Starting phenix.real_space_refine (version: dev) on Thu Feb 16 19:41:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykw_33897/02_2023/7ykw_33897_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykw_33897/02_2023/7ykw_33897.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykw_33897/02_2023/7ykw_33897_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykw_33897/02_2023/7ykw_33897_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykw_33897/02_2023/7ykw_33897_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykw_33897/02_2023/7ykw_33897.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykw_33897/02_2023/7ykw_33897.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykw_33897/02_2023/7ykw_33897_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykw_33897/02_2023/7ykw_33897_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 sd= 0.040 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 Process input model Symmetric amino acids flipped Residue "B ARG 11": "NH1" <-> "NH2" Residue "D ARG 11": "NH1" <-> "NH2" Residue "F ARG 11": "NH1" <-> "NH2" Residue "H ARG 11": "NH1" <-> "NH2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 1908 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 204 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "B" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "C" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 204 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "D" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "E" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 204 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "F" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "G" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 204 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "H" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Time building chain proxies: 1.34, per 1000 atoms: 0.70 Number of scatterers: 1908 At special positions: 0 Unit cell: (86.32, 86.32, 37.44, 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 8 16.00 O 380 8.00 N 356 7.00 C 1164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 2 " - pdb=" SG CYS B 7 " distance=2.03 Simple disulfide: pdb=" SG CYS D 2 " - pdb=" SG CYS D 7 " distance=2.03 Simple disulfide: pdb=" SG CYS F 2 " - pdb=" SG CYS F 7 " distance=2.03 Simple disulfide: pdb=" SG CYS H 2 " - pdb=" SG CYS H 7 " distance=2.03 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: 0.86 Conformation dependent library (CDL) restraints added in 254.5 milliseconds 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 480 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: 0.13 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: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 636 1.33 - 1.45: 405 1.45 - 1.57: 883 1.57 - 1.69: 0 1.69 - 1.81: 8 Bond restraints: 1932 Sorted by residual: bond pdb=" C TYC C 37 " pdb=" NXT TYC C 37 " ideal model delta sigma weight residual 1.451 1.346 0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C TYC E 37 " pdb=" NXT TYC E 37 " ideal model delta sigma weight residual 1.451 1.346 0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" C TYC B 37 " pdb=" NXT TYC B 37 " ideal model delta sigma weight residual 1.451 1.346 0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C TYC G 37 " pdb=" NXT TYC G 37 " ideal model delta sigma weight residual 1.451 1.346 0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C TYC F 37 " pdb=" NXT TYC F 37 " ideal model delta sigma weight residual 1.451 1.346 0.105 2.00e-02 2.50e+03 2.73e+01 ... (remaining 1927 not shown) Histogram of bond angle deviations from ideal: 100.04 - 106.30: 63 106.30 - 112.55: 990 112.55 - 118.81: 460 118.81 - 125.06: 1099 125.06 - 131.31: 12 Bond angle restraints: 2624 Sorted by residual: angle pdb=" N ALA D 5 " pdb=" CA ALA D 5 " pdb=" C ALA D 5 " ideal model delta sigma weight residual 111.36 104.26 7.10 1.09e+00 8.42e-01 4.24e+01 angle pdb=" N ALA F 5 " pdb=" CA ALA F 5 " pdb=" C ALA F 5 " ideal model delta sigma weight residual 111.28 105.14 6.14 1.09e+00 8.42e-01 3.17e+01 angle pdb=" N PHE F 23 " pdb=" CA PHE F 23 " pdb=" C PHE F 23 " ideal model delta sigma weight residual 108.49 100.04 8.45 1.65e+00 3.67e-01 2.62e+01 angle pdb=" N PHE B 23 " pdb=" CA PHE B 23 " pdb=" C PHE B 23 " ideal model delta sigma weight residual 108.49 100.06 8.43 1.65e+00 3.67e-01 2.61e+01 angle pdb=" N PHE D 23 " pdb=" CA PHE D 23 " pdb=" C PHE D 23 " ideal model delta sigma weight residual 108.49 100.07 8.42 1.65e+00 3.67e-01 2.60e+01 ... (remaining 2619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.40: 988 13.40 - 26.80: 72 26.80 - 40.20: 33 40.20 - 53.60: 12 53.60 - 67.00: 3 Dihedral angle restraints: 1108 sinusoidal: 380 harmonic: 728 Sorted by residual: dihedral pdb=" CB CYS D 2 " pdb=" SG CYS D 2 " pdb=" SG CYS D 7 " pdb=" CB CYS D 7 " ideal model delta sinusoidal sigma weight residual -86.00 -153.00 67.00 1 1.00e+01 1.00e-02 5.85e+01 dihedral pdb=" CB CYS F 2 " pdb=" SG CYS F 2 " pdb=" SG CYS F 7 " pdb=" CB CYS F 7 " ideal model delta sinusoidal sigma weight residual -86.00 -142.11 56.11 1 1.00e+01 1.00e-02 4.25e+01 dihedral pdb=" CB CYS H 2 " pdb=" SG CYS H 2 " pdb=" SG CYS H 7 " pdb=" CB CYS H 7 " ideal model delta sinusoidal sigma weight residual -86.00 -141.48 55.48 1 1.00e+01 1.00e-02 4.16e+01 ... (remaining 1105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 158 0.047 - 0.094: 78 0.094 - 0.141: 40 0.141 - 0.189: 24 0.189 - 0.236: 16 Chirality restraints: 316 Sorted by residual: chirality pdb=" CA PHE F 23 " pdb=" N PHE F 23 " pdb=" C PHE F 23 " pdb=" CB PHE F 23 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA PHE B 23 " pdb=" N PHE B 23 " pdb=" C PHE B 23 " pdb=" CB PHE B 23 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA PHE D 23 " pdb=" N PHE D 23 " pdb=" C PHE D 23 " pdb=" CB PHE D 23 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 313 not shown) Planarity restraints: 344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 36 " -0.017 2.00e-02 2.50e+03 3.09e-02 9.54e+00 pdb=" C THR A 36 " 0.053 2.00e-02 2.50e+03 pdb=" O THR A 36 " -0.019 2.00e-02 2.50e+03 pdb=" N TYC A 37 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 36 " -0.017 2.00e-02 2.50e+03 3.08e-02 9.50e+00 pdb=" C THR C 36 " 0.053 2.00e-02 2.50e+03 pdb=" O THR C 36 " -0.019 2.00e-02 2.50e+03 pdb=" N TYC C 37 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 36 " -0.017 2.00e-02 2.50e+03 3.05e-02 9.30e+00 pdb=" C THR E 36 " 0.053 2.00e-02 2.50e+03 pdb=" O THR E 36 " -0.019 2.00e-02 2.50e+03 pdb=" N TYC E 37 " -0.017 2.00e-02 2.50e+03 ... (remaining 341 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 1273 3.01 - 3.48: 1825 3.48 - 3.96: 3330 3.96 - 4.43: 3624 4.43 - 4.90: 6480 Nonbonded interactions: 16532 Sorted by model distance: nonbonded pdb=" N ASN F 3 " pdb=" N THR F 4 " model vdw 2.538 2.560 nonbonded pdb=" N ASN B 3 " pdb=" N THR B 4 " model vdw 2.547 2.560 nonbonded pdb=" C THR B 4 " pdb=" OG1 THR B 4 " model vdw 2.561 2.616 nonbonded pdb=" N ASN D 3 " pdb=" N THR D 4 " model vdw 2.567 2.560 nonbonded pdb=" N ASN B 3 " pdb=" O CYS D 2 " model vdw 2.568 2.520 ... (remaining 16527 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' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 8 5.16 5 C 1164 2.51 5 N 356 2.21 5 O 380 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.920 Check model and map are aligned: 0.020 Process input model: 9.500 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.105 1932 Z= 0.734 Angle : 1.761 9.681 2624 Z= 1.065 Chirality : 0.087 0.236 316 Planarity : 0.004 0.031 344 Dihedral : 11.872 44.566 616 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % 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: -3.01 (0.43), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.33), residues: 232 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.212 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.0589 time to fit residues: 7.4176 Evaluate side-chains 50 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.230 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2851 ------------------------------------------------------------------------------- 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: 1.9990 chunk 15 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 0.0470 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 chunk 19 optimal weight: 0.8980 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 31 ASN B 21 ASN B 31 ASN C 21 ASN C 31 ASN C 35 ASN D 21 ASN D 31 ASN E 21 ASN E 31 ASN F 21 ASN F 31 ASN G 21 ASN G 31 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 ASN H 31 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 1932 Z= 0.250 Angle : 0.604 9.467 2624 Z= 0.293 Chirality : 0.040 0.104 316 Planarity : 0.002 0.011 344 Dihedral : 5.740 20.318 264 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer Outliers : 2.88 % 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: -3.77 (0.39), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.29), residues: 232 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.227 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 61 average time/residue: 0.0686 time to fit residues: 5.4308 Evaluate side-chains 48 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.277 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0210 time to fit residues: 0.3741 ------------------------------------------------------------------------------- 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: 3.9990 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 0.2980 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 1932 Z= 0.166 Angle : 0.504 6.900 2624 Z= 0.247 Chirality : 0.039 0.113 316 Planarity : 0.002 0.013 344 Dihedral : 4.952 16.514 264 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer Outliers : 2.88 % 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: -4.08 (0.37), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.28), residues: 232 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.207 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 53 average time/residue: 0.0640 time to fit residues: 4.4959 Evaluate side-chains 48 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.216 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0234 time to fit residues: 0.3658 ------------------------------------------------------------------------------- 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: 8.9990 chunk 5 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 0 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 14 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.5297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 1932 Z= 0.282 Angle : 0.563 7.783 2624 Z= 0.276 Chirality : 0.040 0.107 316 Planarity : 0.002 0.015 344 Dihedral : 5.285 15.165 264 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (0.36), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.28), residues: 232 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.236 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 51 average time/residue: 0.0645 time to fit residues: 4.4211 Evaluate side-chains 49 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.239 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0218 time to fit residues: 0.3926 ------------------------------------------------------------------------------- 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: 3.9990 chunk 11 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.5687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 1932 Z= 0.296 Angle : 0.525 7.488 2624 Z= 0.263 Chirality : 0.039 0.106 316 Planarity : 0.002 0.008 344 Dihedral : 5.257 15.636 264 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.38 (0.35), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.27), residues: 232 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.222 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 56 average time/residue: 0.0653 time to fit residues: 4.8805 Evaluate side-chains 47 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.227 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0222 time to fit residues: 0.3920 ------------------------------------------------------------------------------- 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: 6.9990 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 10 optimal weight: 0.0670 chunk 16 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.6000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 1932 Z= 0.344 Angle : 0.571 8.431 2624 Z= 0.280 Chirality : 0.041 0.119 316 Planarity : 0.002 0.012 344 Dihedral : 5.452 18.876 264 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 0.96 % 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: -4.59 (0.34), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.26), residues: 232 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.206 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 43 average time/residue: 0.0621 time to fit residues: 3.6212 Evaluate side-chains 40 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.201 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0207 time to fit residues: 0.2871 ------------------------------------------------------------------------------- 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: 0.9990 chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 0.0970 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 0.0570 chunk 17 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.6239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.021 1932 Z= 0.244 Angle : 0.531 7.460 2624 Z= 0.259 Chirality : 0.040 0.117 316 Planarity : 0.002 0.015 344 Dihedral : 5.109 17.254 264 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 0.48 % 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: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (0.27), residues: 232 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.202 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 42 average time/residue: 0.0587 time to fit residues: 3.4032 Evaluate side-chains 40 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.204 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0240 time to fit residues: 0.3541 ------------------------------------------------------------------------------- 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: 4.9990 chunk 5 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 30.0000 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 1 optimal weight: 0.0370 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 35 ASN H 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.6472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.013 1932 Z= 0.142 Angle : 0.503 7.753 2624 Z= 0.234 Chirality : 0.040 0.118 316 Planarity : 0.001 0.008 344 Dihedral : 4.595 15.364 264 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer Outliers : 1.44 % 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: -4.59 (0.35), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.27), residues: 232 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.203 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 46 average time/residue: 0.0583 time to fit residues: 3.6652 Evaluate side-chains 41 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.203 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0205 time to fit residues: 0.3208 ------------------------------------------------------------------------------- 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: 5.9990 chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 2 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 ASN G 35 ASN H 3 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.6587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 1932 Z= 0.293 Angle : 0.558 8.249 2624 Z= 0.270 Chirality : 0.040 0.120 316 Planarity : 0.002 0.009 344 Dihedral : 5.180 22.173 264 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % 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: -4.60 (0.36), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (0.28), residues: 232 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.193 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0619 time to fit residues: 3.4182 Evaluate side-chains 36 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.227 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2641 ------------------------------------------------------------------------------- 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: 0.8980 chunk 10 optimal weight: 9.9990 chunk 13 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 30.0000 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.6768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 1932 Z= 0.275 Angle : 0.545 8.463 2624 Z= 0.262 Chirality : 0.041 0.118 316 Planarity : 0.002 0.008 344 Dihedral : 5.254 27.317 264 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer Outliers : 0.48 % 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: -4.64 (0.36), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.28), residues: 232 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.236 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 39 average time/residue: 0.0652 time to fit residues: 3.5182 Evaluate side-chains 39 residues out of total 208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.246 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2771 ------------------------------------------------------------------------------- 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: 3.9990 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 2 optimal weight: 20.0000 chunk 5 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 30.0000 chunk 7 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.110192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.086966 restraints weight = 5137.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.088786 restraints weight = 2224.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.089885 restraints weight = 1415.021| |-----------------------------------------------------------------------------| r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.6912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 1932 Z= 0.266 Angle : 0.544 8.345 2624 Z= 0.258 Chirality : 0.041 0.116 316 Planarity : 0.002 0.008 344 Dihedral : 5.350 29.771 264 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -4.70 (0.36), residues: 232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.28), residues: 232 =============================================================================== Job complete usr+sys time: 895.36 seconds wall clock time: 16 minutes 56.44 seconds (1016.44 seconds total)