Starting phenix.real_space_refine on Tue Feb 13 06:24:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6k_0690/02_2024/6j6k_0690.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6k_0690/02_2024/6j6k_0690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6k_0690/02_2024/6j6k_0690.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6k_0690/02_2024/6j6k_0690.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6k_0690/02_2024/6j6k_0690.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6k_0690/02_2024/6j6k_0690.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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: 3 Type Number sf(0) Gaussians C 2224 2.51 5 N 620 2.21 5 O 704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 53": "NH1" <-> "NH2" Residue "B ARG 53": "NH1" <-> "NH2" Residue "C ARG 53": "NH1" <-> "NH2" Residue "D ARG 53": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3548 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 2.22, per 1000 atoms: 0.63 Number of scatterers: 3548 At special positions: 0 Unit cell: (70.551, 64.233, 66.339, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 704 8.00 N 620 7.00 C 2224 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 625.2 milliseconds 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 824 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 42.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 4.189A pdb=" N GLY A 41 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 56 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N VAL A 55 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA A 78 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N SER A 88 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP A 108 " --> pdb=" O GLY A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 19 through 21 removed outlier: 4.189A pdb=" N GLY B 41 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 56 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL B 55 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA B 78 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N SER B 88 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP B 108 " --> pdb=" O GLY B 126 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 19 through 21 removed outlier: 4.189A pdb=" N GLY C 41 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C 56 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL C 55 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA C 78 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N SER C 88 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP C 108 " --> pdb=" O GLY C 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 19 through 21 removed outlier: 4.188A pdb=" N GLY D 41 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU D 56 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL D 55 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA D 78 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N SER D 88 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP D 108 " --> pdb=" O GLY D 126 " (cutoff:3.500A) 160 hydrogen bonds defined for protein. 408 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: 0.78 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 572 1.29 - 1.36: 584 1.36 - 1.42: 480 1.42 - 1.49: 623 1.49 - 1.55: 1377 Bond restraints: 3636 Sorted by residual: bond pdb=" N ALA A 50 " pdb=" CA ALA A 50 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.29e-02 6.01e+03 2.31e+00 bond pdb=" N ALA B 50 " pdb=" CA ALA B 50 " ideal model delta sigma weight residual 1.457 1.477 -0.019 1.29e-02 6.01e+03 2.24e+00 bond pdb=" N ALA C 50 " pdb=" CA ALA C 50 " ideal model delta sigma weight residual 1.457 1.477 -0.019 1.29e-02 6.01e+03 2.20e+00 bond pdb=" N ALA D 50 " pdb=" CA ALA D 50 " ideal model delta sigma weight residual 1.457 1.477 -0.019 1.29e-02 6.01e+03 2.20e+00 bond pdb=" C GLU C 44 " pdb=" N SER C 45 " ideal model delta sigma weight residual 1.332 1.352 -0.019 1.40e-02 5.10e+03 1.93e+00 ... (remaining 3631 not shown) Histogram of bond angle deviations from ideal: 103.25 - 109.41: 510 109.41 - 115.56: 1768 115.56 - 121.72: 1699 121.72 - 127.87: 930 127.87 - 134.03: 69 Bond angle restraints: 4976 Sorted by residual: angle pdb=" C SER C 45 " pdb=" N ALA C 46 " pdb=" CA ALA C 46 " ideal model delta sigma weight residual 121.54 133.69 -12.15 1.91e+00 2.74e-01 4.05e+01 angle pdb=" C SER D 45 " pdb=" N ALA D 46 " pdb=" CA ALA D 46 " ideal model delta sigma weight residual 121.54 133.68 -12.14 1.91e+00 2.74e-01 4.04e+01 angle pdb=" C SER B 45 " pdb=" N ALA B 46 " pdb=" CA ALA B 46 " ideal model delta sigma weight residual 121.54 133.68 -12.14 1.91e+00 2.74e-01 4.04e+01 angle pdb=" C SER A 45 " pdb=" N ALA A 46 " pdb=" CA ALA A 46 " ideal model delta sigma weight residual 121.54 133.67 -12.13 1.91e+00 2.74e-01 4.03e+01 angle pdb=" C ALA A 46 " pdb=" N VAL A 47 " pdb=" CA VAL A 47 " ideal model delta sigma weight residual 121.97 133.33 -11.36 1.80e+00 3.09e-01 3.98e+01 ... (remaining 4971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 1860 16.16 - 32.33: 84 32.33 - 48.49: 28 48.49 - 64.65: 4 64.65 - 80.82: 8 Dihedral angle restraints: 1984 sinusoidal: 664 harmonic: 1320 Sorted by residual: dihedral pdb=" CA ALA B 46 " pdb=" C ALA B 46 " pdb=" N VAL B 47 " pdb=" CA VAL B 47 " ideal model delta harmonic sigma weight residual -180.00 -99.18 -80.82 0 5.00e+00 4.00e-02 2.61e+02 dihedral pdb=" CA ALA C 46 " pdb=" C ALA C 46 " pdb=" N VAL C 47 " pdb=" CA VAL C 47 " ideal model delta harmonic sigma weight residual -180.00 -99.21 -80.79 0 5.00e+00 4.00e-02 2.61e+02 dihedral pdb=" CA ALA A 46 " pdb=" C ALA A 46 " pdb=" N VAL A 47 " pdb=" CA VAL A 47 " ideal model delta harmonic sigma weight residual 180.00 -99.24 -80.76 0 5.00e+00 4.00e-02 2.61e+02 ... (remaining 1981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 356 0.042 - 0.084: 120 0.084 - 0.127: 52 0.127 - 0.169: 20 0.169 - 0.211: 8 Chirality restraints: 556 Sorted by residual: chirality pdb=" CA SER C 45 " pdb=" N SER C 45 " pdb=" C SER C 45 " pdb=" CB SER C 45 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA SER D 45 " pdb=" N SER D 45 " pdb=" C SER D 45 " pdb=" CB SER D 45 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA SER A 45 " pdb=" N SER A 45 " pdb=" C SER A 45 " pdb=" CB SER A 45 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 553 not shown) Planarity restraints: 624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 45 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C SER C 45 " -0.037 2.00e-02 2.50e+03 pdb=" O SER C 45 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA C 46 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 45 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.60e+00 pdb=" C SER A 45 " 0.037 2.00e-02 2.50e+03 pdb=" O SER A 45 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA A 46 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 45 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.52e+00 pdb=" C SER B 45 " 0.037 2.00e-02 2.50e+03 pdb=" O SER B 45 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA B 46 " -0.012 2.00e-02 2.50e+03 ... (remaining 621 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 1208 2.87 - 3.37: 2786 3.37 - 3.88: 5801 3.88 - 4.39: 6526 4.39 - 4.90: 12029 Nonbonded interactions: 28350 Sorted by model distance: nonbonded pdb=" O GLY D 34 " pdb=" OH TYR D 60 " model vdw 2.357 2.440 nonbonded pdb=" O GLY A 34 " pdb=" OH TYR A 60 " model vdw 2.357 2.440 nonbonded pdb=" O GLY B 34 " pdb=" OH TYR B 60 " model vdw 2.357 2.440 nonbonded pdb=" O GLY C 34 " pdb=" OH TYR C 60 " model vdw 2.358 2.440 nonbonded pdb=" NE1 TRP D 79 " pdb=" OG1 THR D 90 " model vdw 2.390 2.520 ... (remaining 28345 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 13.740 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3636 Z= 0.312 Angle : 1.220 12.150 4976 Z= 0.681 Chirality : 0.058 0.211 556 Planarity : 0.004 0.022 624 Dihedral : 12.694 80.818 1160 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 2.56 % Allowed : 6.84 % Favored : 90.60 % Rotamer: Outliers : 1.16 % Allowed : 10.47 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.71 % 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: -4.75 (0.27), residues: 468 helix: None (None), residues: 0 sheet: -2.62 (0.25), residues: 264 loop : -3.78 (0.24), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 79 HIS 0.002 0.001 HIS B 87 PHE 0.014 0.003 PHE A 29 TYR 0.014 0.002 TYR A 60 ARG 0.001 0.000 ARG A 59 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.383 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 85 average time/residue: 0.1805 time to fit residues: 18.3703 Evaluate side-chains 46 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 118 ASN B 85 ASN C 82 ASN C 85 ASN D 82 ASN D 85 ASN D 118 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3636 Z= 0.219 Angle : 0.790 7.066 4976 Z= 0.436 Chirality : 0.045 0.155 556 Planarity : 0.003 0.021 624 Dihedral : 8.264 62.054 512 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 1.71 % Allowed : 7.48 % Favored : 90.81 % Rotamer: Outliers : 5.52 % Allowed : 9.01 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % 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: -3.61 (0.31), residues: 468 helix: None (None), residues: 0 sheet: -1.79 (0.27), residues: 288 loop : -3.24 (0.27), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 79 HIS 0.001 0.000 HIS C 127 PHE 0.008 0.002 PHE D 29 TYR 0.006 0.001 TYR B 54 ARG 0.003 0.001 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 61 time to evaluate : 0.392 Fit side-chains REVERT: A 87 HIS cc_start: 0.8163 (m-70) cc_final: 0.7920 (m-70) REVERT: B 87 HIS cc_start: 0.8247 (m-70) cc_final: 0.7992 (m-70) outliers start: 19 outliers final: 11 residues processed: 76 average time/residue: 0.0902 time to fit residues: 9.6240 Evaluate side-chains 59 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 48 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3636 Z= 0.284 Angle : 0.760 6.155 4976 Z= 0.414 Chirality : 0.045 0.162 556 Planarity : 0.003 0.012 624 Dihedral : 7.609 54.370 512 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 1.71 % Allowed : 6.41 % Favored : 91.88 % Rotamer: Outliers : 5.52 % Allowed : 13.37 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % 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: -3.33 (0.32), residues: 468 helix: None (None), residues: 0 sheet: -1.57 (0.28), residues: 292 loop : -3.18 (0.26), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 75 HIS 0.003 0.001 HIS C 127 PHE 0.018 0.004 PHE A 29 TYR 0.007 0.001 TYR D 54 ARG 0.001 0.000 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 58 time to evaluate : 0.390 Fit side-chains outliers start: 19 outliers final: 16 residues processed: 68 average time/residue: 0.0787 time to fit residues: 8.0266 Evaluate side-chains 72 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 56 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 3.9990 chunk 30 optimal weight: 0.0870 chunk 20 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.3562 ------------------------------------------------------------------------------- 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: 0.7930 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3636 Z= 0.179 Angle : 0.667 5.762 4976 Z= 0.364 Chirality : 0.042 0.149 556 Planarity : 0.002 0.018 624 Dihedral : 6.919 47.744 512 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 1.71 % Allowed : 5.34 % Favored : 92.95 % Rotamer: Outliers : 5.23 % Allowed : 14.83 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % 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: -2.96 (0.32), residues: 468 helix: None (None), residues: 0 sheet: -1.32 (0.28), residues: 284 loop : -2.90 (0.26), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 75 HIS 0.002 0.001 HIS B 127 PHE 0.018 0.004 PHE D 29 TYR 0.007 0.001 TYR A 43 ARG 0.001 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 56 time to evaluate : 0.447 Fit side-chains outliers start: 18 outliers final: 13 residues processed: 68 average time/residue: 0.0806 time to fit residues: 8.2752 Evaluate side-chains 65 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 52 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS B 87 HIS D 87 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3636 Z= 0.203 Angle : 0.682 8.141 4976 Z= 0.366 Chirality : 0.043 0.142 556 Planarity : 0.002 0.013 624 Dihedral : 6.499 41.048 512 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 1.28 % Allowed : 5.56 % Favored : 93.16 % Rotamer: Outliers : 6.40 % Allowed : 16.28 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % 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: -2.84 (0.32), residues: 468 helix: None (None), residues: 0 sheet: -1.22 (0.29), residues: 284 loop : -2.84 (0.26), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 75 HIS 0.003 0.001 HIS A 87 PHE 0.015 0.003 PHE C 29 TYR 0.006 0.001 TYR A 43 ARG 0.001 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 53 time to evaluate : 0.383 Fit side-chains outliers start: 22 outliers final: 18 residues processed: 70 average time/residue: 0.0733 time to fit residues: 7.7034 Evaluate side-chains 65 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 47 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS B 87 HIS B 127 HIS D 87 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3636 Z= 0.203 Angle : 0.677 8.154 4976 Z= 0.360 Chirality : 0.042 0.140 556 Planarity : 0.002 0.009 624 Dihedral : 6.030 31.060 512 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.85 % Allowed : 6.84 % Favored : 92.31 % Rotamer: Outliers : 5.81 % Allowed : 18.31 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % 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: -2.89 (0.31), residues: 468 helix: None (None), residues: 0 sheet: -1.28 (0.28), residues: 280 loop : -2.80 (0.26), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 75 HIS 0.003 0.001 HIS D 87 PHE 0.015 0.003 PHE B 29 TYR 0.006 0.001 TYR D 43 ARG 0.001 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 52 time to evaluate : 0.305 Fit side-chains outliers start: 20 outliers final: 16 residues processed: 68 average time/residue: 0.0862 time to fit residues: 8.6188 Evaluate side-chains 64 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 48 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS B 87 HIS D 87 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3636 Z= 0.156 Angle : 0.656 7.262 4976 Z= 0.351 Chirality : 0.041 0.134 556 Planarity : 0.002 0.012 624 Dihedral : 5.518 22.428 512 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.98 % Favored : 93.16 % Rotamer: Outliers : 5.23 % Allowed : 20.64 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.32), residues: 468 helix: None (None), residues: 0 sheet: -1.11 (0.28), residues: 280 loop : -2.64 (0.27), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 108 HIS 0.003 0.001 HIS A 87 PHE 0.016 0.003 PHE A 29 TYR 0.005 0.001 TYR C 43 ARG 0.001 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 56 time to evaluate : 0.577 Fit side-chains outliers start: 18 outliers final: 12 residues processed: 71 average time/residue: 0.0962 time to fit residues: 9.7463 Evaluate side-chains 62 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 50 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 7.9990 chunk 3 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 38 optimal weight: 0.0470 chunk 40 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 overall best weight: 4.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS B 87 HIS ** C 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 3636 Z= 0.462 Angle : 0.784 5.987 4976 Z= 0.420 Chirality : 0.046 0.134 556 Planarity : 0.003 0.017 624 Dihedral : 6.340 24.694 512 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.85 % Allowed : 9.40 % Favored : 89.74 % Rotamer: Outliers : 6.10 % Allowed : 21.51 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.32), residues: 468 helix: None (None), residues: 0 sheet: -0.94 (0.29), residues: 280 loop : -2.78 (0.26), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 92 HIS 0.002 0.001 HIS C 127 PHE 0.011 0.003 PHE C 29 TYR 0.008 0.002 TYR D 43 ARG 0.002 0.000 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 46 time to evaluate : 0.347 Fit side-chains outliers start: 21 outliers final: 15 residues processed: 60 average time/residue: 0.0747 time to fit residues: 6.7546 Evaluate side-chains 59 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 44 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 25 optimal weight: 0.0970 chunk 41 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS B 87 HIS C 87 HIS D 87 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3636 Z= 0.176 Angle : 0.681 7.035 4976 Z= 0.361 Chirality : 0.042 0.128 556 Planarity : 0.002 0.015 624 Dihedral : 5.634 26.018 512 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.98 % Favored : 93.16 % Rotamer: Outliers : 4.36 % Allowed : 22.97 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.32), residues: 468 helix: None (None), residues: 0 sheet: -0.86 (0.29), residues: 276 loop : -2.60 (0.27), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 108 HIS 0.003 0.001 HIS D 87 PHE 0.017 0.003 PHE A 29 TYR 0.005 0.001 TYR A 43 ARG 0.001 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 49 time to evaluate : 0.402 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 61 average time/residue: 0.0827 time to fit residues: 7.4541 Evaluate side-chains 59 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 10 optimal weight: 0.0870 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS A 127 HIS B 87 HIS C 87 HIS D 87 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3636 Z= 0.174 Angle : 0.679 6.551 4976 Z= 0.360 Chirality : 0.042 0.130 556 Planarity : 0.002 0.016 624 Dihedral : 5.269 26.585 512 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.56 % Favored : 93.59 % Rotamer: Outliers : 3.49 % Allowed : 24.42 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.33), residues: 468 helix: None (None), residues: 0 sheet: -0.63 (0.30), residues: 284 loop : -2.49 (0.28), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 108 HIS 0.003 0.001 HIS B 87 PHE 0.015 0.003 PHE C 29 TYR 0.005 0.001 TYR C 43 ARG 0.001 0.000 ARG A 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 53 time to evaluate : 0.374 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 63 average time/residue: 0.0829 time to fit residues: 7.6721 Evaluate side-chains 61 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS B 87 HIS C 87 HIS ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.163735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.130783 restraints weight = 4196.114| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 3.22 r_work: 0.3504 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3636 Z= 0.302 Angle : 0.725 5.867 4976 Z= 0.386 Chirality : 0.043 0.127 556 Planarity : 0.002 0.018 624 Dihedral : 5.733 29.733 512 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.26 % Favored : 91.88 % Rotamer: Outliers : 4.07 % Allowed : 25.00 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.33), residues: 468 helix: None (None), residues: 0 sheet: -0.51 (0.30), residues: 280 loop : -2.65 (0.27), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 75 HIS 0.002 0.001 HIS C 127 PHE 0.012 0.003 PHE D 29 TYR 0.006 0.001 TYR C 43 ARG 0.001 0.000 ARG B 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1037.87 seconds wall clock time: 19 minutes 34.00 seconds (1174.00 seconds total)