 5.074 4624 Z= 0.290 Chirality : 0.044 0.147 495 Planarity : 0.004 0.044 593 Dihedral : 4.740 17.563 472 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 1.38 % Allowed : 24.24 % Favored : 74.38 % 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: -2.18 (0.39), residues: 419 helix: -3.62 (0.78), residues: 24 sheet: 0.01 (0.56), residues: 103 loop : -1.94 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 36 HIS 0.002 0.001 HIS L 93 PHE 0.019 0.001 PHE H 68 TYR 0.017 0.001 TYR H 95 ARG 0.005 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 49 average time/residue: 0.1564 time to fit residues: 9.4007 Evaluate side-chains 42 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.314 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0286 time to fit residues: 0.4663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 28 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.5631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3406 Z= 0.234 Angle : 0.592 5.555 4624 Z= 0.307 Chirality : 0.045 0.144 495 Planarity : 0.004 0.045 593 Dihedral : 4.883 17.979 472 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 2.20 % Allowed : 23.42 % Favored : 74.38 % 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: -2.26 (0.39), residues: 419 helix: -3.54 (0.80), residues: 24 sheet: -0.16 (0.55), residues: 103 loop : -1.97 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 36 HIS 0.002 0.001 HIS L 90 PHE 0.018 0.001 PHE H 68 TYR 0.016 0.001 TYR H 95 ARG 0.005 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 47 average time/residue: 0.1715 time to fit residues: 9.9698 Evaluate side-chains 50 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.387 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0975 time to fit residues: 1.3744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.0040 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 0.1980 chunk 36 optimal weight: 3.9990 chunk 31 optimal weight: 0.0870 chunk 3 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.3170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 moved from start: 0.5633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3406 Z= 0.129 Angle : 0.545 5.545 4624 Z= 0.276 Chirality : 0.043 0.145 495 Planarity : 0.004 0.047 593 Dihedral : 4.327 16.985 472 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 0.83 % Allowed : 23.97 % Favored : 75.21 % 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: 419 helix: -3.81 (0.72), residues: 25 sheet: 0.52 (0.58), residues: 99 loop : -1.91 (0.33), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 36 HIS 0.004 0.001 HIS L 93 PHE 0.014 0.001 PHE H 68 TYR 0.021 0.001 TYR H 95 ARG 0.004 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.385 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 46 average time/residue: 0.1733 time to fit residues: 9.7787 Evaluate side-chains 40 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.391 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0350 time to fit residues: 0.5722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 0.2980 chunk 29 optimal weight: 4.9990 chunk 4 optimal weight: 0.0060 chunk 8 optimal weight: 4.9990 chunk 31 optimal weight: 0.0770 chunk 13 optimal weight: 0.0000 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.2758 ------------------------------------------------------------------------------- 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: 0.6477 moved from start: 0.5729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3406 Z= 0.126 Angle : 0.552 7.021 4624 Z= 0.275 Chirality : 0.044 0.138 495 Planarity : 0.004 0.047 593 Dihedral : 4.192 17.357 472 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 0.83 % Allowed : 26.17 % Favored : 73.00 % 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: -1.86 (0.40), residues: 419 helix: -3.80 (0.73), residues: 25 sheet: 0.41 (0.56), residues: 105 loop : -1.75 (0.34), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.002 0.001 HIS L 93 PHE 0.022 0.001 PHE H 68 TYR 0.020 0.001 TYR H 95 ARG 0.004 0.000 ARG L 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 41 average time/residue: 0.1888 time to fit residues: 9.6168 Evaluate side-chains 42 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.415 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0428 time to fit residues: 0.6623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.0970 chunk 14 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.091400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.073816 restraints weight = 12536.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.076222 restraints weight = 6592.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.077820 restraints weight = 4527.074| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.5785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3406 Z= 0.142 Angle : 0.550 6.531 4624 Z= 0.275 Chirality : 0.044 0.133 495 Planarity : 0.004 0.046 593 Dihedral : 4.210 17.351 472 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 0.28 % Allowed : 26.17 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.40), residues: 419 helix: -3.74 (0.76), residues: 25 sheet: 0.20 (0.56), residues: 109 loop : -1.62 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 36 HIS 0.003 0.001 HIS L 93 PHE 0.021 0.001 PHE H 68 TYR 0.019 0.001 TYR H 95 ARG 0.004 0.000 ARG L 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1274.12 seconds wall clock time: 23 minutes 46.11 seconds (1426.11 seconds total)