Starting phenix.real_space_refine on Sun Mar 10 14:16:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m61_23686/03_2024/7m61_23686_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m61_23686/03_2024/7m61_23686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m61_23686/03_2024/7m61_23686.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m61_23686/03_2024/7m61_23686.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m61_23686/03_2024/7m61_23686_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m61_23686/03_2024/7m61_23686_updated.pdb" } resolution = 3.8 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 ------------------------------------------------------------------------------- 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= 1.000 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 1030 2.51 5 N 305 2.21 5 O 355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 1690 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 185 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "B" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 153 Unusual residues: {'NH2': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 20} Chain: "C" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 185 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "D" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 153 Unusual residues: {'NH2': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 20} Chain: "E" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 185 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "F" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 153 Unusual residues: {'NH2': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 20} Chain: "G" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 185 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "H" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 153 Unusual residues: {'NH2': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 20} Chain: "I" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 185 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "J" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 153 Unusual residues: {'NH2': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 20} Time building chain proxies: 1.03, per 1000 atoms: 0.61 Number of scatterers: 1690 At special positions: 0 Unit cell: (59.08, 51.695, 48.53, 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 355 8.00 N 305 7.00 C 1030 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: 0.97 Conformation dependent library (CDL) restraints added in 323.1 milliseconds 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 420 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 275 1.29 - 1.35: 303 1.35 - 1.42: 232 1.42 - 1.48: 250 1.48 - 1.55: 655 Bond restraints: 1715 Sorted by residual: bond pdb=" CB ILE E 26 " pdb=" CG1 ILE E 26 " ideal model delta sigma weight residual 1.530 1.505 0.025 2.00e-02 2.50e+03 1.53e+00 bond pdb=" CB ILE I 26 " pdb=" CG1 ILE I 26 " ideal model delta sigma weight residual 1.530 1.505 0.025 2.00e-02 2.50e+03 1.52e+00 bond pdb=" CB ILE C 26 " pdb=" CG1 ILE C 26 " ideal model delta sigma weight residual 1.530 1.505 0.025 2.00e-02 2.50e+03 1.52e+00 bond pdb=" CB ILE G 26 " pdb=" CG1 ILE G 26 " ideal model delta sigma weight residual 1.530 1.505 0.025 2.00e-02 2.50e+03 1.51e+00 bond pdb=" CB ILE A 26 " pdb=" CG1 ILE A 26 " ideal model delta sigma weight residual 1.530 1.505 0.025 2.00e-02 2.50e+03 1.51e+00 ... (remaining 1710 not shown) Histogram of bond angle deviations from ideal: 101.48 - 107.42: 40 107.42 - 113.36: 940 113.36 - 119.30: 370 119.30 - 125.24: 975 125.24 - 131.18: 10 Bond angle restraints: 2335 Sorted by residual: angle pdb=" CG1 ILE A 26 " pdb=" CB ILE A 26 " pdb=" CG2 ILE A 26 " ideal model delta sigma weight residual 110.70 101.48 9.22 3.00e+00 1.11e-01 9.45e+00 angle pdb=" CG1 ILE I 26 " pdb=" CB ILE I 26 " pdb=" CG2 ILE I 26 " ideal model delta sigma weight residual 110.70 101.49 9.21 3.00e+00 1.11e-01 9.42e+00 angle pdb=" CG1 ILE G 26 " pdb=" CB ILE G 26 " pdb=" CG2 ILE G 26 " ideal model delta sigma weight residual 110.70 101.51 9.19 3.00e+00 1.11e-01 9.38e+00 angle pdb=" CG1 ILE E 26 " pdb=" CB ILE E 26 " pdb=" CG2 ILE E 26 " ideal model delta sigma weight residual 110.70 101.52 9.18 3.00e+00 1.11e-01 9.37e+00 angle pdb=" CG1 ILE C 26 " pdb=" CB ILE C 26 " pdb=" CG2 ILE C 26 " ideal model delta sigma weight residual 110.70 101.52 9.18 3.00e+00 1.11e-01 9.35e+00 ... (remaining 2330 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.63: 780 8.63 - 17.25: 90 17.25 - 25.87: 40 25.87 - 34.50: 20 34.50 - 43.12: 20 Dihedral angle restraints: 950 sinusoidal: 300 harmonic: 650 Sorted by residual: dihedral pdb=" CA PHE I 15 " pdb=" C PHE I 15 " pdb=" N LEU I 16 " pdb=" CA LEU I 16 " ideal model delta harmonic sigma weight residual 180.00 167.01 12.99 0 5.00e+00 4.00e-02 6.75e+00 dihedral pdb=" CA PHE G 15 " pdb=" C PHE G 15 " pdb=" N LEU G 16 " pdb=" CA LEU G 16 " ideal model delta harmonic sigma weight residual 180.00 167.04 12.96 0 5.00e+00 4.00e-02 6.72e+00 dihedral pdb=" CA PHE A 15 " pdb=" C PHE A 15 " pdb=" N LEU A 16 " pdb=" CA LEU A 16 " ideal model delta harmonic sigma weight residual 180.00 167.07 12.93 0 5.00e+00 4.00e-02 6.69e+00 ... (remaining 947 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.061: 200 0.061 - 0.121: 51 0.121 - 0.181: 9 0.181 - 0.241: 10 0.241 - 0.301: 5 Chirality restraints: 275 Sorted by residual: chirality pdb=" CG LEU B 27 " pdb=" CB LEU B 27 " pdb=" CD1 LEU B 27 " pdb=" CD2 LEU B 27 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CG LEU D 27 " pdb=" CB LEU D 27 " pdb=" CD1 LEU D 27 " pdb=" CD2 LEU D 27 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CG LEU F 27 " pdb=" CB LEU F 27 " pdb=" CD1 LEU F 27 " pdb=" CD2 LEU F 27 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 272 not shown) Planarity restraints: 310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR J 37 " -0.015 2.00e-02 2.50e+03 1.72e-02 5.94e+00 pdb=" CG TYR J 37 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR J 37 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR J 37 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR J 37 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR J 37 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR J 37 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR J 37 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 37 " -0.015 2.00e-02 2.50e+03 1.72e-02 5.93e+00 pdb=" CG TYR F 37 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR F 37 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR F 37 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR F 37 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR F 37 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR F 37 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 37 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 37 " -0.015 2.00e-02 2.50e+03 1.72e-02 5.91e+00 pdb=" CG TYR B 37 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR B 37 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 37 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR B 37 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR B 37 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 37 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 37 " 0.000 2.00e-02 2.50e+03 ... (remaining 307 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 291 2.75 - 3.29: 1820 3.29 - 3.83: 2873 3.83 - 4.36: 3266 4.36 - 4.90: 6151 Nonbonded interactions: 14401 Sorted by model distance: nonbonded pdb=" O SER E 34 " pdb=" OG SER G 34 " model vdw 2.218 2.440 nonbonded pdb=" O SER A 34 " pdb=" OG SER I 34 " model vdw 2.218 2.440 nonbonded pdb=" OG SER A 34 " pdb=" O SER G 34 " model vdw 2.218 2.440 nonbonded pdb=" O SER C 34 " pdb=" OG SER E 34 " model vdw 2.218 2.440 nonbonded pdb=" ND2 ASN G 22 " pdb=" O GLY G 24 " model vdw 2.433 2.520 ... (remaining 14396 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 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.180 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: 0.550 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.840 Find NCS groups from input model: 0.130 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 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 1715 Z= 0.205 Angle : 1.014 9.221 2335 Z= 0.506 Chirality : 0.076 0.301 275 Planarity : 0.003 0.017 310 Dihedral : 12.788 43.118 530 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % 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: -4.63 (0.34), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.26), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 18 PHE 0.005 0.001 PHE H 23 TYR 0.040 0.006 TYR J 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.203 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0660 time to fit residues: 3.5157 Evaluate side-chains 21 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 20.0000 chunk 15 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 1715 Z= 0.167 Angle : 0.701 7.934 2335 Z= 0.340 Chirality : 0.050 0.175 275 Planarity : 0.002 0.009 310 Dihedral : 5.150 14.238 230 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 2.56 % Allowed : 15.90 % Favored : 81.54 % 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: -4.88 (0.32), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.71 (0.24), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 18 PHE 0.013 0.002 PHE F 23 TYR 0.022 0.002 TYR H 37 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 32 time to evaluate : 0.203 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 33 average time/residue: 0.0661 time to fit residues: 2.9385 Evaluate side-chains 20 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 17 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain F residue 37 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 4.9990 chunk 18 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 chunk 17 optimal weight: 8.9990 chunk 13 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1715 Z= 0.151 Angle : 0.658 7.965 2335 Z= 0.316 Chirality : 0.046 0.194 275 Planarity : 0.002 0.009 310 Dihedral : 4.943 14.878 230 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 5.13 % Allowed : 18.46 % Favored : 76.41 % 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: -4.81 (0.33), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.66 (0.25), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 18 PHE 0.016 0.002 PHE H 23 TYR 0.022 0.002 TYR H 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 25 time to evaluate : 0.204 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 31 average time/residue: 0.0678 time to fit residues: 2.8646 Evaluate side-chains 27 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 19 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 31 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 4 optimal weight: 30.0000 chunk 6 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 1715 Z= 0.179 Angle : 0.671 7.895 2335 Z= 0.332 Chirality : 0.046 0.168 275 Planarity : 0.002 0.012 310 Dihedral : 5.382 14.235 230 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 20.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 5.64 % Allowed : 24.10 % Favored : 70.26 % 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: -4.74 (0.35), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.27), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 18 PHE 0.028 0.002 PHE H 23 TYR 0.022 0.002 TYR H 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 24 time to evaluate : 0.224 Fit side-chains REVERT: J 37 TYR cc_start: 0.7643 (m-10) cc_final: 0.4869 (p90) outliers start: 11 outliers final: 6 residues processed: 31 average time/residue: 0.0640 time to fit residues: 2.7205 Evaluate side-chains 21 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 15 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain I residue 31 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 0.0670 chunk 3 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 4 optimal weight: 30.0000 chunk 19 optimal weight: 7.9990 chunk 16 optimal weight: 20.0000 chunk 8 optimal weight: 0.0170 chunk 1 optimal weight: 9.9990 chunk 6 optimal weight: 0.0670 chunk 10 optimal weight: 10.0000 chunk 18 optimal weight: 0.0070 overall best weight: 1.4314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 1715 Z= 0.089 Angle : 0.554 7.665 2335 Z= 0.262 Chirality : 0.041 0.137 275 Planarity : 0.002 0.009 310 Dihedral : 4.033 12.100 230 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 5.13 % Allowed : 25.64 % Favored : 69.23 % 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: -4.59 (0.34), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.26), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 18 PHE 0.010 0.001 PHE H 23 TYR 0.015 0.001 TYR H 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 29 time to evaluate : 0.199 Fit side-chains REVERT: J 37 TYR cc_start: 0.6820 (m-10) cc_final: 0.4779 (p90) outliers start: 10 outliers final: 7 residues processed: 38 average time/residue: 0.0623 time to fit residues: 3.1408 Evaluate side-chains 26 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 19 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 37 TYR Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain H residue 37 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 30.0000 chunk 11 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 16 optimal weight: 30.0000 chunk 19 optimal weight: 9.9990 chunk 12 optimal weight: 30.0000 chunk 8 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 3 optimal weight: 0.0980 overall best weight: 7.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 1715 Z= 0.178 Angle : 0.644 8.369 2335 Z= 0.325 Chirality : 0.044 0.141 275 Planarity : 0.002 0.012 310 Dihedral : 5.226 17.160 230 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 23.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.76 % Favored : 85.24 % Rotamer: Outliers : 7.69 % Allowed : 26.15 % Favored : 66.15 % 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: -4.60 (0.35), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (0.27), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 18 PHE 0.017 0.002 PHE H 23 TYR 0.020 0.002 TYR H 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 21 time to evaluate : 0.198 Fit side-chains REVERT: J 37 TYR cc_start: 0.6817 (m-10) cc_final: 0.4782 (p90) outliers start: 15 outliers final: 11 residues processed: 32 average time/residue: 0.0674 time to fit residues: 2.8777 Evaluate side-chains 28 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 17 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 37 TYR Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain I residue 31 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1715 Z= 0.149 Angle : 0.615 7.573 2335 Z= 0.307 Chirality : 0.044 0.129 275 Planarity : 0.002 0.007 310 Dihedral : 4.950 16.206 230 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 23.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 7.18 % Allowed : 27.18 % Favored : 65.64 % 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: -4.58 (0.35), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.27), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 18 PHE 0.014 0.002 PHE F 23 TYR 0.018 0.002 TYR H 37 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 21 time to evaluate : 0.201 Fit side-chains REVERT: C 31 ASN cc_start: 0.7983 (OUTLIER) cc_final: 0.7292 (p0) REVERT: J 37 TYR cc_start: 0.6273 (m-10) cc_final: 0.4583 (p90) outliers start: 14 outliers final: 12 residues processed: 30 average time/residue: 0.0643 time to fit residues: 2.6313 Evaluate side-chains 32 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 19 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 37 TYR Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain I residue 31 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 17 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 1715 Z= 0.195 Angle : 0.685 8.231 2335 Z= 0.344 Chirality : 0.047 0.225 275 Planarity : 0.002 0.009 310 Dihedral : 5.509 16.226 230 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 26.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.14 % Favored : 82.86 % Rotamer: Outliers : 8.21 % Allowed : 25.64 % Favored : 66.15 % 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: -4.68 (0.34), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.26), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 18 PHE 0.018 0.002 PHE F 23 TYR 0.021 0.002 TYR H 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 19 time to evaluate : 0.203 Fit side-chains REVERT: C 31 ASN cc_start: 0.8078 (OUTLIER) cc_final: 0.7416 (p0) REVERT: J 37 TYR cc_start: 0.6170 (m-10) cc_final: 0.4538 (p90) outliers start: 16 outliers final: 14 residues processed: 31 average time/residue: 0.0651 time to fit residues: 2.7570 Evaluate side-chains 33 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 18 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 37 TYR Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain I residue 31 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 30.0000 chunk 9 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 4 optimal weight: 30.0000 chunk 14 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1715 Z= 0.148 Angle : 0.656 8.366 2335 Z= 0.321 Chirality : 0.047 0.224 275 Planarity : 0.002 0.007 310 Dihedral : 5.109 16.005 230 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 24.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 7.69 % Allowed : 25.13 % Favored : 67.18 % 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: -4.59 (0.34), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.26), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 18 PHE 0.015 0.001 PHE F 23 TYR 0.017 0.002 TYR H 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 22 time to evaluate : 0.224 Fit side-chains REVERT: C 31 ASN cc_start: 0.7889 (OUTLIER) cc_final: 0.7170 (p0) REVERT: J 37 TYR cc_start: 0.6118 (m-10) cc_final: 0.4570 (p90) outliers start: 15 outliers final: 13 residues processed: 33 average time/residue: 0.0665 time to fit residues: 2.9983 Evaluate side-chains 34 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 20 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 37 TYR Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain I residue 31 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 9.9990 chunk 10 optimal weight: 30.0000 chunk 13 optimal weight: 4.9990 chunk 0 optimal weight: 40.0000 chunk 12 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 4 optimal weight: 40.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 1715 Z= 0.157 Angle : 0.685 8.620 2335 Z= 0.330 Chirality : 0.048 0.232 275 Planarity : 0.002 0.008 310 Dihedral : 5.184 15.772 230 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 24.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.14 % Favored : 82.86 % Rotamer: Outliers : 7.18 % Allowed : 26.15 % Favored : 66.67 % 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: -4.62 (0.34), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.26), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 18 PHE 0.015 0.002 PHE F 23 TYR 0.017 0.002 TYR H 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 20 time to evaluate : 0.211 Fit side-chains REVERT: C 31 ASN cc_start: 0.7980 (OUTLIER) cc_final: 0.7297 (p0) REVERT: J 37 TYR cc_start: 0.5862 (m-10) cc_final: 0.4498 (p90) outliers start: 14 outliers final: 13 residues processed: 30 average time/residue: 0.0671 time to fit residues: 2.7126 Evaluate side-chains 34 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 20 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 37 TYR Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain I residue 31 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.100507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.087489 restraints weight = 5024.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.089572 restraints weight = 2693.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.090775 restraints weight = 1827.041| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.5340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1715 Z= 0.175 Angle : 0.696 8.195 2335 Z= 0.340 Chirality : 0.048 0.218 275 Planarity : 0.002 0.008 310 Dihedral : 5.422 17.150 230 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 26.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.24 % Favored : 84.76 % Rotamer: Outliers : 7.69 % Allowed : 25.64 % Favored : 66.67 % 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: -4.59 (0.34), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.26), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 18 PHE 0.016 0.002 PHE F 23 TYR 0.018 0.002 TYR F 37 =============================================================================== Job complete usr+sys time: 637.74 seconds wall clock time: 13 minutes 32.74 seconds (812.74 seconds total)