Starting phenix.real_space_refine on Mon Sep 23 14:59:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqf_28537/09_2024/8eqf_28537.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqf_28537/09_2024/8eqf_28537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqf_28537/09_2024/8eqf_28537.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqf_28537/09_2024/8eqf_28537.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqf_28537/09_2024/8eqf_28537.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqf_28537/09_2024/8eqf_28537.cif" } resolution = 3.16 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= 0.008 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 2133 2.51 5 N 556 2.21 5 O 644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3348 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "H" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 976 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "L" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 808 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 97} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.95, per 1000 atoms: 1.18 Number of scatterers: 3348 At special positions: 0 Unit cell: (54.516, 64.428, 108.206, 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 644 8.00 N 556 7.00 C 2133 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 354 " distance=2.03 Simple disulfide: pdb=" SG CYS A 372 " - pdb=" SG CYS A 425 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 481 " 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 88 " distance=2.03 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 BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 336 " Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 399.5 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 772 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 8 sheets defined 9.5% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 330 through 336 removed outlier: 3.772A pdb=" N VAL A 334 " --> pdb=" O PRO A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 346 removed outlier: 3.509A pdb=" N TRP A 346 " --> pdb=" O VAL A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 403 removed outlier: 4.421A pdb=" N ARG A 401 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 415 removed outlier: 3.529A pdb=" N TYR A 414 " --> pdb=" O LYS A 410 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.980A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.986A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.083A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 347 through 351 Processing sheet with id=AA2, first strand: chain 'A' and resid 354 through 355 removed outlier: 6.928A pdb=" N CYS A 354 " --> pdb=" O CYS A 518 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 445 through 447 Processing sheet with id=AA4, first strand: chain 'A' and resid 466 through 467 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 11 removed outlier: 5.837A pdb=" N GLY H 10 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.062A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.510A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 100 hydrogen bonds defined for protein. 243 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: 1.01 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: 1058 1.34 - 1.46: 917 1.46 - 1.58: 1445 1.58 - 1.70: 0 1.70 - 1.81: 18 Bond restraints: 3438 Sorted by residual: bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.75e+00 bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.439 -0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" CA ASN A 433 " pdb=" CB ASN A 433 " ideal model delta sigma weight residual 1.530 1.514 0.015 1.43e-02 4.89e+03 1.14e+00 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.05e+00 ... (remaining 3433 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 4397 1.09 - 2.18: 227 2.18 - 3.27: 34 3.27 - 4.36: 15 4.36 - 5.45: 1 Bond angle restraints: 4674 Sorted by residual: angle pdb=" N ALA L 51 " pdb=" CA ALA L 51 " pdb=" CB ALA L 51 " ideal model delta sigma weight residual 114.17 110.43 3.74 1.14e+00 7.69e-01 1.07e+01 angle pdb=" C ASP A 357 " pdb=" CA ASP A 357 " pdb=" CB ASP A 357 " ideal model delta sigma weight residual 110.78 114.52 -3.74 1.60e+00 3.91e-01 5.45e+00 angle pdb=" N LEU A 434 " pdb=" CA LEU A 434 " pdb=" CB LEU A 434 " ideal model delta sigma weight residual 114.27 110.50 3.77 1.64e+00 3.72e-01 5.30e+00 angle pdb=" CA ASP A 357 " pdb=" CB ASP A 357 " pdb=" CG ASP A 357 " ideal model delta sigma weight residual 112.60 114.65 -2.05 1.00e+00 1.00e+00 4.21e+00 angle pdb=" C ASN A 433 " pdb=" CA ASN A 433 " pdb=" CB ASN A 433 " ideal model delta sigma weight residual 109.75 112.89 -3.14 1.65e+00 3.67e-01 3.62e+00 ... (remaining 4669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.00: 1916 23.00 - 46.00: 103 46.00 - 69.00: 13 69.00 - 92.00: 2 92.00 - 115.00: 3 Dihedral angle restraints: 2037 sinusoidal: 813 harmonic: 1224 Sorted by residual: dihedral pdb=" CB CYS A 384 " pdb=" SG CYS A 384 " pdb=" SG CYS A 518 " pdb=" CB CYS A 518 " ideal model delta sinusoidal sigma weight residual 93.00 133.02 -40.02 1 1.00e+01 1.00e-02 2.25e+01 dihedral pdb=" C2 NAG B 2 " pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " pdb=" C5 NAG B 2 " ideal model delta sinusoidal sigma weight residual -62.96 52.04 -115.00 1 3.00e+01 1.11e-03 1.52e+01 dihedral pdb=" C1 NAG B 2 " pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " pdb=" C6 NAG B 2 " ideal model delta sinusoidal sigma weight residual 171.16 -78.51 -110.33 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 2034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 307 0.034 - 0.068: 143 0.068 - 0.102: 27 0.102 - 0.136: 19 0.136 - 0.170: 4 Chirality restraints: 500 Sorted by residual: chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 336 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CA ILE A 427 " pdb=" N ILE A 427 " pdb=" C ILE A 427 " pdb=" CB ILE A 427 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.77e-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 2.58 -0.14 2.00e-01 2.50e+01 4.76e-01 ... (remaining 497 not shown) Planarity restraints: 602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 357 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.87e+00 pdb=" CG ASP A 357 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASP A 357 " 0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP A 357 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 336 " -0.013 2.00e-02 2.50e+03 1.27e-02 2.01e+00 pdb=" CG ASN A 336 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN A 336 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 336 " 0.019 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 357 " 0.006 2.00e-02 2.50e+03 1.23e-02 1.52e+00 pdb=" C ASP A 357 " -0.021 2.00e-02 2.50e+03 pdb=" O ASP A 357 " 0.008 2.00e-02 2.50e+03 pdb=" N TYR A 358 " 0.007 2.00e-02 2.50e+03 ... (remaining 599 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 30 2.58 - 3.16: 2736 3.16 - 3.74: 4913 3.74 - 4.32: 7512 4.32 - 4.90: 12547 Nonbonded interactions: 27738 Sorted by model distance: nonbonded pdb=" O4 NAG B 1 " pdb=" O6 NAG B 2 " model vdw 1.998 3.040 nonbonded pdb=" O3 NAG B 1 " pdb=" O7 NAG B 1 " model vdw 2.012 3.040 nonbonded pdb=" O ASP H 62 " pdb=" OG SER H 63 " model vdw 2.038 3.040 nonbonded pdb=" O ASP A 357 " pdb=" OD1 ASP A 357 " model vdw 2.142 3.040 nonbonded pdb=" OH TYR A 482 " pdb=" O TYR L 92 " model vdw 2.289 3.040 ... (remaining 27733 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.050 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: 23.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 3438 Z= 0.323 Angle : 0.571 5.445 4674 Z= 0.317 Chirality : 0.043 0.170 500 Planarity : 0.003 0.026 601 Dihedral : 14.570 115.000 1247 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.38 (0.42), residues: 416 helix: -4.44 (0.43), residues: 27 sheet: -0.01 (0.44), residues: 136 loop : 0.23 (0.41), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 429 HIS 0.002 0.001 HIS L 100 PHE 0.008 0.001 PHE A 393 TYR 0.011 0.001 TYR H 95 ARG 0.003 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.386 Fit side-chains REVERT: A 436 SER cc_start: 0.8112 (m) cc_final: 0.7883 (m) REVERT: A 488 TYR cc_start: 0.8303 (m-80) cc_final: 0.7914 (m-80) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1693 time to fit residues: 10.6963 Evaluate side-chains 50 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.0970 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.1980 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 GLN H 57 ASN L 30 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 3438 Z= 0.469 Angle : 0.677 9.619 4674 Z= 0.342 Chirality : 0.049 0.190 500 Planarity : 0.004 0.031 601 Dihedral : 6.813 47.470 513 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.10 % Allowed : 4.97 % Favored : 93.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.33 (0.41), residues: 416 helix: -4.56 (0.40), residues: 27 sheet: 0.17 (0.45), residues: 135 loop : 0.18 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 429 HIS 0.002 0.001 HIS L 30 PHE 0.012 0.002 PHE A 393 TYR 0.014 0.002 TYR A 362 ARG 0.007 0.001 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.381 Fit side-chains REVERT: A 488 TYR cc_start: 0.8393 (m-80) cc_final: 0.7996 (m-80) outliers start: 4 outliers final: 3 residues processed: 55 average time/residue: 0.1444 time to fit residues: 10.0628 Evaluate side-chains 55 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 30 optimal weight: 0.1980 chunk 25 optimal weight: 0.0980 chunk 10 optimal weight: 0.1980 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 0.0870 chunk 33 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 chunk 12 optimal weight: 0.6980 chunk 29 optimal weight: 0.2980 overall best weight: 0.1758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 ASN L 30 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3438 Z= 0.228 Angle : 0.557 5.898 4674 Z= 0.287 Chirality : 0.044 0.162 500 Planarity : 0.004 0.034 601 Dihedral : 6.167 45.508 513 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.38 % Allowed : 5.52 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.23 (0.41), residues: 416 helix: -4.44 (0.45), residues: 27 sheet: 0.05 (0.44), residues: 136 loop : 0.38 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 429 HIS 0.001 0.000 HIS L 100 PHE 0.008 0.001 PHE L 98 TYR 0.010 0.001 TYR A 501 ARG 0.006 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.379 Fit side-chains REVERT: A 488 TYR cc_start: 0.8363 (m-80) cc_final: 0.7950 (m-80) REVERT: H 95 TYR cc_start: 0.8536 (m-80) cc_final: 0.8291 (m-80) outliers start: 5 outliers final: 4 residues processed: 59 average time/residue: 0.1412 time to fit residues: 10.5132 Evaluate side-chains 59 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 487 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 0.0570 chunk 17 optimal weight: 0.0670 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 35 optimal weight: 0.0970 chunk 10 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 overall best weight: 0.2234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3438 Z= 0.265 Angle : 0.557 4.934 4674 Z= 0.287 Chirality : 0.044 0.163 500 Planarity : 0.004 0.035 601 Dihedral : 5.888 45.214 513 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.38 % Allowed : 7.73 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.04 (0.42), residues: 416 helix: -4.02 (0.70), residues: 20 sheet: 0.20 (0.44), residues: 136 loop : 0.41 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 429 HIS 0.001 0.000 HIS L 100 PHE 0.008 0.001 PHE A 393 TYR 0.014 0.001 TYR A 501 ARG 0.003 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.369 Fit side-chains REVERT: A 488 TYR cc_start: 0.8364 (m-80) cc_final: 0.7902 (m-80) REVERT: H 95 TYR cc_start: 0.8564 (m-80) cc_final: 0.8324 (m-80) outliers start: 5 outliers final: 3 residues processed: 57 average time/residue: 0.1385 time to fit residues: 9.9535 Evaluate side-chains 57 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 507 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 chunk 29 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 27 optimal weight: 0.0970 chunk 20 optimal weight: 0.4980 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.2980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 ASN L 30 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 3438 Z= 0.423 Angle : 0.610 5.414 4674 Z= 0.316 Chirality : 0.046 0.160 500 Planarity : 0.004 0.038 601 Dihedral : 5.917 46.462 513 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.10 % Allowed : 9.67 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.29 (0.40), residues: 416 helix: -4.28 (0.56), residues: 27 sheet: 0.23 (0.45), residues: 129 loop : 0.17 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 47 HIS 0.001 0.000 HIS L 100 PHE 0.012 0.002 PHE A 393 TYR 0.019 0.002 TYR A 501 ARG 0.006 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 0.388 Fit side-chains REVERT: A 488 TYR cc_start: 0.8407 (m-80) cc_final: 0.8047 (m-80) REVERT: H 95 TYR cc_start: 0.8591 (m-80) cc_final: 0.8238 (m-80) REVERT: L 91 SER cc_start: 0.8251 (p) cc_final: 0.8036 (m) outliers start: 4 outliers final: 3 residues processed: 59 average time/residue: 0.1206 time to fit residues: 9.2588 Evaluate side-chains 60 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 507 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.3980 chunk 9 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 18 optimal weight: 0.0770 chunk 3 optimal weight: 0.0870 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 0.1980 chunk 38 optimal weight: 0.0980 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 0.1980 overall best weight: 0.1316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3438 Z= 0.183 Angle : 0.524 4.676 4674 Z= 0.273 Chirality : 0.043 0.159 500 Planarity : 0.004 0.035 601 Dihedral : 5.375 44.303 513 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.38 % Allowed : 9.67 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.02 (0.42), residues: 416 helix: -3.97 (0.75), residues: 20 sheet: 0.22 (0.44), residues: 136 loop : 0.36 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 429 HIS 0.001 0.000 HIS L 100 PHE 0.008 0.001 PHE L 98 TYR 0.014 0.001 TYR A 501 ARG 0.006 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.375 Fit side-chains REVERT: A 348 ARG cc_start: 0.8562 (ttm170) cc_final: 0.8154 (ttm170) REVERT: A 488 TYR cc_start: 0.8356 (m-80) cc_final: 0.7919 (m-80) REVERT: H 95 TYR cc_start: 0.8545 (m-80) cc_final: 0.8317 (m-80) REVERT: L 91 SER cc_start: 0.8342 (p) cc_final: 0.8118 (m) outliers start: 5 outliers final: 4 residues processed: 61 average time/residue: 0.1519 time to fit residues: 11.6714 Evaluate side-chains 60 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 487 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.5980 chunk 22 optimal weight: 0.0980 chunk 33 optimal weight: 0.9990 chunk 39 optimal weight: 0.3980 chunk 24 optimal weight: 0.0470 chunk 18 optimal weight: 0.0060 chunk 15 optimal weight: 0.0670 chunk 23 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.2980 chunk 25 optimal weight: 0.0980 overall best weight: 0.0632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 ASN L 30 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3438 Z= 0.138 Angle : 0.494 4.339 4674 Z= 0.259 Chirality : 0.042 0.162 500 Planarity : 0.003 0.034 601 Dihedral : 5.001 41.870 513 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.10 % Allowed : 10.22 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.14 (0.42), residues: 416 helix: -4.01 (0.73), residues: 20 sheet: 0.35 (0.44), residues: 137 loop : 0.43 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 429 HIS 0.001 0.000 HIS L 100 PHE 0.006 0.001 PHE L 98 TYR 0.012 0.001 TYR A 501 ARG 0.005 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 0.356 Fit side-chains REVERT: A 348 ARG cc_start: 0.8530 (ttm170) cc_final: 0.8120 (ttm170) REVERT: A 488 TYR cc_start: 0.8271 (m-80) cc_final: 0.7822 (m-80) outliers start: 4 outliers final: 3 residues processed: 59 average time/residue: 0.1471 time to fit residues: 10.8545 Evaluate side-chains 59 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 487 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 0.0270 chunk 31 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 chunk 37 optimal weight: 0.6980 chunk 34 optimal weight: 0.2980 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 0.2980 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 overall best weight: 0.2838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3438 Z= 0.315 Angle : 0.557 4.881 4674 Z= 0.292 Chirality : 0.044 0.170 500 Planarity : 0.004 0.035 601 Dihedral : 5.392 45.993 513 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.38 % Allowed : 11.33 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.02 (0.42), residues: 416 helix: -3.77 (0.72), residues: 26 sheet: 0.37 (0.44), residues: 130 loop : 0.31 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 429 HIS 0.001 0.000 HIS L 30 PHE 0.010 0.001 PHE A 393 TYR 0.021 0.001 TYR A 501 ARG 0.003 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.323 Fit side-chains REVERT: A 488 TYR cc_start: 0.8370 (m-80) cc_final: 0.8027 (m-80) outliers start: 5 outliers final: 5 residues processed: 60 average time/residue: 0.1252 time to fit residues: 9.7669 Evaluate side-chains 60 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 64 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 chunk 24 optimal weight: 0.0870 chunk 38 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 0.0870 chunk 27 optimal weight: 0.2980 chunk 40 optimal weight: 0.3980 chunk 37 optimal weight: 0.4980 overall best weight: 0.2736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3438 Z= 0.300 Angle : 0.548 4.892 4674 Z= 0.287 Chirality : 0.044 0.163 500 Planarity : 0.004 0.035 601 Dihedral : 5.370 45.102 513 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.93 % Allowed : 10.77 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.10 (0.41), residues: 416 helix: -3.80 (0.71), residues: 26 sheet: 0.33 (0.44), residues: 130 loop : 0.25 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 429 HIS 0.001 0.000 HIS L 30 PHE 0.010 0.001 PHE A 393 TYR 0.021 0.001 TYR A 501 ARG 0.010 0.001 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 0.367 Fit side-chains REVERT: A 488 TYR cc_start: 0.8377 (m-80) cc_final: 0.7976 (m-80) outliers start: 7 outliers final: 5 residues processed: 59 average time/residue: 0.1250 time to fit residues: 9.5941 Evaluate side-chains 58 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 64 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.6980 chunk 3 optimal weight: 0.0470 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 0.4980 chunk 29 optimal weight: 0.1980 chunk 4 optimal weight: 0.3980 chunk 13 optimal weight: 0.3980 chunk 33 optimal weight: 0.4980 chunk 6 optimal weight: 0.1980 overall best weight: 0.2478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3438 Z= 0.281 Angle : 0.543 4.845 4674 Z= 0.285 Chirality : 0.044 0.163 500 Planarity : 0.004 0.038 601 Dihedral : 5.356 45.168 513 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.38 % Allowed : 11.05 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.21 (0.41), residues: 416 helix: -4.11 (0.57), residues: 33 sheet: 0.34 (0.44), residues: 130 loop : 0.29 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 429 HIS 0.001 0.000 HIS L 100 PHE 0.009 0.001 PHE A 393 TYR 0.023 0.001 TYR A 501 ARG 0.006 0.000 ARG H 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.373 Fit side-chains REVERT: A 488 TYR cc_start: 0.8364 (m-80) cc_final: 0.7967 (m-80) outliers start: 5 outliers final: 5 residues processed: 61 average time/residue: 0.1349 time to fit residues: 10.5430 Evaluate side-chains 62 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 64 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.6980 chunk 1 optimal weight: 0.0970 chunk 23 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 0.0870 chunk 27 optimal weight: 0.0870 chunk 26 optimal weight: 0.0980 chunk 24 optimal weight: 0.0970 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.1980 chunk 40 optimal weight: 0.1980 overall best weight: 0.0932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.109827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.100582 restraints weight = 5068.481| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.99 r_work: 0.3130 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3438 Z= 0.152 Angle : 0.499 5.418 4674 Z= 0.261 Chirality : 0.042 0.162 500 Planarity : 0.003 0.034 601 Dihedral : 5.009 42.735 513 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.38 % Allowed : 11.33 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.03 (0.42), residues: 416 helix: -3.82 (0.70), residues: 26 sheet: 0.46 (0.44), residues: 130 loop : 0.33 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 429 HIS 0.001 0.000 HIS L 100 PHE 0.007 0.001 PHE L 98 TYR 0.017 0.001 TYR A 501 ARG 0.007 0.000 ARG H 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1766.60 seconds wall clock time: 31 minutes 50.58 seconds (1910.58 seconds total)