Starting phenix.real_space_refine on Thu Dec 7 16:37:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynp_33968/12_2023/7ynp_33968_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynp_33968/12_2023/7ynp_33968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynp_33968/12_2023/7ynp_33968.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynp_33968/12_2023/7ynp_33968.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynp_33968/12_2023/7ynp_33968_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynp_33968/12_2023/7ynp_33968_neut_updated.pdb" } resolution = 2.8 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 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 2 5.16 5 C 1620 2.51 5 N 444 2.21 5 O 502 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 46": "OE1" <-> "OE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "F GLU 46": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2568 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "B" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "C" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "D" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "E" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "F" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'IZM': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'IZM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.88, per 1000 atoms: 0.73 Number of scatterers: 2568 At special positions: 0 Unit cell: (97.11, 105.41, 31.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 2 16.00 O 502 8.00 N 444 7.00 C 1620 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 540.2 milliseconds 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 624 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: 0.45 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: 1.22 - 1.30: 432 1.30 - 1.37: 424 1.37 - 1.45: 260 1.45 - 1.53: 1331 1.53 - 1.61: 137 Bond restraints: 2584 Sorted by residual: bond pdb=" C10 IZM D 201 " pdb=" S17 IZM D 201 " ideal model delta sigma weight residual 1.748 1.575 0.173 2.00e-02 2.50e+03 7.46e+01 bond pdb=" C10 IZM F 201 " pdb=" S17 IZM F 201 " ideal model delta sigma weight residual 1.748 1.576 0.172 2.00e-02 2.50e+03 7.40e+01 bond pdb=" C09 IZM D 201 " pdb=" C10 IZM D 201 " ideal model delta sigma weight residual 1.433 1.574 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C09 IZM F 201 " pdb=" C10 IZM F 201 " ideal model delta sigma weight residual 1.433 1.573 -0.140 2.00e-02 2.50e+03 4.90e+01 bond pdb=" C13 IZM D 201 " pdb=" S17 IZM D 201 " ideal model delta sigma weight residual 1.744 1.608 0.136 2.00e-02 2.50e+03 4.60e+01 ... (remaining 2579 not shown) Histogram of bond angle deviations from ideal: 99.25 - 106.30: 10 106.30 - 113.36: 1624 113.36 - 120.41: 851 120.41 - 127.46: 1001 127.46 - 134.52: 10 Bond angle restraints: 3496 Sorted by residual: angle pdb=" C08 IZM F 201 " pdb=" C09 IZM F 201 " pdb=" C10 IZM F 201 " ideal model delta sigma weight residual 125.57 112.89 12.68 3.00e+00 1.11e-01 1.79e+01 angle pdb=" C08 IZM D 201 " pdb=" C09 IZM D 201 " pdb=" C10 IZM D 201 " ideal model delta sigma weight residual 125.57 112.97 12.60 3.00e+00 1.11e-01 1.76e+01 angle pdb=" C07 IZM F 201 " pdb=" C08 IZM F 201 " pdb=" C09 IZM F 201 " ideal model delta sigma weight residual 123.72 111.56 12.16 3.00e+00 1.11e-01 1.64e+01 angle pdb=" C07 IZM D 201 " pdb=" C08 IZM D 201 " pdb=" C09 IZM D 201 " ideal model delta sigma weight residual 123.72 111.57 12.15 3.00e+00 1.11e-01 1.64e+01 angle pdb=" C10 IZM F 201 " pdb=" S17 IZM F 201 " pdb=" C13 IZM F 201 " ideal model delta sigma weight residual 89.24 99.25 -10.01 3.00e+00 1.11e-01 1.11e+01 ... (remaining 3491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.28: 1322 16.28 - 32.57: 138 32.57 - 48.85: 30 48.85 - 65.13: 0 65.13 - 81.42: 4 Dihedral angle restraints: 1494 sinusoidal: 504 harmonic: 990 Sorted by residual: dihedral pdb=" CB LYS D 60 " pdb=" CG LYS D 60 " pdb=" CD LYS D 60 " pdb=" CE LYS D 60 " ideal model delta sinusoidal sigma weight residual 180.00 140.70 39.30 3 1.50e+01 4.44e-03 6.96e+00 dihedral pdb=" CB LYS B 60 " pdb=" CG LYS B 60 " pdb=" CD LYS B 60 " pdb=" CE LYS B 60 " ideal model delta sinusoidal sigma weight residual 180.00 140.77 39.23 3 1.50e+01 4.44e-03 6.94e+00 dihedral pdb=" CB LYS A 60 " pdb=" CG LYS A 60 " pdb=" CD LYS A 60 " pdb=" CE LYS A 60 " ideal model delta sinusoidal sigma weight residual 180.00 140.78 39.22 3 1.50e+01 4.44e-03 6.94e+00 ... (remaining 1491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 210 0.032 - 0.064: 134 0.064 - 0.097: 52 0.097 - 0.129: 54 0.129 - 0.161: 6 Chirality restraints: 456 Sorted by residual: chirality pdb=" CB THR D 72 " pdb=" CA THR D 72 " pdb=" OG1 THR D 72 " pdb=" CG2 THR D 72 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.48e-01 chirality pdb=" CB THR A 72 " pdb=" CA THR A 72 " pdb=" OG1 THR A 72 " pdb=" CG2 THR A 72 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CB THR E 72 " pdb=" CA THR E 72 " pdb=" OG1 THR E 72 " pdb=" CG2 THR E 72 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 453 not shown) Planarity restraints: 428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 50 " 0.009 2.00e-02 2.50e+03 8.58e-03 1.10e+00 pdb=" CG HIS A 50 " -0.018 2.00e-02 2.50e+03 pdb=" ND1 HIS A 50 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS A 50 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS A 50 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS A 50 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 50 " -0.009 2.00e-02 2.50e+03 8.28e-03 1.03e+00 pdb=" CG HIS F 50 " 0.018 2.00e-02 2.50e+03 pdb=" ND1 HIS F 50 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS F 50 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS F 50 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS F 50 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 50 " -0.009 2.00e-02 2.50e+03 8.24e-03 1.02e+00 pdb=" CG HIS E 50 " 0.018 2.00e-02 2.50e+03 pdb=" ND1 HIS E 50 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS E 50 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS E 50 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS E 50 " -0.002 2.00e-02 2.50e+03 ... (remaining 425 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 556 2.79 - 3.32: 2112 3.32 - 3.85: 4028 3.85 - 4.37: 4471 4.37 - 4.90: 9061 Nonbonded interactions: 20228 Sorted by model distance: nonbonded pdb=" OE1 GLU D 46 " pdb=" NZ LYS D 80 " model vdw 2.265 2.520 nonbonded pdb=" OE1 GLU E 46 " pdb=" NZ LYS E 80 " model vdw 2.266 2.520 nonbonded pdb=" OE1 GLU F 46 " pdb=" NZ LYS F 80 " model vdw 2.266 2.520 nonbonded pdb=" OE1 GLU C 46 " pdb=" NZ LYS C 80 " model vdw 2.266 2.520 nonbonded pdb=" OE1 GLU A 46 " pdb=" NZ LYS A 80 " model vdw 2.266 2.520 ... (remaining 20223 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' and resid 37 through 97) selection = chain 'E' selection = (chain 'F' and resid 37 through 97) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.900 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: 9.230 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.490 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 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 : 0.012 0.173 2584 Z= 0.603 Angle : 0.965 12.679 3496 Z= 0.479 Chirality : 0.056 0.161 456 Planarity : 0.003 0.009 428 Dihedral : 13.694 81.418 870 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % 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: -3.88 (0.34), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.26), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.005 HIS A 50 PHE 0.012 0.004 PHE D 94 TYR 0.011 0.003 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.280 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 1.4786 time to fit residues: 30.4545 Evaluate side-chains 19 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.295 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN B 65 ASN B 79 GLN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2584 Z= 0.189 Angle : 0.464 2.559 3496 Z= 0.267 Chirality : 0.050 0.121 456 Planarity : 0.002 0.007 428 Dihedral : 6.117 41.945 378 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.10 % Allowed : 13.18 % Favored : 83.72 % 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: -3.50 (0.37), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.28), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS A 50 PHE 0.009 0.002 PHE B 94 TYR 0.008 0.002 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 26 time to evaluate : 0.286 Fit side-chains outliers start: 8 outliers final: 1 residues processed: 32 average time/residue: 0.9292 time to fit residues: 30.8163 Evaluate side-chains 23 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.268 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0307 time to fit residues: 0.4558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN B 65 ASN B 79 GLN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2584 Z= 0.130 Angle : 0.385 2.549 3496 Z= 0.227 Chirality : 0.050 0.119 456 Planarity : 0.002 0.015 428 Dihedral : 3.960 14.488 378 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.10 % Allowed : 15.12 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.004 HIS A 50 PHE 0.007 0.002 PHE A 94 TYR 0.006 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 24 time to evaluate : 0.277 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 25 average time/residue: 1.2082 time to fit residues: 31.1874 Evaluate side-chains 23 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 18 time to evaluate : 0.277 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2984 time to fit residues: 1.9678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN B 65 ASN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2584 Z= 0.093 Angle : 0.336 1.993 3496 Z= 0.201 Chirality : 0.050 0.118 456 Planarity : 0.002 0.012 428 Dihedral : 3.434 11.650 378 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.33 % Allowed : 17.05 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.42), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 50 PHE 0.005 0.001 PHE B 94 TYR 0.005 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 19 time to evaluate : 0.278 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 19 average time/residue: 1.3854 time to fit residues: 27.1729 Evaluate side-chains 22 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 18 time to evaluate : 0.258 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0280 time to fit residues: 0.5886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN B 65 ASN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2584 Z= 0.150 Angle : 0.394 2.633 3496 Z= 0.234 Chirality : 0.050 0.121 456 Planarity : 0.002 0.010 428 Dihedral : 4.026 14.764 378 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 5.43 % Allowed : 16.28 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS C 50 PHE 0.005 0.001 PHE C 94 TYR 0.006 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 17 time to evaluate : 0.245 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 23 average time/residue: 1.0850 time to fit residues: 25.8603 Evaluate side-chains 26 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 16 time to evaluate : 0.254 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 5 average time/residue: 0.6021 time to fit residues: 3.4432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 33 optimal weight: 0.4980 chunk 3 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 0.3980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN B 65 ASN C 65 ASN E 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.010 2584 Z= 0.070 Angle : 0.312 2.012 3496 Z= 0.187 Chirality : 0.050 0.118 456 Planarity : 0.001 0.009 428 Dihedral : 3.188 10.230 378 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.88 % Allowed : 18.99 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 50 PHE 0.004 0.001 PHE B 94 TYR 0.004 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 17 time to evaluate : 0.278 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 22 average time/residue: 1.1464 time to fit residues: 26.1430 Evaluate side-chains 22 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 14 time to evaluate : 0.260 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.0254 time to fit residues: 0.4971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 4.9990 chunk 29 optimal weight: 0.4980 chunk 34 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2584 Z= 0.090 Angle : 0.327 2.245 3496 Z= 0.196 Chirality : 0.049 0.118 456 Planarity : 0.001 0.008 428 Dihedral : 3.222 10.151 378 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.49 % Allowed : 18.60 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.005 0.001 PHE B 94 TYR 0.004 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 15 time to evaluate : 0.288 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 20 average time/residue: 1.0748 time to fit residues: 22.3717 Evaluate side-chains 22 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 14 time to evaluate : 0.269 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 0.0248 time to fit residues: 0.5009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 9.9990 chunk 3 optimal weight: 0.4980 chunk 27 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 32 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2584 Z= 0.133 Angle : 0.374 2.405 3496 Z= 0.223 Chirality : 0.049 0.119 456 Planarity : 0.002 0.008 428 Dihedral : 3.686 11.968 378 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.71 % Allowed : 20.16 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.42), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 50 PHE 0.005 0.001 PHE B 94 TYR 0.005 0.001 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 17 time to evaluate : 0.270 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 23 average time/residue: 1.0381 time to fit residues: 24.8253 Evaluate side-chains 22 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 16 time to evaluate : 0.311 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.3995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 35 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.009 2584 Z= 0.065 Angle : 0.303 1.996 3496 Z= 0.182 Chirality : 0.050 0.119 456 Planarity : 0.001 0.008 428 Dihedral : 2.970 9.043 378 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.10 % Allowed : 19.38 % Favored : 77.52 % 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: -1.96 (0.43), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 50 PHE 0.004 0.001 PHE B 94 TYR 0.004 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 17 time to evaluate : 0.289 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 23 average time/residue: 1.0686 time to fit residues: 25.5030 Evaluate side-chains 21 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 14 time to evaluate : 0.259 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.0253 time to fit residues: 0.4299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2584 Z= 0.115 Angle : 0.349 2.332 3496 Z= 0.208 Chirality : 0.049 0.118 456 Planarity : 0.001 0.007 428 Dihedral : 3.389 10.827 378 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.10 % Allowed : 20.16 % Favored : 76.74 % 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: -1.98 (0.43), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 50 PHE 0.004 0.001 PHE B 94 TYR 0.004 0.001 TYR E 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 15 time to evaluate : 0.252 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 21 average time/residue: 0.9985 time to fit residues: 21.8128 Evaluate side-chains 22 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 15 time to evaluate : 0.250 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 1.2835 time to fit residues: 1.6415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.188815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.151825 restraints weight = 2523.604| |-----------------------------------------------------------------------------| r_work (start): 0.4446 rms_B_bonded: 2.82 r_work: 0.4340 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.4194 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 2584 Z= 0.201 Angle : 0.454 2.838 3496 Z= 0.267 Chirality : 0.050 0.117 456 Planarity : 0.002 0.008 428 Dihedral : 4.251 13.732 378 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.71 % Allowed : 20.16 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.42), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.005 HIS A 50 PHE 0.005 0.002 PHE E 94 TYR 0.006 0.002 TYR E 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1365.52 seconds wall clock time: 24 minutes 55.24 seconds (1495.24 seconds total)