Starting phenix.real_space_refine on Thu Nov 14 02:27:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjn_40095/11_2024/8gjn_40095.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjn_40095/11_2024/8gjn_40095.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/8gjn_40095/11_2024/8gjn_40095.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjn_40095/11_2024/8gjn_40095.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjn_40095/11_2024/8gjn_40095.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjn_40095/11_2024/8gjn_40095.cif" } 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= 0.000 sd= 0.011 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 15 5.16 5 C 2102 2.51 5 N 550 2.21 5 O 652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 3319 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 934 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "B" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1552 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.48, per 1000 atoms: 1.35 Number of scatterers: 3319 At special positions: 0 Unit cell: (86.625, 54.45, 107.25, 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 15 16.00 O 652 8.00 N 550 7.00 C 2102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 115 " distance=2.04 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 108 " distance=2.05 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG C 601 " - " ASN C 343 " Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 435.1 milliseconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 8 sheets defined 13.1% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.719A pdb=" N TYR A 51 " --> pdb=" O PHE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 85 removed outlier: 4.450A pdb=" N GLY A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.758A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.106A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.074A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 411 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.661A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 6.213A pdb=" N GLU A 29 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N MET A 53 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY A 69 " --> pdb=" O MET A 53 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP A 55 " --> pdb=" O ILE A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 42 Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 26 removed outlier: 4.157A pdb=" N VAL B 39 " --> pdb=" O ILE B 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 30 through 33 removed outlier: 6.388A pdb=" N TRP B 55 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 33 Processing sheet with id=AA6, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'C' and resid 452 through 454 108 hydrogen bonds defined for protein. 249 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: 0.90 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 801 1.33 - 1.46: 791 1.46 - 1.58: 1791 1.58 - 1.70: 0 1.70 - 1.82: 18 Bond restraints: 3401 Sorted by residual: bond pdb=" N ILE C 472 " pdb=" CA ILE C 472 " ideal model delta sigma weight residual 1.456 1.497 -0.040 1.19e-02 7.06e+03 1.14e+01 bond pdb=" N CYS A 115 " pdb=" CA CYS A 115 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.17e-02 7.31e+03 1.12e+01 bond pdb=" N VAL A 37 " pdb=" CA VAL A 37 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.17e-02 7.31e+03 1.04e+01 bond pdb=" N ARG C 457 " pdb=" CA ARG C 457 " ideal model delta sigma weight residual 1.455 1.493 -0.037 1.18e-02 7.18e+03 9.94e+00 bond pdb=" N VAL C 524 " pdb=" CA VAL C 524 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.10e-02 8.26e+03 9.93e+00 ... (remaining 3396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 3361 1.75 - 3.50: 1059 3.50 - 5.25: 180 5.25 - 7.00: 13 7.00 - 8.75: 2 Bond angle restraints: 4615 Sorted by residual: angle pdb=" N PHE C 490 " pdb=" CA PHE C 490 " pdb=" C PHE C 490 " ideal model delta sigma weight residual 109.24 100.49 8.75 1.39e+00 5.18e-01 3.96e+01 angle pdb=" N CYS C 488 " pdb=" CA CYS C 488 " pdb=" C CYS C 488 " ideal model delta sigma weight residual 109.54 101.74 7.80 1.37e+00 5.33e-01 3.25e+01 angle pdb=" N TYR C 489 " pdb=" CA TYR C 489 " pdb=" C TYR C 489 " ideal model delta sigma weight residual 110.43 116.65 -6.22 1.31e+00 5.83e-01 2.25e+01 angle pdb=" C GLY A 27 " pdb=" N PRO A 28 " pdb=" CA PRO A 28 " ideal model delta sigma weight residual 119.90 124.65 -4.75 1.02e+00 9.61e-01 2.16e+01 angle pdb=" C LYS B 80 " pdb=" CA LYS B 80 " pdb=" CB LYS B 80 " ideal model delta sigma weight residual 116.54 111.44 5.10 1.15e+00 7.56e-01 1.97e+01 ... (remaining 4610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 1851 17.49 - 34.98: 134 34.98 - 52.47: 21 52.47 - 69.95: 21 69.95 - 87.44: 2 Dihedral angle restraints: 2029 sinusoidal: 809 harmonic: 1220 Sorted by residual: dihedral pdb=" CA ASP B 61 " pdb=" C ASP B 61 " pdb=" N GLY B 62 " pdb=" CA GLY B 62 " ideal model delta harmonic sigma weight residual 180.00 150.37 29.63 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA SER B 97 " pdb=" C SER B 97 " pdb=" N PRO B 98 " pdb=" CA PRO B 98 " ideal model delta harmonic sigma weight residual 180.00 153.41 26.59 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA ALA A 111 " pdb=" C ALA A 111 " pdb=" N VAL A 112 " pdb=" CA VAL A 112 " ideal model delta harmonic sigma weight residual 180.00 153.44 26.56 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 2026 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 226 0.060 - 0.120: 168 0.120 - 0.180: 80 0.180 - 0.240: 17 0.240 - 0.300: 5 Chirality restraints: 496 Sorted by residual: chirality pdb=" CA PHE C 464 " pdb=" N PHE C 464 " pdb=" C PHE C 464 " pdb=" CB PHE C 464 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA PRO A 33 " pdb=" N PRO A 33 " pdb=" C PRO A 33 " pdb=" CB PRO A 33 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA LEU C 461 " pdb=" N LEU C 461 " pdb=" C LEU C 461 " pdb=" CB LEU C 461 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 493 not shown) Planarity restraints: 596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 601 " -0.104 2.00e-02 2.50e+03 8.66e-02 9.37e+01 pdb=" C7 NAG C 601 " 0.024 2.00e-02 2.50e+03 pdb=" C8 NAG C 601 " -0.076 2.00e-02 2.50e+03 pdb=" N2 NAG C 601 " 0.142 2.00e-02 2.50e+03 pdb=" O7 NAG C 601 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 380 " -0.094 2.00e-02 2.50e+03 5.01e-02 5.01e+01 pdb=" CG TYR C 380 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR C 380 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TYR C 380 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR C 380 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR C 380 " 0.029 2.00e-02 2.50e+03 pdb=" CZ TYR C 380 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 380 " -0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 69 " -0.071 2.00e-02 2.50e+03 4.07e-02 3.31e+01 pdb=" CG TYR B 69 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR B 69 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TYR B 69 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR B 69 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR B 69 " 0.034 2.00e-02 2.50e+03 pdb=" CZ TYR B 69 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 69 " -0.063 2.00e-02 2.50e+03 ... (remaining 593 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 1409 2.92 - 3.42: 3062 3.42 - 3.91: 5638 3.91 - 4.41: 6166 4.41 - 4.90: 10475 Nonbonded interactions: 26750 Sorted by model distance: nonbonded pdb=" O TYR B 111 " pdb=" OG1 THR C 478 " model vdw 2.431 3.040 nonbonded pdb=" OG1 THR C 333 " pdb=" N ASN C 334 " model vdw 2.451 3.120 nonbonded pdb=" O GLN A 24 " pdb=" N LYS A 42 " model vdw 2.470 3.120 nonbonded pdb=" OH TYR C 453 " pdb=" OE1 GLN C 493 " model vdw 2.482 3.040 nonbonded pdb=" OD1 ASP C 442 " pdb=" OH TYR C 451 " model vdw 2.506 3.040 ... (remaining 26745 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.010 Normalize map: mean=0, sd=1: 6.650 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.410 Find NCS groups from input model: 0.040 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 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 : 0.013 0.046 3401 Z= 0.832 Angle : 1.648 8.747 4615 Z= 1.119 Chirality : 0.093 0.300 496 Planarity : 0.013 0.098 595 Dihedral : 14.166 87.440 1237 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 1.10 % Allowed : 7.40 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -2.73 (0.37), residues: 415 helix: -3.89 (0.58), residues: 26 sheet: -1.56 (0.46), residues: 116 loop : -1.77 (0.33), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.009 TRP C 353 HIS 0.001 0.000 HIS C 519 PHE 0.062 0.008 PHE C 464 TYR 0.094 0.014 TYR C 380 ARG 0.009 0.001 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 LYS cc_start: 0.7469 (tttt) cc_final: 0.7225 (tttt) REVERT: C 367 VAL cc_start: 0.8406 (t) cc_final: 0.8095 (p) outliers start: 4 outliers final: 0 residues processed: 70 average time/residue: 0.1618 time to fit residues: 13.9381 Evaluate side-chains 62 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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: 0.5980 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 0.0980 chunk 12 optimal weight: 0.0010 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 36 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 overall best weight: 0.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 62 GLN B 57 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3401 Z= 0.196 Angle : 0.597 8.968 4615 Z= 0.313 Chirality : 0.043 0.196 496 Planarity : 0.004 0.032 595 Dihedral : 5.291 35.193 488 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.19 % Allowed : 10.68 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.85 (0.39), residues: 415 helix: -3.79 (0.62), residues: 27 sheet: -1.23 (0.45), residues: 133 loop : -0.87 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 353 HIS 0.001 0.000 HIS C 519 PHE 0.016 0.002 PHE C 497 TYR 0.017 0.002 TYR C 380 ARG 0.004 0.000 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7156 (tttt) cc_final: 0.6884 (tttt) REVERT: B 83 SER cc_start: 0.6779 (p) cc_final: 0.6513 (p) REVERT: C 354 ASN cc_start: 0.8145 (m-40) cc_final: 0.7895 (m110) REVERT: C 423 TYR cc_start: 0.8262 (t80) cc_final: 0.8045 (t80) REVERT: C 492 LEU cc_start: 0.8426 (mp) cc_final: 0.8192 (mp) REVERT: C 508 TYR cc_start: 0.8622 (m-10) cc_final: 0.8354 (m-10) outliers start: 8 outliers final: 4 residues processed: 75 average time/residue: 0.1313 time to fit residues: 12.7041 Evaluate side-chains 74 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 493 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.0670 chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 39 optimal weight: 0.0670 chunk 32 optimal weight: 0.0870 chunk 12 optimal weight: 0.5980 chunk 29 optimal weight: 0.1980 chunk 35 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 18 optimal weight: 0.0170 overall best weight: 0.0872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN B 57 GLN C 360 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3401 Z= 0.125 Angle : 0.514 7.564 4615 Z= 0.265 Chirality : 0.042 0.204 496 Planarity : 0.004 0.037 595 Dihedral : 4.386 29.359 488 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.64 % Allowed : 14.52 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.40 (0.39), residues: 415 helix: -3.08 (0.76), residues: 27 sheet: -0.78 (0.45), residues: 130 loop : -0.71 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.001 0.000 HIS C 519 PHE 0.010 0.001 PHE C 497 TYR 0.010 0.001 TYR C 380 ARG 0.002 0.000 ARG A 119 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 438 SER cc_start: 0.8581 (m) cc_final: 0.7996 (p) REVERT: C 492 LEU cc_start: 0.8365 (mp) cc_final: 0.8139 (mp) REVERT: C 508 TYR cc_start: 0.8638 (m-10) cc_final: 0.8413 (m-10) REVERT: C 514 SER cc_start: 0.8445 (t) cc_final: 0.8210 (p) outliers start: 6 outliers final: 5 residues processed: 80 average time/residue: 0.1220 time to fit residues: 12.6001 Evaluate side-chains 83 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 493 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 0.0050 chunk 10 optimal weight: 0.5980 chunk 32 optimal weight: 0.2980 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3401 Z= 0.247 Angle : 0.572 10.302 4615 Z= 0.293 Chirality : 0.043 0.214 496 Planarity : 0.004 0.039 595 Dihedral : 4.927 39.218 488 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.92 % Allowed : 15.62 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.50 (0.39), residues: 415 helix: -2.95 (0.74), residues: 34 sheet: -0.70 (0.43), residues: 143 loop : -0.80 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 55 HIS 0.000 0.000 HIS C 519 PHE 0.010 0.002 PHE C 486 TYR 0.021 0.002 TYR C 423 ARG 0.002 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: C 478 THR cc_start: 0.8125 (m) cc_final: 0.7802 (p) REVERT: C 503 VAL cc_start: 0.8366 (t) cc_final: 0.7975 (p) outliers start: 7 outliers final: 6 residues processed: 76 average time/residue: 0.1218 time to fit residues: 12.0916 Evaluate side-chains 75 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 493 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 26 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 0.0980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3401 Z= 0.203 Angle : 0.543 7.456 4615 Z= 0.274 Chirality : 0.042 0.223 496 Planarity : 0.004 0.038 595 Dihedral : 4.793 34.555 488 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.19 % Allowed : 16.99 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.49 (0.39), residues: 415 helix: -2.99 (0.74), residues: 34 sheet: -0.72 (0.43), residues: 143 loop : -0.77 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.001 0.000 HIS A 60 PHE 0.008 0.001 PHE C 400 TYR 0.019 0.001 TYR C 423 ARG 0.001 0.000 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: C 353 TRP cc_start: 0.8770 (p-90) cc_final: 0.8117 (p-90) REVERT: C 478 THR cc_start: 0.8141 (m) cc_final: 0.7811 (p) REVERT: C 508 TYR cc_start: 0.8668 (m-10) cc_final: 0.8441 (m-10) outliers start: 8 outliers final: 7 residues processed: 75 average time/residue: 0.1230 time to fit residues: 12.0682 Evaluate side-chains 75 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 493 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 0.0970 chunk 28 optimal weight: 0.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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: 0.6904 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3401 Z= 0.265 Angle : 0.581 7.175 4615 Z= 0.295 Chirality : 0.043 0.236 496 Planarity : 0.004 0.042 595 Dihedral : 5.172 37.218 488 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.56 % Allowed : 16.44 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.47 (0.40), residues: 415 helix: -3.17 (0.71), residues: 34 sheet: -0.61 (0.45), residues: 136 loop : -0.80 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.001 0.000 HIS A 60 PHE 0.010 0.001 PHE C 400 TYR 0.019 0.002 TYR C 423 ARG 0.003 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 HIS cc_start: 0.8476 (OUTLIER) cc_final: 0.8176 (p-80) REVERT: C 478 THR cc_start: 0.8075 (m) cc_final: 0.7776 (p) outliers start: 13 outliers final: 12 residues processed: 76 average time/residue: 0.1091 time to fit residues: 11.0389 Evaluate side-chains 77 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 511 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 0.0970 chunk 23 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 3401 Z= 0.293 Angle : 0.595 8.088 4615 Z= 0.305 Chirality : 0.043 0.132 496 Planarity : 0.004 0.043 595 Dihedral : 5.314 34.754 488 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.11 % Allowed : 15.34 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.68 (0.40), residues: 415 helix: -3.28 (0.71), residues: 34 sheet: -0.77 (0.43), residues: 143 loop : -0.93 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 128 HIS 0.001 0.000 HIS A 60 PHE 0.011 0.001 PHE C 400 TYR 0.021 0.002 TYR C 423 ARG 0.006 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 HIS cc_start: 0.8439 (OUTLIER) cc_final: 0.8215 (p-80) REVERT: A 116 THR cc_start: 0.7182 (OUTLIER) cc_final: 0.6938 (m) REVERT: B 65 LYS cc_start: 0.7543 (tptt) cc_final: 0.7234 (tptt) REVERT: C 478 THR cc_start: 0.8061 (m) cc_final: 0.7764 (p) outliers start: 15 outliers final: 10 residues processed: 70 average time/residue: 0.1402 time to fit residues: 12.3551 Evaluate side-chains 70 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 493 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 3401 Z= 0.313 Angle : 0.605 8.695 4615 Z= 0.310 Chirality : 0.044 0.263 496 Planarity : 0.004 0.042 595 Dihedral : 5.416 35.902 488 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.84 % Allowed : 16.16 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.66 (0.40), residues: 415 helix: -3.19 (0.73), residues: 34 sheet: -0.68 (0.43), residues: 143 loop : -0.99 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 55 HIS 0.001 0.000 HIS A 60 PHE 0.011 0.002 PHE C 400 TYR 0.022 0.002 TYR C 423 ARG 0.005 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 65 LYS cc_start: 0.7500 (tptt) cc_final: 0.7167 (tptt) REVERT: C 478 THR cc_start: 0.8033 (m) cc_final: 0.7731 (p) outliers start: 14 outliers final: 13 residues processed: 67 average time/residue: 0.1501 time to fit residues: 12.5823 Evaluate side-chains 72 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 511 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.0870 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.0970 chunk 26 optimal weight: 0.2980 chunk 39 optimal weight: 0.5980 chunk 36 optimal weight: 0.0870 chunk 31 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 overall best weight: 0.1734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3401 Z= 0.148 Angle : 0.554 8.884 4615 Z= 0.280 Chirality : 0.043 0.261 496 Planarity : 0.004 0.037 595 Dihedral : 4.843 31.092 488 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.29 % Allowed : 16.71 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.49 (0.40), residues: 415 helix: -3.23 (0.68), residues: 34 sheet: -0.59 (0.42), residues: 144 loop : -0.83 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 55 HIS 0.002 0.001 HIS A 60 PHE 0.009 0.001 PHE C 497 TYR 0.006 0.001 TYR B 106 ARG 0.003 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 423 TYR cc_start: 0.8457 (t80) cc_final: 0.8192 (t80) REVERT: C 478 THR cc_start: 0.7979 (m) cc_final: 0.7607 (p) outliers start: 12 outliers final: 10 residues processed: 72 average time/residue: 0.1494 time to fit residues: 13.4577 Evaluate side-chains 73 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 32 optimal weight: 0.0050 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3401 Z= 0.262 Angle : 0.604 9.187 4615 Z= 0.305 Chirality : 0.044 0.284 496 Planarity : 0.004 0.042 595 Dihedral : 5.181 34.430 488 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.47 % Allowed : 17.81 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.50 (0.40), residues: 415 helix: -3.09 (0.74), residues: 34 sheet: -0.64 (0.42), residues: 145 loop : -0.82 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 55 HIS 0.001 0.000 HIS A 60 PHE 0.016 0.002 PHE A 127 TYR 0.015 0.001 TYR B 111 ARG 0.004 0.000 ARG C 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 423 TYR cc_start: 0.8517 (t80) cc_final: 0.8020 (t80) REVERT: C 478 THR cc_start: 0.8011 (m) cc_final: 0.7686 (p) outliers start: 9 outliers final: 8 residues processed: 64 average time/residue: 0.1502 time to fit residues: 12.0604 Evaluate side-chains 67 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.1980 chunk 36 optimal weight: 0.0470 chunk 21 optimal weight: 0.0470 chunk 27 optimal weight: 0.0870 chunk 1 optimal weight: 0.0570 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 39 optimal weight: 0.2980 overall best weight: 0.0872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.163177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.137407 restraints weight = 5779.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.141730 restraints weight = 2906.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.144408 restraints weight = 1758.426| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3401 Z= 0.149 Angle : 0.594 9.141 4615 Z= 0.300 Chirality : 0.042 0.146 496 Planarity : 0.004 0.034 595 Dihedral : 4.722 27.631 488 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.19 % Allowed : 18.36 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.23 (0.40), residues: 415 helix: -3.04 (0.68), residues: 34 sheet: -0.31 (0.45), residues: 131 loop : -0.72 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 55 HIS 0.000 0.000 HIS A 60 PHE 0.028 0.001 PHE A 127 TYR 0.006 0.001 TYR C 380 ARG 0.002 0.000 ARG C 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1541.10 seconds wall clock time: 28 minutes 38.73 seconds (1718.73 seconds total)