Starting phenix.real_space_refine on Mon Nov 13 15:11:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bg9_16027/11_2023/8bg9_16027_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bg9_16027/11_2023/8bg9_16027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bg9_16027/11_2023/8bg9_16027.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bg9_16027/11_2023/8bg9_16027.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bg9_16027/11_2023/8bg9_16027_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bg9_16027/11_2023/8bg9_16027_neut.pdb" } resolution = 3.5 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= 0.005 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 6 5.16 5 C 1074 2.51 5 N 300 2.21 5 O 312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 3": "OE1" <-> "OE2" Residue "B ASP 7": "OD1" <-> "OD2" Residue "C GLU 3": "OE1" <-> "OE2" Residue "D ASP 7": "OD1" <-> "OD2" Residue "E GLU 3": "OE1" <-> "OE2" Residue "F ASP 7": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 1692 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 1.43, per 1000 atoms: 0.85 Number of scatterers: 1692 At special positions: 0 Unit cell: (86.688, 62.608, 30.1, 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 6 16.00 O 312 8.00 N 300 7.00 C 1074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 339.8 milliseconds 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 372 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: 0.29 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 525 1.34 - 1.46: 483 1.46 - 1.58: 708 1.58 - 1.70: 0 1.70 - 1.82: 12 Bond restraints: 1728 Sorted by residual: bond pdb=" CA SER A 8 " pdb=" CB SER A 8 " ideal model delta sigma weight residual 1.529 1.494 0.036 1.78e-02 3.16e+03 4.06e+00 bond pdb=" CA SER E 8 " pdb=" CB SER E 8 " ideal model delta sigma weight residual 1.529 1.494 0.036 1.78e-02 3.16e+03 4.04e+00 bond pdb=" CA SER D 8 " pdb=" CB SER D 8 " ideal model delta sigma weight residual 1.529 1.494 0.036 1.78e-02 3.16e+03 3.98e+00 bond pdb=" CA SER C 8 " pdb=" CB SER C 8 " ideal model delta sigma weight residual 1.529 1.494 0.036 1.78e-02 3.16e+03 3.98e+00 bond pdb=" CA SER F 8 " pdb=" CB SER F 8 " ideal model delta sigma weight residual 1.529 1.494 0.035 1.78e-02 3.16e+03 3.92e+00 ... (remaining 1723 not shown) Histogram of bond angle deviations from ideal: 100.91 - 107.20: 42 107.20 - 113.49: 827 113.49 - 119.78: 611 119.78 - 126.07: 812 126.07 - 132.36: 18 Bond angle restraints: 2310 Sorted by residual: angle pdb=" C TYR E 10 " pdb=" CA TYR E 10 " pdb=" CB TYR E 10 " ideal model delta sigma weight residual 109.72 118.61 -8.89 1.73e+00 3.34e-01 2.64e+01 angle pdb=" C TYR C 10 " pdb=" CA TYR C 10 " pdb=" CB TYR C 10 " ideal model delta sigma weight residual 109.72 118.60 -8.88 1.73e+00 3.34e-01 2.64e+01 angle pdb=" C TYR A 10 " pdb=" CA TYR A 10 " pdb=" CB TYR A 10 " ideal model delta sigma weight residual 109.72 118.60 -8.88 1.73e+00 3.34e-01 2.63e+01 angle pdb=" CB GLU F 11 " pdb=" CG GLU F 11 " pdb=" CD GLU F 11 " ideal model delta sigma weight residual 112.60 120.28 -7.68 1.70e+00 3.46e-01 2.04e+01 angle pdb=" CB GLU D 11 " pdb=" CG GLU D 11 " pdb=" CD GLU D 11 " ideal model delta sigma weight residual 112.60 120.28 -7.68 1.70e+00 3.46e-01 2.04e+01 ... (remaining 2305 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 11.61: 780 11.61 - 23.22: 120 23.22 - 34.82: 42 34.82 - 46.43: 9 46.43 - 58.03: 9 Dihedral angle restraints: 960 sinusoidal: 366 harmonic: 594 Sorted by residual: dihedral pdb=" CA SER F 8 " pdb=" C SER F 8 " pdb=" N GLY F 9 " pdb=" CA GLY F 9 " ideal model delta harmonic sigma weight residual 180.00 159.62 20.38 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA SER B 8 " pdb=" C SER B 8 " pdb=" N GLY B 9 " pdb=" CA GLY B 9 " ideal model delta harmonic sigma weight residual 180.00 159.63 20.37 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA SER D 8 " pdb=" C SER D 8 " pdb=" N GLY D 9 " pdb=" CA GLY D 9 " ideal model delta harmonic sigma weight residual 180.00 159.66 20.34 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 957 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.045: 87 0.045 - 0.087: 62 0.087 - 0.129: 46 0.129 - 0.171: 24 0.171 - 0.213: 15 Chirality restraints: 234 Sorted by residual: chirality pdb=" CA VAL C 18 " pdb=" N VAL C 18 " pdb=" C VAL C 18 " pdb=" CB VAL C 18 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA VAL A 18 " pdb=" N VAL A 18 " pdb=" C VAL A 18 " pdb=" CB VAL A 18 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA VAL E 18 " pdb=" N VAL E 18 " pdb=" C VAL E 18 " pdb=" CB VAL E 18 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 231 not shown) Planarity restraints: 306 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 8 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.60e+00 pdb=" C SER D 8 " -0.028 2.00e-02 2.50e+03 pdb=" O SER D 8 " 0.010 2.00e-02 2.50e+03 pdb=" N GLY D 9 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 8 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C SER B 8 " -0.028 2.00e-02 2.50e+03 pdb=" O SER B 8 " 0.010 2.00e-02 2.50e+03 pdb=" N GLY B 9 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 8 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.58e+00 pdb=" C SER F 8 " -0.028 2.00e-02 2.50e+03 pdb=" O SER F 8 " 0.010 2.00e-02 2.50e+03 pdb=" N GLY F 9 " 0.009 2.00e-02 2.50e+03 ... (remaining 303 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.97: 809 2.97 - 3.45: 1558 3.45 - 3.93: 2520 3.93 - 4.42: 2733 4.42 - 4.90: 4413 Nonbonded interactions: 12033 Sorted by model distance: nonbonded pdb=" OD1 ASP B 7 " pdb=" N GLY B 9 " model vdw 2.484 2.520 nonbonded pdb=" OD1 ASP A 7 " pdb=" N GLY A 9 " model vdw 2.484 2.520 nonbonded pdb=" OD1 ASP D 7 " pdb=" N GLY D 9 " model vdw 2.485 2.520 nonbonded pdb=" OD1 ASP E 7 " pdb=" N GLY E 9 " model vdw 2.485 2.520 nonbonded pdb=" OD1 ASP C 7 " pdb=" N GLY C 9 " model vdw 2.485 2.520 ... (remaining 12028 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 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: 1.630 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.680 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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 0.037 1728 Z= 0.474 Angle : 1.465 8.889 2310 Z= 0.953 Chirality : 0.091 0.213 234 Planarity : 0.007 0.043 306 Dihedral : 14.959 58.032 588 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 2.86 % Allowed : 17.14 % Favored : 80.00 % Rotamer: Outliers : 12.50 % Allowed : 23.21 % Favored : 64.29 % 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: -5.16 (0.32), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.24), residues: 210 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 35 time to evaluate : 0.199 Fit side-chains outliers start: 21 outliers final: 11 residues processed: 55 average time/residue: 0.1364 time to fit residues: 8.6149 Evaluate side-chains 35 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 24 time to evaluate : 0.214 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0318 time to fit residues: 0.7800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 15 GLN B 13 HIS C 13 HIS C 14 HIS D 13 HIS D 14 HIS E 13 HIS E 15 GLN F 13 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1728 Z= 0.136 Angle : 0.670 6.578 2310 Z= 0.352 Chirality : 0.052 0.145 234 Planarity : 0.003 0.031 306 Dihedral : 4.662 13.495 228 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.57 % Allowed : 18.45 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.82 (0.29), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.67 (0.22), residues: 210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 18 time to evaluate : 0.200 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 24 average time/residue: 0.1486 time to fit residues: 4.2294 Evaluate side-chains 19 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 14 time to evaluate : 0.197 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0258 time to fit residues: 0.4551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 0.0980 chunk 5 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 1728 Z= 0.147 Angle : 0.627 5.564 2310 Z= 0.338 Chirality : 0.052 0.143 234 Planarity : 0.002 0.009 306 Dihedral : 4.543 14.888 228 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 5.36 % Allowed : 16.67 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.13 (0.36), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.28), residues: 210 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 21 time to evaluate : 0.196 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 28 average time/residue: 0.0956 time to fit residues: 3.3686 Evaluate side-chains 24 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 18 time to evaluate : 0.195 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0217 time to fit residues: 0.4709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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: 0.7925 moved from start: 0.5893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1728 Z= 0.110 Angle : 0.514 4.866 2310 Z= 0.271 Chirality : 0.049 0.132 234 Planarity : 0.002 0.009 306 Dihedral : 3.987 12.423 228 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.98 % Allowed : 16.67 % Favored : 80.36 % 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: -3.78 (0.39), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.30), residues: 210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 18 time to evaluate : 0.198 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 22 average time/residue: 0.0614 time to fit residues: 1.9919 Evaluate side-chains 21 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 18 time to evaluate : 0.204 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0198 time to fit residues: 0.3556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.6588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 1728 Z= 0.186 Angle : 0.607 5.563 2310 Z= 0.324 Chirality : 0.051 0.134 234 Planarity : 0.002 0.011 306 Dihedral : 4.775 17.207 228 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 3.57 % Allowed : 18.45 % Favored : 77.98 % 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 (0.40), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.30), residues: 210 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 23 time to evaluate : 0.219 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 27 average time/residue: 0.1158 time to fit residues: 3.8210 Evaluate side-chains 23 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.196 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0243 time to fit residues: 0.3969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 17 optimal weight: 0.0870 chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 11 optimal weight: 0.5980 overall best weight: 3.5364 ------------------------------------------------------------------------------- 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: 0.8016 moved from start: 0.7080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 1728 Z= 0.187 Angle : 0.602 5.293 2310 Z= 0.324 Chirality : 0.052 0.138 234 Planarity : 0.002 0.010 306 Dihedral : 4.892 17.673 228 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.79 % Allowed : 23.81 % Favored : 74.40 % 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: -3.98 (0.40), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.31), residues: 210 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.192 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 23 average time/residue: 0.0958 time to fit residues: 2.8823 Evaluate side-chains 23 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.205 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0213 time to fit residues: 0.3798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 0.0770 chunk 8 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 16 optimal weight: 0.0870 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 overall best weight: 1.8322 ------------------------------------------------------------------------------- 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: 0.7971 moved from start: 0.7364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1728 Z= 0.111 Angle : 0.534 5.859 2310 Z= 0.277 Chirality : 0.049 0.124 234 Planarity : 0.001 0.009 306 Dihedral : 4.339 13.216 228 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.60 % Allowed : 23.21 % Favored : 76.19 % 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: -3.74 (0.43), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.32), residues: 210 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.208 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 21 average time/residue: 0.0627 time to fit residues: 1.9382 Evaluate side-chains 21 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.206 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0192 time to fit residues: 0.2878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 0.0570 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 17 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 11 optimal weight: 0.5980 chunk 14 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 overall best weight: 0.8102 ------------------------------------------------------------------------------- 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: 0.7914 moved from start: 0.7621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1728 Z= 0.078 Angle : 0.510 5.484 2310 Z= 0.253 Chirality : 0.047 0.120 234 Planarity : 0.001 0.006 306 Dihedral : 3.847 10.421 228 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.60 % Allowed : 23.81 % Favored : 75.60 % 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: -3.37 (0.46), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.35), residues: 210 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.145 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 21 average time/residue: 0.0828 time to fit residues: 2.2028 Evaluate side-chains 19 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 18 time to evaluate : 0.153 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0179 time to fit residues: 0.2185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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: 0.8022 moved from start: 0.7645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 1728 Z= 0.213 Angle : 0.634 6.967 2310 Z= 0.332 Chirality : 0.052 0.133 234 Planarity : 0.003 0.021 306 Dihedral : 5.067 18.368 228 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 1.19 % Allowed : 25.00 % Favored : 73.81 % 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: -3.72 (0.43), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.33), residues: 210 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 21 time to evaluate : 0.203 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 23 average time/residue: 0.0649 time to fit residues: 2.1264 Evaluate side-chains 22 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.197 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0197 time to fit residues: 0.2919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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: 0.8045 moved from start: 0.7957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 1728 Z= 0.237 Angle : 0.676 7.632 2310 Z= 0.355 Chirality : 0.053 0.135 234 Planarity : 0.003 0.018 306 Dihedral : 5.481 19.582 228 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 27.98 % Favored : 72.02 % 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: -3.97 (0.41), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.31), residues: 210 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.211 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0657 time to fit residues: 1.9245 Evaluate side-chains 18 residues out of total 174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.188 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.5007 r_free = 0.5007 target = 0.334626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.5512 r_free = 0.5512 target = 0.267368 restraints weight = 2260.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.5536 r_free = 0.5536 target = 0.269479 restraints weight = 1068.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.5550 r_free = 0.5550 target = 0.270678 restraints weight = 601.334| |-----------------------------------------------------------------------------| r_work (final): 0.4615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.8096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 1728 Z= 0.228 Angle : 0.658 7.135 2310 Z= 0.346 Chirality : 0.053 0.132 234 Planarity : 0.003 0.018 306 Dihedral : 5.483 19.757 228 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 0.60 % Allowed : 27.38 % Favored : 72.02 % 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: -4.03 (0.41), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.31), residues: 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 844.11 seconds wall clock time: 18 minutes 26.21 seconds (1106.21 seconds total)