Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 09:53:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m61_23686/08_2023/7m61_23686_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m61_23686/08_2023/7m61_23686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m61_23686/08_2023/7m61_23686.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m61_23686/08_2023/7m61_23686.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m61_23686/08_2023/7m61_23686_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m61_23686/08_2023/7m61_23686_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1030 2.51 5 N 305 2.21 5 O 355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 1690 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 185 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "B" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 153 Unusual residues: {'NH2': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 20} Chain: "C" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 185 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "D" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 153 Unusual residues: {'NH2': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 20} Chain: "E" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 185 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "F" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 153 Unusual residues: {'NH2': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 20} Chain: "G" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 185 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "H" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 153 Unusual residues: {'NH2': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 20} Chain: "I" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 185 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "J" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 153 Unusual residues: {'NH2': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 20} Time building chain proxies: 1.16, per 1000 atoms: 0.69 Number of scatterers: 1690 At special positions: 0 Unit cell: (59.08, 51.695, 48.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 355 8.00 N 305 7.00 C 1030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 236.5 milliseconds 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 420 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 275 1.29 - 1.35: 303 1.35 - 1.42: 232 1.42 - 1.48: 250 1.48 - 1.55: 655 Bond restraints: 1715 Sorted by residual: bond pdb=" CB ILE E 26 " pdb=" CG1 ILE E 26 " ideal model delta sigma weight residual 1.530 1.505 0.025 2.00e-02 2.50e+03 1.53e+00 bond pdb=" CB ILE I 26 " pdb=" CG1 ILE I 26 " ideal model delta sigma weight residual 1.530 1.505 0.025 2.00e-02 2.50e+03 1.52e+00 bond pdb=" CB ILE C 26 " pdb=" CG1 ILE C 26 " ideal model delta sigma weight residual 1.530 1.505 0.025 2.00e-02 2.50e+03 1.52e+00 bond pdb=" CB ILE G 26 " pdb=" CG1 ILE G 26 " ideal model delta sigma weight residual 1.530 1.505 0.025 2.00e-02 2.50e+03 1.51e+00 bond pdb=" CB ILE A 26 " pdb=" CG1 ILE A 26 " ideal model delta sigma weight residual 1.530 1.505 0.025 2.00e-02 2.50e+03 1.51e+00 ... (remaining 1710 not shown) Histogram of bond angle deviations from ideal: 101.48 - 107.42: 40 107.42 - 113.36: 940 113.36 - 119.30: 370 119.30 - 125.24: 975 125.24 - 131.18: 10 Bond angle restraints: 2335 Sorted by residual: angle pdb=" CG1 ILE A 26 " pdb=" CB ILE A 26 " pdb=" CG2 ILE A 26 " ideal model delta sigma weight residual 110.70 101.48 9.22 3.00e+00 1.11e-01 9.45e+00 angle pdb=" CG1 ILE I 26 " pdb=" CB ILE I 26 " pdb=" CG2 ILE I 26 " ideal model delta sigma weight residual 110.70 101.49 9.21 3.00e+00 1.11e-01 9.42e+00 angle pdb=" CG1 ILE G 26 " pdb=" CB ILE G 26 " pdb=" CG2 ILE G 26 " ideal model delta sigma weight residual 110.70 101.51 9.19 3.00e+00 1.11e-01 9.38e+00 angle pdb=" CG1 ILE E 26 " pdb=" CB ILE E 26 " pdb=" CG2 ILE E 26 " ideal model delta sigma weight residual 110.70 101.52 9.18 3.00e+00 1.11e-01 9.37e+00 angle pdb=" CG1 ILE C 26 " pdb=" CB ILE C 26 " pdb=" CG2 ILE C 26 " ideal model delta sigma weight residual 110.70 101.52 9.18 3.00e+00 1.11e-01 9.35e+00 ... (remaining 2330 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.63: 780 8.63 - 17.25: 90 17.25 - 25.87: 40 25.87 - 34.50: 20 34.50 - 43.12: 20 Dihedral angle restraints: 950 sinusoidal: 300 harmonic: 650 Sorted by residual: dihedral pdb=" CA PHE I 15 " pdb=" C PHE I 15 " pdb=" N LEU I 16 " pdb=" CA LEU I 16 " ideal model delta harmonic sigma weight residual 180.00 167.01 12.99 0 5.00e+00 4.00e-02 6.75e+00 dihedral pdb=" CA PHE G 15 " pdb=" C PHE G 15 " pdb=" N LEU G 16 " pdb=" CA LEU G 16 " ideal model delta harmonic sigma weight residual 180.00 167.04 12.96 0 5.00e+00 4.00e-02 6.72e+00 dihedral pdb=" CA PHE A 15 " pdb=" C PHE A 15 " pdb=" N LEU A 16 " pdb=" CA LEU A 16 " ideal model delta harmonic sigma weight residual 180.00 167.07 12.93 0 5.00e+00 4.00e-02 6.69e+00 ... (remaining 947 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.061: 200 0.061 - 0.121: 51 0.121 - 0.181: 9 0.181 - 0.241: 10 0.241 - 0.301: 5 Chirality restraints: 275 Sorted by residual: chirality pdb=" CG LEU B 27 " pdb=" CB LEU B 27 " pdb=" CD1 LEU B 27 " pdb=" CD2 LEU B 27 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CG LEU D 27 " pdb=" CB LEU D 27 " pdb=" CD1 LEU D 27 " pdb=" CD2 LEU D 27 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CG LEU F 27 " pdb=" CB LEU F 27 " pdb=" CD1 LEU F 27 " pdb=" CD2 LEU F 27 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 272 not shown) Planarity restraints: 310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR J 37 " -0.015 2.00e-02 2.50e+03 1.72e-02 5.94e+00 pdb=" CG TYR J 37 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR J 37 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR J 37 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR J 37 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR J 37 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR J 37 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR J 37 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 37 " -0.015 2.00e-02 2.50e+03 1.72e-02 5.93e+00 pdb=" CG TYR F 37 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR F 37 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR F 37 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR F 37 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR F 37 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR F 37 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 37 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 37 " -0.015 2.00e-02 2.50e+03 1.72e-02 5.91e+00 pdb=" CG TYR B 37 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR B 37 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 37 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR B 37 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR B 37 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 37 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 37 " 0.000 2.00e-02 2.50e+03 ... (remaining 307 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 291 2.75 - 3.29: 1820 3.29 - 3.83: 2873 3.83 - 4.36: 3266 4.36 - 4.90: 6151 Nonbonded interactions: 14401 Sorted by model distance: nonbonded pdb=" O SER E 34 " pdb=" OG SER G 34 " model vdw 2.218 2.440 nonbonded pdb=" O SER A 34 " pdb=" OG SER I 34 " model vdw 2.218 2.440 nonbonded pdb=" OG SER A 34 " pdb=" O SER G 34 " model vdw 2.218 2.440 nonbonded pdb=" O SER C 34 " pdb=" OG SER E 34 " model vdw 2.218 2.440 nonbonded pdb=" ND2 ASN G 22 " pdb=" O GLY G 24 " model vdw 2.433 2.520 ... (remaining 14396 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.590 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.290 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 1715 Z= 0.205 Angle : 1.014 9.221 2335 Z= 0.506 Chirality : 0.076 0.301 275 Planarity : 0.003 0.017 310 Dihedral : 12.788 43.118 530 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.63 (0.34), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.26), residues: 210 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.196 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0628 time to fit residues: 3.3432 Evaluate side-chains 21 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.195 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 20.0000 chunk 15 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 1715 Z= 0.167 Angle : 0.701 7.934 2335 Z= 0.340 Chirality : 0.050 0.175 275 Planarity : 0.002 0.009 310 Dihedral : 5.150 14.238 230 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer Outliers : 2.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.88 (0.32), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.71 (0.24), residues: 210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 32 time to evaluate : 0.196 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 33 average time/residue: 0.0679 time to fit residues: 2.9924 Evaluate side-chains 20 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 17 time to evaluate : 0.197 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0240 time to fit residues: 0.3489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 4.9990 chunk 18 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 chunk 17 optimal weight: 8.9990 chunk 13 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 1715 Z= 0.177 Angle : 0.678 7.790 2335 Z= 0.332 Chirality : 0.047 0.196 275 Planarity : 0.002 0.009 310 Dihedral : 5.215 14.861 230 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 20.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer Outliers : 4.10 % 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: -4.83 (0.33), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.68 (0.25), 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 31 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 23 time to evaluate : 0.215 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 29 average time/residue: 0.0662 time to fit residues: 2.6290 Evaluate side-chains 21 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 16 time to evaluate : 0.204 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0232 time to fit residues: 0.4218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 4 optimal weight: 30.0000 chunk 6 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 1715 Z= 0.168 Angle : 0.640 7.996 2335 Z= 0.322 Chirality : 0.046 0.172 275 Planarity : 0.002 0.012 310 Dihedral : 5.285 14.017 230 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer Outliers : 2.56 % 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: -4.75 (0.35), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.26), 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 27 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 22 time to evaluate : 0.207 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 25 average time/residue: 0.0661 time to fit residues: 2.3207 Evaluate side-chains 18 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 15 time to evaluate : 0.202 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0251 time to fit residues: 0.3609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 4 optimal weight: 40.0000 chunk 19 optimal weight: 5.9990 chunk 16 optimal weight: 30.0000 chunk 8 optimal weight: 30.0000 chunk 1 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 18 optimal weight: 0.3980 overall best weight: 5.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 1715 Z= 0.151 Angle : 0.613 7.978 2335 Z= 0.305 Chirality : 0.044 0.135 275 Planarity : 0.002 0.008 310 Dihedral : 5.123 14.246 230 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer Outliers : 3.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.62 (0.36), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.27), 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 26 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 20 time to evaluate : 0.143 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 26 average time/residue: 0.0535 time to fit residues: 1.9705 Evaluate side-chains 16 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 13 time to evaluate : 0.195 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0211 time to fit residues: 0.3254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 16 optimal weight: 0.0570 chunk 19 optimal weight: 20.0000 chunk 12 optimal weight: 30.0000 chunk 8 optimal weight: 20.0000 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 3 optimal weight: 0.9980 overall best weight: 3.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 1715 Z= 0.117 Angle : 0.604 8.506 2335 Z= 0.292 Chirality : 0.042 0.121 275 Planarity : 0.002 0.008 310 Dihedral : 4.594 12.821 230 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer Outliers : 3.08 % 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: -4.57 (0.35), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.27), 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 30 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 24 time to evaluate : 0.199 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 29 average time/residue: 0.0660 time to fit residues: 2.6196 Evaluate side-chains 19 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 17 time to evaluate : 0.200 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0259 time to fit residues: 0.3257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 30.0000 chunk 12 optimal weight: 7.9990 chunk 13 optimal weight: 30.0000 chunk 9 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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: 0.7413 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 1715 Z= 0.171 Angle : 0.660 7.637 2335 Z= 0.328 Chirality : 0.044 0.135 275 Planarity : 0.002 0.010 310 Dihedral : 5.217 16.630 230 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.71 % Favored : 84.29 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.60 (0.35), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (0.26), 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 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 19 time to evaluate : 0.199 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 22 average time/residue: 0.0636 time to fit residues: 2.0075 Evaluate side-chains 19 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 17 time to evaluate : 0.205 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0207 time to fit residues: 0.3067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 chunk 16 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- 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: 0.7358 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 1715 Z= 0.136 Angle : 0.621 7.412 2335 Z= 0.304 Chirality : 0.042 0.127 275 Planarity : 0.002 0.009 310 Dihedral : 4.854 15.105 230 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer Outliers : 3.08 % 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: -4.56 (0.35), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.26), 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 27 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 21 time to evaluate : 0.211 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 24 average time/residue: 0.0692 time to fit residues: 2.3338 Evaluate side-chains 21 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 19 time to evaluate : 0.199 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0209 time to fit residues: 0.3021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 30.0000 chunk 9 optimal weight: 30.0000 chunk 16 optimal weight: 0.6980 chunk 4 optimal weight: 30.0000 chunk 14 optimal weight: 0.0050 chunk 2 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 30.0000 chunk 13 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 overall best weight: 3.3400 ------------------------------------------------------------------------------- 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: 0.7297 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 1715 Z= 0.115 Angle : 0.664 8.572 2335 Z= 0.312 Chirality : 0.046 0.242 275 Planarity : 0.002 0.014 310 Dihedral : 4.549 14.422 230 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.55 (0.34), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.26), 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 21 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.203 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0659 time to fit residues: 1.9717 Evaluate side-chains 21 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.194 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 chunk 12 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 4 optimal weight: 40.0000 overall best weight: 8.9996 ------------------------------------------------------------------------------- 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: 0.7436 moved from start: 0.5430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.030 1715 Z= 0.217 Angle : 0.752 8.660 2335 Z= 0.369 Chirality : 0.049 0.232 275 Planarity : 0.002 0.010 310 Dihedral : 5.575 16.602 230 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 25.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer Outliers : 0.51 % 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: -4.69 (0.34), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.26), 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 18 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.207 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 18 average time/residue: 0.0644 time to fit residues: 1.6930 Evaluate side-chains 16 residues out of total 195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.191 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 overall best weight: 5.9788 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.118919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.094639 restraints weight = 5653.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.096973 restraints weight = 3230.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.098476 restraints weight = 2215.521| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.5490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 1715 Z= 0.156 Angle : 0.718 8.465 2335 Z= 0.341 Chirality : 0.047 0.225 275 Planarity : 0.002 0.011 310 Dihedral : 5.194 16.439 230 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.65 (0.34), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.26), residues: 210 =============================================================================== Job complete usr+sys time: 658.28 seconds wall clock time: 13 minutes 43.13 seconds (823.13 seconds total)