Starting phenix.real_space_refine on Thu Dec 7 16:12:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrf_11380/12_2023/6zrf_11380_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrf_11380/12_2023/6zrf_11380.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrf_11380/12_2023/6zrf_11380_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrf_11380/12_2023/6zrf_11380_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrf_11380/12_2023/6zrf_11380_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrf_11380/12_2023/6zrf_11380.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrf_11380/12_2023/6zrf_11380.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrf_11380/12_2023/6zrf_11380_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrf_11380/12_2023/6zrf_11380_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 1368 2.51 5 N 396 2.21 5 O 456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2220 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 185 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "C" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 185 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "E" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 185 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "G" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 185 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "I" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 185 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "K" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 185 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "B" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 185 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "D" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 185 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "F" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 185 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "H" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 185 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "J" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 185 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "L" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 185 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Time building chain proxies: 1.61, per 1000 atoms: 0.73 Number of scatterers: 2220 At special positions: 0 Unit cell: (64.965, 47.925, 47.925, 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 456 8.00 N 396 7.00 C 1368 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: 1.01 Conformation dependent library (CDL) restraints added in 365.6 milliseconds 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 552 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: 0.34 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: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 360 1.28 - 1.34: 384 1.34 - 1.41: 276 1.41 - 1.47: 373 1.47 - 1.54: 863 Bond restraints: 2256 Sorted by residual: bond pdb=" C TYC H 37 " pdb=" NXT TYC H 37 " ideal model delta sigma weight residual 1.451 1.327 0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" C TYC J 37 " pdb=" NXT TYC J 37 " ideal model delta sigma weight residual 1.451 1.327 0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" C TYC G 37 " pdb=" NXT TYC G 37 " ideal model delta sigma weight residual 1.451 1.327 0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" C TYC B 37 " pdb=" NXT TYC B 37 " ideal model delta sigma weight residual 1.451 1.327 0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" C TYC I 37 " pdb=" NXT TYC I 37 " ideal model delta sigma weight residual 1.451 1.327 0.124 2.00e-02 2.50e+03 3.82e+01 ... (remaining 2251 not shown) Histogram of bond angle deviations from ideal: 102.97 - 108.68: 192 108.68 - 114.38: 1130 114.38 - 120.09: 653 120.09 - 125.79: 1085 125.79 - 131.50: 12 Bond angle restraints: 3072 Sorted by residual: angle pdb=" C PHE J 23 " pdb=" CA PHE J 23 " pdb=" CB PHE J 23 " ideal model delta sigma weight residual 110.65 102.97 7.68 1.95e+00 2.63e-01 1.55e+01 angle pdb=" C PHE B 23 " pdb=" CA PHE B 23 " pdb=" CB PHE B 23 " ideal model delta sigma weight residual 110.65 103.84 6.81 1.95e+00 2.63e-01 1.22e+01 angle pdb=" C PHE I 23 " pdb=" CA PHE I 23 " pdb=" CB PHE I 23 " ideal model delta sigma weight residual 110.65 103.84 6.81 1.95e+00 2.63e-01 1.22e+01 angle pdb=" C PHE A 23 " pdb=" CA PHE A 23 " pdb=" CB PHE A 23 " ideal model delta sigma weight residual 110.65 103.86 6.79 1.95e+00 2.63e-01 1.21e+01 angle pdb=" C PHE K 23 " pdb=" CA PHE K 23 " pdb=" CB PHE K 23 " ideal model delta sigma weight residual 110.65 103.86 6.79 1.95e+00 2.63e-01 1.21e+01 ... (remaining 3067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.49: 997 11.49 - 22.99: 155 22.99 - 34.48: 84 34.48 - 45.97: 0 45.97 - 57.46: 12 Dihedral angle restraints: 1248 sinusoidal: 408 harmonic: 840 Sorted by residual: dihedral pdb=" CA ALA F 25 " pdb=" C ALA F 25 " pdb=" N ILE F 26 " pdb=" CA ILE F 26 " ideal model delta harmonic sigma weight residual 180.00 161.97 18.03 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ALA A 25 " pdb=" C ALA A 25 " pdb=" N ILE A 26 " pdb=" CA ILE A 26 " ideal model delta harmonic sigma weight residual 180.00 161.98 18.02 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ALA D 25 " pdb=" C ALA D 25 " pdb=" N ILE D 26 " pdb=" CA ILE D 26 " ideal model delta harmonic sigma weight residual 180.00 161.99 18.01 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 1245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 147 0.026 - 0.052: 163 0.052 - 0.078: 14 0.078 - 0.103: 12 0.103 - 0.129: 24 Chirality restraints: 360 Sorted by residual: chirality pdb=" CA TYC F 37 " pdb=" N TYC F 37 " pdb=" C TYC F 37 " pdb=" CB TYC F 37 " both_signs ideal model delta sigma weight residual False 2.61 2.48 0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA ILE F 26 " pdb=" N ILE F 26 " pdb=" C ILE F 26 " pdb=" CB ILE F 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA ILE G 26 " pdb=" N ILE G 26 " pdb=" C ILE G 26 " pdb=" CB ILE G 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.07e-01 ... (remaining 357 not shown) Planarity restraints: 408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 23 " 0.012 2.00e-02 2.50e+03 1.04e-02 1.90e+00 pdb=" CG PHE C 23 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE C 23 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE C 23 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 23 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 23 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 23 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 23 " 0.012 2.00e-02 2.50e+03 1.04e-02 1.89e+00 pdb=" CG PHE B 23 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE B 23 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE B 23 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 23 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 23 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 23 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 23 " 0.012 2.00e-02 2.50e+03 1.04e-02 1.88e+00 pdb=" CG PHE I 23 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE I 23 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE I 23 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE I 23 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE I 23 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE I 23 " 0.002 2.00e-02 2.50e+03 ... (remaining 405 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 78 2.57 - 3.16: 2248 3.16 - 3.74: 3211 3.74 - 4.32: 4612 4.32 - 4.90: 8142 Nonbonded interactions: 18291 Sorted by model distance: nonbonded pdb=" O SER H 20 " pdb=" OG SER J 20 " model vdw 1.993 2.440 nonbonded pdb=" ND2 ASN C 31 " pdb=" OD1 ASN C 35 " model vdw 2.148 2.520 nonbonded pdb=" ND2 ASN B 31 " pdb=" OD1 ASN B 35 " model vdw 2.148 2.520 nonbonded pdb=" ND2 ASN E 31 " pdb=" OD1 ASN E 35 " model vdw 2.148 2.520 nonbonded pdb=" ND2 ASN G 31 " pdb=" OD1 ASN G 35 " model vdw 2.148 2.520 ... (remaining 18286 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' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 0.350 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: 1.680 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.810 Find NCS groups from input model: 0.170 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 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 : 0.014 0.124 2256 Z= 0.692 Angle : 1.284 9.584 3072 Z= 0.601 Chirality : 0.046 0.129 360 Planarity : 0.003 0.010 408 Dihedral : 15.234 57.462 696 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 42.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % 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: -6.22 (0.32), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.73 (0.24), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 18 PHE 0.024 0.005 PHE C 23 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.249 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0645 time to fit residues: 4.3790 Evaluate side-chains 21 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.242 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2256 Z= 0.137 Angle : 0.671 6.962 3072 Z= 0.329 Chirality : 0.045 0.131 360 Planarity : 0.002 0.007 408 Dihedral : 11.679 56.962 324 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 22.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.33 % Allowed : 12.92 % Favored : 83.75 % 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: -5.95 (0.33), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.53 (0.25), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 18 PHE 0.010 0.002 PHE E 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.243 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 55 average time/residue: 0.0540 time to fit residues: 4.3502 Evaluate side-chains 42 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.244 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0242 time to fit residues: 0.3784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 10 optimal weight: 0.0870 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2256 Z= 0.163 Angle : 0.649 7.501 3072 Z= 0.317 Chirality : 0.044 0.127 360 Planarity : 0.002 0.006 408 Dihedral : 11.358 56.674 324 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 21.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 2.92 % Allowed : 23.75 % Favored : 73.33 % 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: -5.93 (0.34), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.51 (0.26), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 18 PHE 0.011 0.002 PHE K 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.239 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 45 average time/residue: 0.0516 time to fit residues: 3.4822 Evaluate side-chains 35 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 31 time to evaluate : 0.228 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0263 time to fit residues: 0.4638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 13 optimal weight: 0.0670 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.3720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.021 2256 Z= 0.214 Angle : 0.658 6.821 3072 Z= 0.326 Chirality : 0.045 0.131 360 Planarity : 0.002 0.006 408 Dihedral : 11.524 59.790 324 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 26.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Rotamer: Outliers : 1.25 % Allowed : 27.08 % Favored : 71.67 % 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: -5.93 (0.35), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.52 (0.27), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 18 PHE 0.012 0.003 PHE K 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 time to evaluate : 0.245 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 34 average time/residue: 0.0505 time to fit residues: 2.7102 Evaluate side-chains 32 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 0.246 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0245 time to fit residues: 0.3363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 HIS ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 2256 Z= 0.265 Angle : 0.663 4.691 3072 Z= 0.337 Chirality : 0.046 0.130 360 Planarity : 0.002 0.006 408 Dihedral : 11.778 58.535 324 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 30.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 1.67 % Allowed : 26.67 % Favored : 71.67 % 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: -5.95 (0.35), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.53 (0.27), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 18 PHE 0.013 0.003 PHE K 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 31 time to evaluate : 0.264 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 33 average time/residue: 0.0524 time to fit residues: 2.6936 Evaluate side-chains 30 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 29 time to evaluate : 0.214 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0252 time to fit residues: 0.3032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2256 Z= 0.206 Angle : 0.633 6.004 3072 Z= 0.314 Chirality : 0.046 0.133 360 Planarity : 0.002 0.005 408 Dihedral : 11.435 58.797 324 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 24.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Rotamer: Outliers : 1.25 % Allowed : 28.75 % Favored : 70.00 % 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: -5.92 (0.36), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.51 (0.28), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 18 PHE 0.011 0.002 PHE K 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 0.238 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 32 average time/residue: 0.0513 time to fit residues: 2.5746 Evaluate side-chains 32 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 0.238 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0258 time to fit residues: 0.3758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 0.0030 chunk 2 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2256 Z= 0.120 Angle : 0.563 6.043 3072 Z= 0.274 Chirality : 0.045 0.126 360 Planarity : 0.001 0.007 408 Dihedral : 10.819 58.884 324 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Rotamer: Outliers : 2.08 % Allowed : 27.08 % Favored : 70.83 % 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: -5.92 (0.36), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.51 (0.28), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 18 PHE 0.007 0.002 PHE K 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.237 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 38 average time/residue: 0.0528 time to fit residues: 3.0563 Evaluate side-chains 35 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.215 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0270 time to fit residues: 0.3980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2256 Z= 0.144 Angle : 0.620 6.288 3072 Z= 0.291 Chirality : 0.045 0.129 360 Planarity : 0.001 0.008 408 Dihedral : 10.840 59.936 324 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 20.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Rotamer: Outliers : 0.83 % Allowed : 25.42 % Favored : 73.75 % 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: -5.92 (0.36), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.50 (0.28), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 18 PHE 0.008 0.002 PHE K 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.248 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 34 average time/residue: 0.0507 time to fit residues: 2.6987 Evaluate side-chains 31 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.237 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 7 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 2256 Z= 0.169 Angle : 0.614 6.805 3072 Z= 0.293 Chirality : 0.045 0.131 360 Planarity : 0.001 0.007 408 Dihedral : 11.085 59.727 324 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 22.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 0.83 % Allowed : 26.25 % Favored : 72.92 % 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: -5.91 (0.37), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.50 (0.28), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 18 PHE 0.009 0.002 PHE K 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.242 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 33 average time/residue: 0.0508 time to fit residues: 2.6308 Evaluate side-chains 32 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.237 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 0.0570 chunk 0 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2256 Z= 0.098 Angle : 0.567 6.587 3072 Z= 0.265 Chirality : 0.045 0.127 360 Planarity : 0.001 0.007 408 Dihedral : 10.522 59.129 324 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 0.42 % Allowed : 26.67 % Favored : 72.92 % 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: -5.81 (0.36), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.42 (0.28), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS E 18 PHE 0.006 0.001 PHE K 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.242 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 37 average time/residue: 0.0522 time to fit residues: 2.9651 Evaluate side-chains 34 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.239 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.157650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.132799 restraints weight = 3761.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.136305 restraints weight = 1990.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.138616 restraints weight = 1316.503| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 2256 Z= 0.200 Angle : 0.623 6.152 3072 Z= 0.300 Chirality : 0.045 0.131 360 Planarity : 0.001 0.005 408 Dihedral : 11.083 59.531 324 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 22.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.26 % Favored : 86.74 % Rotamer: Outliers : 0.42 % Allowed : 26.25 % Favored : 73.33 % 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: -5.85 (0.37), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.45 (0.28), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 18 PHE 0.011 0.002 PHE K 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 933.62 seconds wall clock time: 17 minutes 31.32 seconds (1051.32 seconds total)