Starting phenix.real_space_refine on Tue Feb 13 04:59:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wr9_32719/02_2024/7wr9_32719.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wr9_32719/02_2024/7wr9_32719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wr9_32719/02_2024/7wr9_32719.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wr9_32719/02_2024/7wr9_32719.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wr9_32719/02_2024/7wr9_32719.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wr9_32719/02_2024/7wr9_32719.pdb" } resolution = 3.24 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= 0.032 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 2074 2.51 5 N 539 2.21 5 O 638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 28": "NH1" <-> "NH2" Residue "A ARG 56": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 98": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 38": "NH1" <-> "NH2" Residue "B TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B GLU 80": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3266 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 973 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain: "B" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 780 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 9, 'TRANS': 94} Chain: "F" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1450 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 167} Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" 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: 2.48, per 1000 atoms: 0.76 Number of scatterers: 3266 At special positions: 0 Unit cell: (90.48, 63.44, 74.88, 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 638 8.00 N 539 7.00 C 2074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.02 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 87 " distance=2.03 Simple disulfide: pdb=" SG CYS F 323 " - pdb=" SG CYS F 348 " distance=2.03 Simple disulfide: pdb=" SG CYS F 366 " - pdb=" SG CYS F 419 " distance=2.03 Simple disulfide: pdb=" SG CYS F 467 " - pdb=" SG CYS F 474 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " BETA1-6 " NAG C 1 " - " FUC C 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG C 1 " - " ASN F 330 " " NAG F 601 " - " ASN F 357 " Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 525.8 milliseconds 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 748 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 8 sheets defined 3.9% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 87 through 91 removed outlier: 4.057A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 397 Processing helix chain 'F' and resid 425 through 430 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.997A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11 removed outlier: 3.518A pdb=" N ALA A 92 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE A 34 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LYS A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR A 59 " --> pdb=" O LYS A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 20 Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 5 Processing sheet with id=AA5, first strand: chain 'B' and resid 9 through 10 removed outlier: 3.541A pdb=" N VAL B 10 " --> pdb=" O LYS B 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 44 through 47 removed outlier: 6.485A pdb=" N TRP B 34 " --> pdb=" O VAL B 46 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 341 through 345 removed outlier: 4.027A pdb=" N GLU F 341 " --> pdb=" O SER F 386 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN F 381 " --> pdb=" O GLU F 502 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 439 through 441 82 hydrogen bonds defined for protein. 207 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: 0.74 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 525 1.32 - 1.45: 1011 1.45 - 1.57: 1802 1.57 - 1.70: 0 1.70 - 1.82: 19 Bond restraints: 3357 Sorted by residual: bond pdb=" C PRO A 102 " pdb=" O PRO A 102 " ideal model delta sigma weight residual 1.235 1.196 0.039 1.30e-02 5.92e+03 9.14e+00 bond pdb=" CA TYR A 107 " pdb=" C TYR A 107 " ideal model delta sigma weight residual 1.529 1.498 0.031 1.04e-02 9.25e+03 9.05e+00 bond pdb=" N PRO A 102 " pdb=" CA PRO A 102 " ideal model delta sigma weight residual 1.469 1.432 0.036 1.28e-02 6.10e+03 8.02e+00 bond pdb=" N SER A 104 " pdb=" CA SER A 104 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.46e+00 bond pdb=" N ASP A 105 " pdb=" CA ASP A 105 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.41e-02 5.03e+03 6.45e+00 ... (remaining 3352 not shown) Histogram of bond angle deviations from ideal: 92.17 - 100.65: 4 100.65 - 109.13: 348 109.13 - 117.61: 2081 117.61 - 126.10: 2082 126.10 - 134.58: 64 Bond angle restraints: 4579 Sorted by residual: angle pdb=" N PRO A 106 " pdb=" CA PRO A 106 " pdb=" CB PRO A 106 " ideal model delta sigma weight residual 103.25 92.17 11.08 1.05e+00 9.07e-01 1.11e+02 angle pdb=" C PRO A 106 " pdb=" CA PRO A 106 " pdb=" CB PRO A 106 " ideal model delta sigma weight residual 111.56 120.78 -9.22 1.65e+00 3.67e-01 3.12e+01 angle pdb=" CA LEU B 27 " pdb=" CB LEU B 27 " pdb=" CG LEU B 27 " ideal model delta sigma weight residual 116.30 134.58 -18.28 3.50e+00 8.16e-02 2.73e+01 angle pdb=" C ASP B 91 " pdb=" N ALA B 92 " pdb=" CA ALA B 92 " ideal model delta sigma weight residual 121.54 130.69 -9.15 1.91e+00 2.74e-01 2.30e+01 angle pdb=" C TYR A 107 " pdb=" CA TYR A 107 " pdb=" CB TYR A 107 " ideal model delta sigma weight residual 111.43 105.49 5.94 1.24e+00 6.50e-01 2.29e+01 ... (remaining 4574 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.95: 1912 24.95 - 49.89: 95 49.89 - 74.83: 11 74.83 - 99.78: 10 99.78 - 124.72: 5 Dihedral angle restraints: 2033 sinusoidal: 847 harmonic: 1186 Sorted by residual: dihedral pdb=" CA LEU B 27 " pdb=" C LEU B 27 " pdb=" N PRO B 28 " pdb=" CA PRO B 28 " ideal model delta harmonic sigma weight residual 180.00 145.93 34.07 0 5.00e+00 4.00e-02 4.64e+01 dihedral pdb=" CB CYS F 467 " pdb=" SG CYS F 467 " pdb=" SG CYS F 474 " pdb=" CB CYS F 474 " ideal model delta sinusoidal sigma weight residual -86.00 -130.82 44.82 1 1.00e+01 1.00e-02 2.79e+01 dihedral pdb=" CA ALA B 92 " pdb=" C ALA B 92 " pdb=" N SER B 93 " pdb=" CA SER B 93 " ideal model delta harmonic sigma weight residual 180.00 154.30 25.70 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 2030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 398 0.061 - 0.121: 86 0.121 - 0.181: 14 0.181 - 0.242: 4 0.242 - 0.302: 3 Chirality restraints: 505 Sorted by residual: chirality pdb=" CA ARG A 100 " pdb=" N ARG A 100 " pdb=" C ARG A 100 " pdb=" CB ARG A 100 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA TYR A 107 " pdb=" N TYR A 107 " pdb=" C TYR A 107 " pdb=" CB TYR A 107 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 502 not shown) Planarity restraints: 587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 109 " 0.017 2.00e-02 2.50e+03 2.81e-02 1.97e+01 pdb=" CG TRP A 109 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP A 109 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP A 109 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 109 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 109 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 109 " 0.021 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 109 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 109 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 109 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 105 " 0.018 2.00e-02 2.50e+03 3.61e-02 1.31e+01 pdb=" C ASP A 105 " -0.063 2.00e-02 2.50e+03 pdb=" O ASP A 105 " 0.023 2.00e-02 2.50e+03 pdb=" N PRO A 106 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 118 " 0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C VAL A 118 " -0.059 2.00e-02 2.50e+03 pdb=" O VAL A 118 " 0.023 2.00e-02 2.50e+03 pdb=" N TRP A 119 " 0.020 2.00e-02 2.50e+03 ... (remaining 584 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1152 2.86 - 3.37: 2584 3.37 - 3.88: 5412 3.88 - 4.39: 6083 4.39 - 4.90: 10951 Nonbonded interactions: 26182 Sorted by model distance: nonbonded pdb=" O VAL A 108 " pdb=" OG SER A 111 " model vdw 2.350 2.440 nonbonded pdb=" O ALA F 430 " pdb=" OG1 THR F 485 " model vdw 2.389 2.440 nonbonded pdb=" OG SER B 93 " pdb=" OG1 THR B 95 " model vdw 2.408 2.440 nonbonded pdb=" O GLY B 76 " pdb=" NE2 GLN B 78 " model vdw 2.413 2.520 nonbonded pdb=" O SER B 62 " pdb=" OG SER B 62 " model vdw 2.421 2.440 ... (remaining 26177 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 9.730 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.550 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 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 : 0.006 0.043 3357 Z= 0.377 Angle : 1.051 18.280 4579 Z= 0.592 Chirality : 0.058 0.302 505 Planarity : 0.009 0.075 585 Dihedral : 17.104 124.722 1270 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.49 % Allowed : 9.63 % Favored : 89.88 % Rotamer: Outliers : 1.15 % Allowed : 0.86 % Favored : 97.99 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -2.72 (0.39), residues: 405 helix: -4.46 (0.69), residues: 25 sheet: -1.38 (0.43), residues: 131 loop : -1.78 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.004 TRP A 109 HIS 0.002 0.001 HIS B 97 PHE 0.030 0.003 PHE F 364 TYR 0.040 0.002 TYR F 442 ARG 0.013 0.001 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 80 GLU cc_start: 0.6819 (pm20) cc_final: 0.6519 (pt0) outliers start: 4 outliers final: 1 residues processed: 66 average time/residue: 0.1897 time to fit residues: 15.0389 Evaluate side-chains 55 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.2980 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 0.2980 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 12 optimal weight: 0.0670 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- 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: 0.7863 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 3357 Z= 0.184 Angle : 0.653 9.103 4579 Z= 0.330 Chirality : 0.046 0.152 505 Planarity : 0.008 0.118 585 Dihedral : 12.962 109.155 561 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.40 % Favored : 91.36 % Rotamer: Outliers : 1.15 % Allowed : 8.62 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -2.40 (0.41), residues: 405 helix: -4.58 (0.62), residues: 27 sheet: -1.19 (0.43), residues: 133 loop : -1.46 (0.40), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 109 HIS 0.003 0.001 HIS A 35 PHE 0.011 0.001 PHE F 334 TYR 0.013 0.001 TYR F 356 ARG 0.002 0.000 ARG F 426 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 105 ASP cc_start: 0.6891 (OUTLIER) cc_final: 0.6628 (p0) outliers start: 4 outliers final: 2 residues processed: 70 average time/residue: 0.1777 time to fit residues: 14.8999 Evaluate side-chains 64 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 109 TRP Chi-restraints excluded: chain B residue 44 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 29 optimal weight: 0.2980 chunk 35 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7896 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 3357 Z= 0.213 Angle : 0.611 7.454 4579 Z= 0.305 Chirality : 0.045 0.146 505 Planarity : 0.007 0.116 585 Dihedral : 10.332 103.237 558 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.14 % Favored : 90.62 % Rotamer: Outliers : 1.44 % Allowed : 11.78 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -2.19 (0.42), residues: 405 helix: -4.74 (0.47), residues: 27 sheet: -1.08 (0.44), residues: 133 loop : -1.25 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 109 HIS 0.003 0.001 HIS A 35 PHE 0.013 0.001 PHE F 334 TYR 0.013 0.001 TYR F 356 ARG 0.002 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 109 TRP cc_start: 0.7077 (OUTLIER) cc_final: 0.6551 (t60) REVERT: B 41 GLN cc_start: 0.7206 (pm20) cc_final: 0.6960 (pm20) outliers start: 5 outliers final: 4 residues processed: 72 average time/residue: 0.2031 time to fit residues: 17.3742 Evaluate side-chains 71 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 109 TRP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 404 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.0970 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 10 optimal weight: 0.1980 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 3357 Z= 0.178 Angle : 0.574 7.052 4579 Z= 0.286 Chirality : 0.044 0.148 505 Planarity : 0.007 0.113 585 Dihedral : 9.288 99.242 558 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.16 % Favored : 92.59 % Rotamer: Outliers : 3.74 % Allowed : 13.79 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.99 (0.43), residues: 405 helix: -4.73 (0.46), residues: 27 sheet: -0.89 (0.44), residues: 133 loop : -1.13 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 109 HIS 0.002 0.000 HIS A 35 PHE 0.010 0.001 PHE A 101 TYR 0.012 0.001 TYR F 356 ARG 0.001 0.000 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.357 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 75 average time/residue: 0.1742 time to fit residues: 15.5584 Evaluate side-chains 76 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 TRP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain F residue 376 ASP Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 467 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.0970 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.2980 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7935 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 3357 Z= 0.257 Angle : 0.638 12.009 4579 Z= 0.311 Chirality : 0.045 0.154 505 Planarity : 0.007 0.113 585 Dihedral : 9.643 102.091 558 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.14 % Favored : 90.62 % Rotamer: Outliers : 3.74 % Allowed : 15.52 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.43), residues: 405 helix: -4.84 (0.38), residues: 27 sheet: -0.88 (0.44), residues: 133 loop : -1.13 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 109 HIS 0.003 0.001 HIS A 35 PHE 0.013 0.001 PHE F 334 TYR 0.013 0.001 TYR F 356 ARG 0.003 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 0.453 Fit side-chains REVERT: F 366 CYS cc_start: 0.6233 (m) cc_final: 0.5787 (m) outliers start: 13 outliers final: 11 residues processed: 71 average time/residue: 0.1828 time to fit residues: 15.4906 Evaluate side-chains 77 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 109 TRP Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 467 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 0.0070 chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 0.0170 chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 3357 Z= 0.183 Angle : 0.594 9.636 4579 Z= 0.292 Chirality : 0.044 0.155 505 Planarity : 0.007 0.110 585 Dihedral : 9.207 98.033 558 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.65 % Favored : 92.10 % Rotamer: Outliers : 3.16 % Allowed : 18.10 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.88 (0.43), residues: 405 helix: -4.80 (0.39), residues: 27 sheet: -0.80 (0.44), residues: 133 loop : -1.05 (0.44), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 109 HIS 0.002 0.001 HIS A 35 PHE 0.010 0.001 PHE A 101 TYR 0.012 0.001 TYR F 356 ARG 0.001 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.371 Fit side-chains REVERT: F 366 CYS cc_start: 0.6183 (m) cc_final: 0.5753 (m) outliers start: 11 outliers final: 10 residues processed: 69 average time/residue: 0.1891 time to fit residues: 15.5063 Evaluate side-chains 73 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 109 TRP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 467 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.0870 chunk 24 optimal weight: 0.0000 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.0870 chunk 15 optimal weight: 0.4980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.2740 ------------------------------------------------------------------------------- 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: 0.7856 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 3357 Z= 0.154 Angle : 0.572 8.691 4579 Z= 0.279 Chirality : 0.043 0.152 505 Planarity : 0.006 0.108 585 Dihedral : 8.642 92.231 558 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.41 % Favored : 92.35 % Rotamer: Outliers : 2.87 % Allowed : 18.10 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.74 (0.43), residues: 405 helix: -4.83 (0.34), residues: 27 sheet: -0.59 (0.45), residues: 133 loop : -1.01 (0.44), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 109 HIS 0.001 0.000 HIS A 35 PHE 0.009 0.001 PHE A 101 TYR 0.011 0.001 TYR F 356 ARG 0.002 0.000 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.403 Fit side-chains REVERT: F 366 CYS cc_start: 0.6188 (m) cc_final: 0.5747 (m) outliers start: 10 outliers final: 10 residues processed: 66 average time/residue: 0.1890 time to fit residues: 14.8282 Evaluate side-chains 71 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 109 TRP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain F residue 376 ASP Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 467 CYS 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: 1.9990 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 0.0970 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 32 optimal weight: 0.1980 chunk 23 optimal weight: 0.7980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 3357 Z= 0.200 Angle : 0.586 7.511 4579 Z= 0.287 Chirality : 0.044 0.157 505 Planarity : 0.006 0.109 585 Dihedral : 8.725 93.125 558 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.15 % Favored : 91.60 % Rotamer: Outliers : 3.45 % Allowed : 18.10 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.69 (0.44), residues: 405 helix: -4.82 (0.36), residues: 27 sheet: -0.55 (0.45), residues: 133 loop : -0.98 (0.44), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 109 HIS 0.002 0.001 HIS A 35 PHE 0.009 0.001 PHE A 101 TYR 0.011 0.001 TYR F 356 ARG 0.002 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.367 Fit side-chains REVERT: B 78 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7201 (mt0) REVERT: F 366 CYS cc_start: 0.6206 (m) cc_final: 0.5771 (m) outliers start: 12 outliers final: 11 residues processed: 68 average time/residue: 0.1869 time to fit residues: 15.1848 Evaluate side-chains 73 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 109 TRP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain F residue 376 ASP Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 467 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 36 optimal weight: 0.0020 chunk 31 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.3980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 GLN F 457 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 3357 Z= 0.186 Angle : 0.581 7.207 4579 Z= 0.285 Chirality : 0.044 0.157 505 Planarity : 0.006 0.108 585 Dihedral : 8.697 92.662 558 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.41 % Favored : 92.35 % Rotamer: Outliers : 3.45 % Allowed : 18.10 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.64 (0.44), residues: 405 helix: -4.83 (0.35), residues: 27 sheet: -0.53 (0.45), residues: 133 loop : -0.93 (0.44), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 109 HIS 0.002 0.000 HIS A 35 PHE 0.009 0.001 PHE A 101 TYR 0.011 0.001 TYR F 356 ARG 0.002 0.000 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: F 366 CYS cc_start: 0.6213 (m) cc_final: 0.5774 (m) outliers start: 12 outliers final: 12 residues processed: 67 average time/residue: 0.1776 time to fit residues: 14.2722 Evaluate side-chains 74 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 109 TRP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain F residue 376 ASP Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 467 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.0980 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 0.1980 chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 chunk 1 optimal weight: 2.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 3357 Z= 0.180 Angle : 0.577 7.213 4579 Z= 0.283 Chirality : 0.044 0.157 505 Planarity : 0.006 0.108 585 Dihedral : 8.643 92.022 558 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.90 % Favored : 91.85 % Rotamer: Outliers : 3.45 % Allowed : 18.39 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.64 (0.44), residues: 405 helix: -4.83 (0.35), residues: 27 sheet: -0.53 (0.45), residues: 133 loop : -0.93 (0.44), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 109 HIS 0.002 0.000 HIS A 35 PHE 0.009 0.001 PHE A 101 TYR 0.011 0.001 TYR F 356 ARG 0.002 0.000 ARG A 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: F 366 CYS cc_start: 0.6215 (m) cc_final: 0.5776 (m) outliers start: 12 outliers final: 12 residues processed: 63 average time/residue: 0.1879 time to fit residues: 14.2099 Evaluate side-chains 69 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 109 TRP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain F residue 376 ASP Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 467 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 0.0970 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.0070 chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.149643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.124335 restraints weight = 3884.068| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.18 r_work: 0.3234 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 3357 Z= 0.168 Angle : 0.572 7.145 4579 Z= 0.280 Chirality : 0.044 0.157 505 Planarity : 0.006 0.107 585 Dihedral : 8.548 90.919 558 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.41 % Favored : 92.35 % Rotamer: Outliers : 3.45 % Allowed : 18.39 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.61 (0.44), residues: 405 helix: -4.81 (0.36), residues: 27 sheet: -0.51 (0.45), residues: 133 loop : -0.90 (0.45), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 109 HIS 0.001 0.000 HIS A 35 PHE 0.009 0.001 PHE A 101 TYR 0.011 0.001 TYR F 356 ARG 0.002 0.000 ARG A 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1364.86 seconds wall clock time: 25 minutes 21.16 seconds (1521.16 seconds total)