Starting phenix.real_space_refine on Sun Mar 10 15:05:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yno_33967/03_2024/7yno_33967_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yno_33967/03_2024/7yno_33967.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/7yno_33967/03_2024/7yno_33967.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yno_33967/03_2024/7yno_33967.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yno_33967/03_2024/7yno_33967_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yno_33967/03_2024/7yno_33967_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= 0.003 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: 4 Type Number sf(0) Gaussians S 2 5.16 5 C 1618 2.51 5 N 442 2.21 5 O 500 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-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2562 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: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'IZV': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'IZV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.76, per 1000 atoms: 0.69 Number of scatterers: 2562 At special positions: 0 Unit cell: (100.43, 107.07, 32.37, 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 500 8.00 N 442 7.00 C 1618 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: 1.06 Conformation dependent library (CDL) restraints added in 483.6 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: 0.32 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: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.31: 432 1.31 - 1.40: 512 1.40 - 1.49: 476 1.49 - 1.58: 1154 1.58 - 1.67: 4 Bond restraints: 2578 Sorted by residual: bond pdb=" C07 IZV A 201 " pdb=" S16 IZV A 201 " ideal model delta sigma weight residual 1.766 1.670 0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C07 IZV C 201 " pdb=" S16 IZV C 201 " ideal model delta sigma weight residual 1.766 1.670 0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C11 IZV A 201 " pdb=" N12 IZV A 201 " ideal model delta sigma weight residual 1.351 1.442 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" C11 IZV C 201 " pdb=" N12 IZV C 201 " ideal model delta sigma weight residual 1.351 1.442 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C07 IZV C 201 " pdb=" N06 IZV C 201 " ideal model delta sigma weight residual 1.290 1.373 -0.083 2.00e-02 2.50e+03 1.74e+01 ... (remaining 2573 not shown) Histogram of bond angle deviations from ideal: 99.59 - 106.71: 22 106.71 - 113.83: 1641 113.83 - 120.95: 965 120.95 - 128.08: 852 128.08 - 135.20: 8 Bond angle restraints: 3488 Sorted by residual: angle pdb=" C07 IZV A 201 " pdb=" S16 IZV A 201 " pdb=" C17 IZV A 201 " ideal model delta sigma weight residual 89.25 99.61 -10.36 3.00e+00 1.11e-01 1.19e+01 angle pdb=" C07 IZV C 201 " pdb=" S16 IZV C 201 " pdb=" C17 IZV C 201 " ideal model delta sigma weight residual 89.25 99.59 -10.34 3.00e+00 1.11e-01 1.19e+01 angle pdb=" C18 IZV A 201 " pdb=" C17 IZV A 201 " pdb=" S16 IZV A 201 " ideal model delta sigma weight residual 128.49 135.20 -6.71 3.00e+00 1.11e-01 5.00e+00 angle pdb=" C18 IZV C 201 " pdb=" C17 IZV C 201 " pdb=" S16 IZV C 201 " ideal model delta sigma weight residual 128.49 135.18 -6.69 3.00e+00 1.11e-01 4.97e+00 angle pdb=" N06 IZV A 201 " pdb=" C07 IZV A 201 " pdb=" S16 IZV A 201 " ideal model delta sigma weight residual 114.50 109.15 5.35 3.00e+00 1.11e-01 3.18e+00 ... (remaining 3483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.81: 1332 13.81 - 27.62: 120 27.62 - 41.43: 24 41.43 - 55.24: 0 55.24 - 69.04: 6 Dihedral angle restraints: 1482 sinusoidal: 492 harmonic: 990 Sorted by residual: dihedral pdb=" CA ALA F 90 " pdb=" C ALA F 90 " pdb=" N ALA F 91 " pdb=" CA ALA F 91 " ideal model delta harmonic sigma weight residual 180.00 165.63 14.37 0 5.00e+00 4.00e-02 8.26e+00 dihedral pdb=" CA ALA E 90 " pdb=" C ALA E 90 " pdb=" N ALA E 91 " pdb=" CA ALA E 91 " ideal model delta harmonic sigma weight residual 180.00 165.66 14.34 0 5.00e+00 4.00e-02 8.23e+00 dihedral pdb=" CA ALA B 90 " pdb=" C ALA B 90 " pdb=" N ALA B 91 " pdb=" CA ALA B 91 " ideal model delta harmonic sigma weight residual 180.00 165.67 14.33 0 5.00e+00 4.00e-02 8.22e+00 ... (remaining 1479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 194 0.026 - 0.052: 139 0.052 - 0.078: 45 0.078 - 0.104: 41 0.104 - 0.130: 37 Chirality restraints: 456 Sorted by residual: chirality pdb=" CA VAL A 49 " pdb=" N VAL A 49 " pdb=" C VAL A 49 " pdb=" CB VAL A 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA VAL D 49 " pdb=" N VAL D 49 " pdb=" C VAL D 49 " pdb=" CB VAL D 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA VAL C 49 " pdb=" N VAL C 49 " pdb=" C VAL C 49 " pdb=" CB VAL C 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 453 not shown) Planarity restraints: 424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C07 IZV A 201 " -0.042 2.00e-02 2.50e+03 2.44e-02 1.19e+01 pdb=" C08 IZV A 201 " 0.014 2.00e-02 2.50e+03 pdb=" C09 IZV A 201 " 0.014 2.00e-02 2.50e+03 pdb=" C10 IZV A 201 " 0.014 2.00e-02 2.50e+03 pdb=" C11 IZV A 201 " 0.014 2.00e-02 2.50e+03 pdb=" C14 IZV A 201 " 0.014 2.00e-02 2.50e+03 pdb=" C15 IZV A 201 " 0.014 2.00e-02 2.50e+03 pdb=" N12 IZV A 201 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C07 IZV C 201 " 0.041 2.00e-02 2.50e+03 2.44e-02 1.19e+01 pdb=" C08 IZV C 201 " -0.014 2.00e-02 2.50e+03 pdb=" C09 IZV C 201 " -0.014 2.00e-02 2.50e+03 pdb=" C10 IZV C 201 " -0.014 2.00e-02 2.50e+03 pdb=" C11 IZV C 201 " -0.015 2.00e-02 2.50e+03 pdb=" C14 IZV C 201 " -0.014 2.00e-02 2.50e+03 pdb=" C15 IZV C 201 " -0.014 2.00e-02 2.50e+03 pdb=" N12 IZV C 201 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 38 " 0.005 2.00e-02 2.50e+03 9.44e-03 8.90e-01 pdb=" C LEU C 38 " -0.016 2.00e-02 2.50e+03 pdb=" O LEU C 38 " 0.006 2.00e-02 2.50e+03 pdb=" N TYR C 39 " 0.005 2.00e-02 2.50e+03 ... (remaining 421 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 433 2.78 - 3.31: 2400 3.31 - 3.84: 3908 3.84 - 4.37: 4354 4.37 - 4.90: 8997 Nonbonded interactions: 20092 Sorted by model distance: nonbonded pdb=" ND2 ASN E 65 " pdb=" O GLY E 68 " model vdw 2.252 2.520 nonbonded pdb=" ND2 ASN C 65 " pdb=" O GLY C 68 " model vdw 2.252 2.520 nonbonded pdb=" ND2 ASN D 65 " pdb=" O GLY D 68 " model vdw 2.252 2.520 nonbonded pdb=" ND2 ASN F 65 " pdb=" O GLY F 68 " model vdw 2.252 2.520 nonbonded pdb=" ND2 ASN A 65 " pdb=" O GLY A 68 " model vdw 2.252 2.520 ... (remaining 20087 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' and resid 37 through 97) selection = chain 'B' selection = (chain 'C' and resid 37 through 97) selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 9.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.270 Find NCS groups from input model: 0.180 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:12.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 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 : 0.008 0.096 2578 Z= 0.382 Angle : 0.788 10.355 3488 Z= 0.409 Chirality : 0.054 0.130 456 Planarity : 0.003 0.024 424 Dihedral : 12.187 69.044 858 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 22.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % 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: -3.47 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.004 HIS D 50 PHE 0.003 0.002 PHE B 94 TYR 0.006 0.002 TYR B 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 25 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.287 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.7565 time to fit residues: 19.9603 Evaluate side-chains 17 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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: 9.9990 chunk 27 optimal weight: 0.4980 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 0.0020 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2578 Z= 0.091 Angle : 0.437 2.336 3488 Z= 0.250 Chirality : 0.052 0.127 456 Planarity : 0.002 0.010 424 Dihedral : 4.764 11.181 366 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.71 % Allowed : 7.36 % Favored : 89.92 % 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: -2.69 (0.44), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 50 PHE 0.002 0.001 PHE E 94 TYR 0.003 0.001 TYR F 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 36 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 29 time to evaluate : 0.285 Fit side-chains REVERT: A 38 LEU cc_start: 0.6291 (OUTLIER) cc_final: 0.5954 (tm) REVERT: B 38 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6667 (tm) REVERT: C 38 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.6024 (tm) REVERT: D 38 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6545 (tm) REVERT: E 38 LEU cc_start: 0.6158 (OUTLIER) cc_final: 0.5871 (tm) outliers start: 7 outliers final: 0 residues processed: 36 average time/residue: 0.7465 time to fit residues: 28.1575 Evaluate side-chains 28 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 23 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain E residue 38 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 32 optimal weight: 0.0050 chunk 35 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 overall best weight: 3.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 2578 Z= 0.241 Angle : 0.601 5.406 3488 Z= 0.348 Chirality : 0.054 0.136 456 Planarity : 0.003 0.012 424 Dihedral : 5.482 15.232 366 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 2.33 % Allowed : 10.47 % Favored : 87.21 % 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: -2.52 (0.44), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 50 PHE 0.005 0.002 PHE E 94 TYR 0.009 0.002 TYR B 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 30 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 24 time to evaluate : 0.254 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 30 average time/residue: 0.3566 time to fit residues: 11.7612 Evaluate side-chains 22 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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: 2.9990 chunk 3 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.0870 chunk 34 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2578 Z= 0.088 Angle : 0.419 4.192 3488 Z= 0.241 Chirality : 0.052 0.128 456 Planarity : 0.002 0.010 424 Dihedral : 4.486 11.819 366 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.33 % Allowed : 12.40 % Favored : 85.27 % 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: -2.44 (0.44), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 50 PHE 0.001 0.001 PHE D 94 TYR 0.004 0.001 TYR F 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 31 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 25 time to evaluate : 0.272 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 31 average time/residue: 0.5032 time to fit residues: 16.6625 Evaluate side-chains 22 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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: 10.0000 chunk 25 optimal weight: 0.0020 chunk 14 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 8 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 overall best weight: 4.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.039 2578 Z= 0.362 Angle : 0.823 8.307 3488 Z= 0.443 Chirality : 0.060 0.154 456 Planarity : 0.004 0.012 424 Dihedral : 6.049 15.889 366 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.28 % Favored : 86.72 % Rotamer: Outliers : 2.71 % Allowed : 13.95 % Favored : 83.33 % 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: -2.29 (0.46), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS D 50 PHE 0.009 0.003 PHE E 94 TYR 0.011 0.003 TYR A 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 28 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 21 time to evaluate : 0.268 Fit side-chains outliers start: 7 outliers final: 0 residues processed: 27 average time/residue: 0.2207 time to fit residues: 6.9382 Evaluate side-chains 21 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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: 1.9990 chunk 34 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 25 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2578 Z= 0.092 Angle : 0.515 6.080 3488 Z= 0.267 Chirality : 0.054 0.132 456 Planarity : 0.002 0.010 424 Dihedral : 4.663 13.917 366 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.33 % Allowed : 15.12 % Favored : 82.56 % 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: -2.28 (0.45), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 50 PHE 0.002 0.001 PHE F 94 TYR 0.004 0.001 TYR E 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 31 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 25 time to evaluate : 0.278 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 31 average time/residue: 0.3565 time to fit residues: 12.1243 Evaluate side-chains 26 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain D residue 38 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 0.0030 chunk 29 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 6 optimal weight: 0.0770 chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.9952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2578 Z= 0.099 Angle : 0.519 7.299 3488 Z= 0.263 Chirality : 0.053 0.126 456 Planarity : 0.002 0.010 424 Dihedral : 4.308 11.930 366 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.33 % Allowed : 16.28 % Favored : 81.40 % 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: -2.10 (0.45), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 50 PHE 0.002 0.001 PHE F 94 TYR 0.005 0.001 TYR F 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 32 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 26 time to evaluate : 0.270 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 32 average time/residue: 0.5664 time to fit residues: 19.2176 Evaluate side-chains 28 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 24 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain D residue 38 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 33 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 25 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2578 Z= 0.088 Angle : 0.517 7.923 3488 Z= 0.256 Chirality : 0.053 0.128 456 Planarity : 0.002 0.011 424 Dihedral : 4.084 12.773 366 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.71 % Allowed : 17.44 % Favored : 79.84 % 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 (0.45), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 50 PHE 0.001 0.001 PHE D 94 TYR 0.003 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 36 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 29 time to evaluate : 0.256 Fit side-chains REVERT: C 62 GLN cc_start: 0.5687 (tt0) cc_final: 0.5395 (tt0) outliers start: 7 outliers final: 5 residues processed: 35 average time/residue: 0.6465 time to fit residues: 23.7547 Evaluate side-chains 30 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 25 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2578 Z= 0.130 Angle : 0.559 8.094 3488 Z= 0.285 Chirality : 0.054 0.141 456 Planarity : 0.002 0.011 424 Dihedral : 4.383 13.269 366 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.10 % Allowed : 18.99 % 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: -1.98 (0.45), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.002 0.001 PHE E 94 TYR 0.005 0.001 TYR E 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 34 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 26 time to evaluate : 0.275 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 32 average time/residue: 0.4594 time to fit residues: 15.7972 Evaluate side-chains 28 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 25 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain D residue 38 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2578 Z= 0.185 Angle : 0.611 6.934 3488 Z= 0.322 Chirality : 0.055 0.135 456 Planarity : 0.002 0.010 424 Dihedral : 4.838 13.283 366 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.33 % Allowed : 19.77 % 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: -2.06 (0.45), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 50 PHE 0.004 0.002 PHE E 94 TYR 0.005 0.001 TYR F 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 30 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 24 time to evaluate : 0.275 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 30 average time/residue: 0.2832 time to fit residues: 9.5523 Evaluate side-chains 26 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain D residue 38 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 0.0010 chunk 5 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 0.0570 chunk 24 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.8110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4934 r_free = 0.4934 target = 0.225754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.187841 restraints weight = 2838.977| |-----------------------------------------------------------------------------| r_work (start): 0.4558 rms_B_bonded: 2.48 r_work: 0.4445 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2578 Z= 0.146 Angle : 0.599 8.543 3488 Z= 0.302 Chirality : 0.054 0.151 456 Planarity : 0.002 0.012 424 Dihedral : 4.615 12.798 366 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.94 % Allowed : 20.16 % 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: -2.04 (0.45), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 50 PHE 0.003 0.001 PHE E 94 TYR 0.006 0.001 TYR E 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1227.99 seconds wall clock time: 22 minutes 37.04 seconds (1357.04 seconds total)