Starting phenix.real_space_refine on Thu Dec 7 17:38:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wr9_32719/12_2023/7wr9_32719.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wr9_32719/12_2023/7wr9_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_32719/12_2023/7wr9_32719.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wr9_32719/12_2023/7wr9_32719.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wr9_32719/12_2023/7wr9_32719.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wr9_32719/12_2023/7wr9_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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 6 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: 2.21, per 1000 atoms: 0.68 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: 1.52 Conformation dependent library (CDL) restraints added in 607.6 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: 0.33 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: 0.75 Time building geometry restraints manager: 1.58 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 - 17.01: 1789 17.01 - 34.02: 163 34.02 - 51.03: 36 51.03 - 68.04: 6 68.04 - 85.05: 3 Dihedral angle restraints: 1997 sinusoidal: 811 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 1994 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: 2.320 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: 9.560 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.870 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.630 ------------------------------------------------------------------------------- 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 : 13.558 85.052 1234 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 : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 66 average time/residue: 0.1892 time to fit residues: 14.9557 Evaluate side-chains 55 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.392 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0306 time to fit residues: 0.5814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.2980 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 12 optimal weight: 0.0670 chunk 19 optimal weight: 0.0570 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.2636 ------------------------------------------------------------------------------- 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: 0.7846 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 3357 Z= 0.161 Angle : 0.633 8.638 4579 Z= 0.324 Chirality : 0.044 0.149 505 Planarity : 0.008 0.114 585 Dihedral : 5.887 50.427 522 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.15 % Favored : 91.60 % Rotamer: Outliers : 0.86 % Allowed : 9.20 % Favored : 89.94 % 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: -2.39 (0.41), residues: 405 helix: -4.50 (0.68), residues: 27 sheet: -1.18 (0.43), residues: 133 loop : -1.47 (0.40), 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 0.009 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: 3 poor density : 68 time to evaluate : 0.399 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 70 average time/residue: 0.1836 time to fit residues: 15.7601 Evaluate side-chains 62 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.419 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0416 time to fit residues: 0.6395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.0030 chunk 29 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.0020 chunk 18 optimal weight: 3.9990 overall best weight: 0.4800 ------------------------------------------------------------------------------- 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: 0.7879 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 3357 Z= 0.193 Angle : 0.588 7.101 4579 Z= 0.297 Chirality : 0.044 0.144 505 Planarity : 0.007 0.118 585 Dihedral : 5.465 47.871 522 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.90 % Favored : 91.85 % Rotamer: Outliers : 1.44 % Allowed : 12.07 % Favored : 86.49 % 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: -2.18 (0.42), residues: 405 helix: -4.60 (0.60), residues: 27 sheet: -1.05 (0.44), residues: 133 loop : -1.28 (0.42), 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 0.014 0.001 PHE F 334 TYR 0.013 0.001 TYR F 356 ARG 0.002 0.000 ARG B 53 *********************** 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 73 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.369 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 71 average time/residue: 0.1865 time to fit residues: 15.7707 Evaluate side-chains 67 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.365 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0333 time to fit residues: 0.7350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.0370 chunk 24 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 19 optimal weight: 0.2980 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 21 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 overall best weight: 0.3858 ------------------------------------------------------------------------------- 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: 0.7872 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 : 0.003 0.074 3357 Z= 0.165 Angle : 0.557 6.488 4579 Z= 0.281 Chirality : 0.043 0.146 505 Planarity : 0.007 0.115 585 Dihedral : 5.211 46.900 522 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.16 % Favored : 92.59 % Rotamer: Outliers : 1.44 % Allowed : 13.79 % Favored : 84.77 % 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: -4.70 (0.49), residues: 27 sheet: -0.88 (0.44), residues: 133 loop : -1.14 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 109 HIS 0.001 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 100 *********************** 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 73 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.389 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 71 average time/residue: 0.1870 time to fit residues: 15.8090 Evaluate side-chains 69 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.388 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0351 time to fit residues: 0.7064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 0.0970 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.7946 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 3357 Z= 0.289 Angle : 0.654 12.434 4579 Z= 0.320 Chirality : 0.044 0.155 505 Planarity : 0.007 0.116 585 Dihedral : 5.380 47.236 522 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.14 % Favored : 90.62 % Rotamer: Outliers : 1.72 % Allowed : 16.67 % Favored : 81.61 % 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: -2.05 (0.43), residues: 405 helix: -4.86 (0.37), residues: 27 sheet: -0.95 (0.44), residues: 133 loop : -1.15 (0.44), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 423 HIS 0.004 0.001 HIS A 35 PHE 0.016 0.002 PHE F 334 TYR 0.013 0.001 TYR F 356 ARG 0.003 0.000 ARG F 342 *********************** 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 73 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.377 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 69 average time/residue: 0.1881 time to fit residues: 15.4724 Evaluate side-chains 72 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.354 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0334 time to fit residues: 0.7592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 0.0010 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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: 0.7921 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 3357 Z= 0.218 Angle : 0.604 10.772 4579 Z= 0.298 Chirality : 0.044 0.158 505 Planarity : 0.007 0.115 585 Dihedral : 5.328 48.275 522 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.65 % Favored : 92.10 % Rotamer: Outliers : 1.15 % Allowed : 18.10 % 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: -1.97 (0.43), residues: 405 helix: -4.85 (0.36), residues: 27 sheet: -0.86 (0.44), residues: 133 loop : -1.11 (0.44), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 109 HIS 0.003 0.001 HIS A 35 PHE 0.011 0.001 PHE A 101 TYR 0.013 0.001 TYR F 356 ARG 0.002 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 71 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.416 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 69 average time/residue: 0.1862 time to fit residues: 15.3857 Evaluate side-chains 68 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 0.341 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0379 time to fit residues: 0.7073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.0370 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 0.0770 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 11 optimal weight: 0.2980 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 0.0870 overall best weight: 0.2194 ------------------------------------------------------------------------------- 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: 0.7863 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 3357 Z= 0.146 Angle : 0.565 9.257 4579 Z= 0.279 Chirality : 0.043 0.154 505 Planarity : 0.007 0.112 585 Dihedral : 5.062 46.619 522 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.41 % Favored : 92.35 % Rotamer: Outliers : 0.29 % Allowed : 19.83 % Favored : 79.89 % 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: -1.79 (0.43), residues: 405 helix: -4.83 (0.34), residues: 27 sheet: -0.67 (0.44), residues: 133 loop : -1.03 (0.44), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 119 HIS 0.001 0.000 HIS A 35 PHE 0.010 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 59 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.343 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 58 average time/residue: 0.2119 time to fit residues: 14.5268 Evaluate side-chains 57 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.397 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0337 time to fit residues: 0.5465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7899 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 3357 Z= 0.216 Angle : 0.584 8.472 4579 Z= 0.290 Chirality : 0.044 0.156 505 Planarity : 0.007 0.112 585 Dihedral : 5.068 46.404 522 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.90 % Favored : 91.85 % Rotamer: Outliers : 0.29 % Allowed : 20.69 % 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: -1.76 (0.44), residues: 405 helix: -4.83 (0.34), residues: 27 sheet: -0.63 (0.44), residues: 133 loop : -1.01 (0.44), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 423 HIS 0.002 0.001 HIS A 35 PHE 0.010 0.001 PHE F 334 TYR 0.011 0.001 TYR F 356 ARG 0.003 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 57 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.329 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 56 average time/residue: 0.2115 time to fit residues: 13.9048 Evaluate side-chains 55 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.396 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 36 optimal weight: 0.0050 chunk 31 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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: 0.7892 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 3357 Z= 0.194 Angle : 0.574 7.920 4579 Z= 0.286 Chirality : 0.043 0.156 505 Planarity : 0.006 0.112 585 Dihedral : 5.046 46.570 522 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.65 % Favored : 92.10 % Rotamer: Outliers : 0.00 % Allowed : 21.26 % 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: -1.73 (0.43), residues: 405 helix: -4.83 (0.34), residues: 27 sheet: -0.59 (0.44), residues: 133 loop : -1.00 (0.44), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 423 HIS 0.002 0.001 HIS A 35 PHE 0.009 0.001 PHE A 101 TYR 0.012 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 54 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.387 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2099 time to fit residues: 13.4786 Evaluate side-chains 54 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.402 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 31 optimal weight: 0.3980 chunk 13 optimal weight: 0.5980 chunk 32 optimal weight: 0.3980 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 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: 0.7899 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 3357 Z= 0.207 Angle : 0.578 7.832 4579 Z= 0.288 Chirality : 0.043 0.156 505 Planarity : 0.006 0.111 585 Dihedral : 5.029 46.670 522 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.15 % Favored : 91.60 % Rotamer: Outliers : 0.00 % Allowed : 20.69 % Favored : 79.31 % 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: -1.72 (0.44), residues: 405 helix: -4.83 (0.34), residues: 27 sheet: -0.58 (0.45), residues: 133 loop : -0.98 (0.44), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 423 HIS 0.002 0.001 HIS A 35 PHE 0.009 0.001 PHE A 101 TYR 0.012 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 56 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.369 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1980 time to fit residues: 13.2579 Evaluate side-chains 55 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.388 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.9980 chunk 36 optimal weight: 0.0000 chunk 21 optimal weight: 0.2980 chunk 27 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.150543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.125029 restraints weight = 3876.249| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.21 r_work: 0.3248 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 3357 Z= 0.158 Angle : 0.543 7.327 4579 Z= 0.269 Chirality : 0.043 0.152 505 Planarity : 0.006 0.109 585 Dihedral : 4.924 45.537 522 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.16 % Favored : 92.59 % Rotamer: Outliers : 0.00 % Allowed : 20.69 % Favored : 79.31 % 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: -1.59 (0.44), residues: 405 helix: -4.77 (0.37), residues: 27 sheet: -0.50 (0.44), residues: 133 loop : -0.89 (0.44), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 109 HIS 0.001 0.000 HIS A 35 PHE 0.010 0.001 PHE A 101 TYR 0.012 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: 1395.87 seconds wall clock time: 25 minutes 52.85 seconds (1552.85 seconds total)