Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:36:44 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f1z_4172/11_2022/6f1z_4172_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f1z_4172/11_2022/6f1z_4172.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f1z_4172/11_2022/6f1z_4172.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f1z_4172/11_2022/6f1z_4172.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f1z_4172/11_2022/6f1z_4172_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f1z_4172/11_2022/6f1z_4172_neut.pdb" } resolution = 3.4 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= -0.000 sd= 0.004 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "o ARG 205": "NH1" <-> "NH2" Residue "p GLU 185": "OE1" <-> "OE2" Residue "p GLU 186": "OE1" <-> "OE2" Residue "p ARG 205": "NH1" <-> "NH2" Residue "p ARG 209": "NH1" <-> "NH2" Residue "s ARG 10": "NH1" <-> "NH2" Residue "s ARG 54": "NH1" <-> "NH2" Residue "s ARG 72": "NH1" <-> "NH2" Residue "t ARG 10": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 2138 Number of models: 1 Model: "" Number of chains: 4 Chain: "o" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 304 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "p" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 350 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 42} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "s" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 742 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 5, 'TRANS': 87} Chain: "t" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 742 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 5, 'TRANS': 87} Time building chain proxies: 1.68, per 1000 atoms: 0.79 Number of scatterers: 2138 At special positions: 0 Unit cell: (57.62, 76.38, 64.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 417 8.00 N 365 7.00 C 1350 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: 0.83 Conformation dependent library (CDL) restraints added in 280.7 milliseconds 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 516 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 1 sheets defined 46.0% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'o' and resid 183 through 192 Processing helix chain 'o' and resid 195 through 210 removed outlier: 4.273A pdb=" N PHE o 199 " --> pdb=" O GLU o 195 " (cutoff:3.500A) Processing helix chain 'p' and resid 187 through 193 removed outlier: 3.946A pdb=" N LEU p 191 " --> pdb=" O LYS p 187 " (cutoff:3.500A) Processing helix chain 'p' and resid 195 through 211 Processing helix chain 's' and resid 4 through 11 Processing helix chain 's' and resid 35 through 61 removed outlier: 4.395A pdb=" N TYR s 42 " --> pdb=" O THR s 38 " (cutoff:3.500A) Processing helix chain 't' and resid 4 through 13 Processing helix chain 't' and resid 35 through 61 removed outlier: 4.042A pdb=" N GLN t 41 " --> pdb=" O PRO t 37 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR t 42 " --> pdb=" O THR t 38 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 's' and resid 17 through 20 removed outlier: 5.997A pdb=" N THR s 67 " --> pdb=" O PRO s 82 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL t 90 " --> pdb=" O MET t 79 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ILE t 91 " --> pdb=" O GLN t 18 " (cutoff:3.500A) 111 hydrogen bonds defined for protein. 327 hydrogen bond angles 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: 0.50 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 696 1.34 - 1.46: 247 1.46 - 1.57: 1213 1.57 - 1.69: 0 1.69 - 1.80: 12 Bond restraints: 2168 Sorted by residual: bond pdb=" C ASN t 36 " pdb=" N PRO t 37 " ideal model delta sigma weight residual 1.336 1.349 -0.013 1.23e-02 6.61e+03 1.20e+00 bond pdb=" CA ASN s 36 " pdb=" C ASN s 36 " ideal model delta sigma weight residual 1.521 1.533 -0.012 1.14e-02 7.69e+03 1.10e+00 bond pdb=" C ASN s 36 " pdb=" N PRO s 37 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 9.53e-01 bond pdb=" C MET t 46 " pdb=" O MET t 46 " ideal model delta sigma weight residual 1.236 1.223 0.013 1.29e-02 6.01e+03 9.53e-01 bond pdb=" CB PHE s 87 " pdb=" CG PHE s 87 " ideal model delta sigma weight residual 1.502 1.524 -0.022 2.30e-02 1.89e+03 9.25e-01 ... (remaining 2163 not shown) Histogram of bond angle deviations from ideal: 99.89 - 106.43: 52 106.43 - 112.97: 1172 112.97 - 119.50: 646 119.50 - 126.04: 1040 126.04 - 132.57: 15 Bond angle restraints: 2925 Sorted by residual: angle pdb=" N GLN p 188 " pdb=" CA GLN p 188 " pdb=" C GLN p 188 " ideal model delta sigma weight residual 111.28 121.15 -9.87 1.09e+00 8.42e-01 8.19e+01 angle pdb=" N THR p 183 " pdb=" CA THR p 183 " pdb=" C THR p 183 " ideal model delta sigma weight residual 111.07 119.17 -8.10 1.07e+00 8.73e-01 5.73e+01 angle pdb=" N GLN p 189 " pdb=" CA GLN p 189 " pdb=" C GLN p 189 " ideal model delta sigma weight residual 111.28 115.58 -4.30 1.09e+00 8.42e-01 1.56e+01 angle pdb=" N LYS p 187 " pdb=" CA LYS p 187 " pdb=" C LYS p 187 " ideal model delta sigma weight residual 111.36 115.22 -3.86 1.09e+00 8.42e-01 1.25e+01 angle pdb=" N GLU p 195 " pdb=" CA GLU p 195 " pdb=" C GLU p 195 " ideal model delta sigma weight residual 114.04 110.39 3.65 1.24e+00 6.50e-01 8.68e+00 ... (remaining 2920 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.74: 1260 14.74 - 29.49: 58 29.49 - 44.23: 23 44.23 - 58.97: 4 58.97 - 73.72: 2 Dihedral angle restraints: 1347 sinusoidal: 566 harmonic: 781 Sorted by residual: dihedral pdb=" CA PHE t 49 " pdb=" C PHE t 49 " pdb=" N ILE t 50 " pdb=" CA ILE t 50 " ideal model delta harmonic sigma weight residual 180.00 159.38 20.62 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA THR s 39 " pdb=" C THR s 39 " pdb=" N THR s 40 " pdb=" CA THR s 40 " ideal model delta harmonic sigma weight residual -180.00 -160.65 -19.35 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA TYR t 86 " pdb=" C TYR t 86 " pdb=" N PHE t 87 " pdb=" CA PHE t 87 " ideal model delta harmonic sigma weight residual 180.00 -161.45 -18.55 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 1344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 264 0.068 - 0.135: 70 0.135 - 0.202: 9 0.202 - 0.269: 1 0.269 - 0.336: 2 Chirality restraints: 346 Sorted by residual: chirality pdb=" CB ILE s 20 " pdb=" CA ILE s 20 " pdb=" CG1 ILE s 20 " pdb=" CG2 ILE s 20 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA GLN p 188 " pdb=" N GLN p 188 " pdb=" C GLN p 188 " pdb=" CB GLN p 188 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA THR p 183 " pdb=" N THR p 183 " pdb=" C THR p 183 " pdb=" CB THR p 183 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 343 not shown) Planarity restraints: 377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA t 81 " -0.035 5.00e-02 4.00e+02 5.31e-02 4.51e+00 pdb=" N PRO t 82 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO t 82 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO t 82 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE o 200 " 0.011 2.00e-02 2.50e+03 1.59e-02 4.44e+00 pdb=" CG PHE o 200 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE o 200 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE o 200 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE o 200 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE o 200 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE o 200 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU t 45 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.19e+00 pdb=" C LEU t 45 " -0.035 2.00e-02 2.50e+03 pdb=" O LEU t 45 " 0.013 2.00e-02 2.50e+03 pdb=" N MET t 46 " 0.012 2.00e-02 2.50e+03 ... (remaining 374 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 495 2.79 - 3.32: 2025 3.32 - 3.85: 3496 3.85 - 4.37: 3838 4.37 - 4.90: 6630 Nonbonded interactions: 16484 Sorted by model distance: nonbonded pdb=" O ASN t 36 " pdb=" OG1 THR t 40 " model vdw 2.264 2.440 nonbonded pdb=" NZ LYS s 75 " pdb=" OD1 ASP t 61 " model vdw 2.275 2.520 nonbonded pdb=" OG SER s 73 " pdb=" OD1 ASN s 76 " model vdw 2.281 2.440 nonbonded pdb=" OG1 THR t 25 " pdb=" O ASP t 85 " model vdw 2.281 2.440 nonbonded pdb=" O GLU p 195 " pdb=" OG SER p 198 " model vdw 2.289 2.440 ... (remaining 16479 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 's' selection = chain 't' } 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 6 5.16 5 C 1350 2.51 5 N 365 2.21 5 O 417 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.160 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: 41.600 Check model and map are aligned: 0.030 Convert atoms to be neutral: 0.030 Process input model: 14.200 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 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 : 0.004 0.037 2168 Z= 0.271 Angle : 0.973 9.866 2925 Z= 0.571 Chirality : 0.063 0.336 346 Planarity : 0.007 0.053 377 Dihedral : 11.170 73.718 831 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.40), residues: 257 helix: -2.50 (0.36), residues: 105 sheet: -1.50 (0.75), residues: 40 loop : -3.56 (0.45), residues: 112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 97 average time/residue: 0.2219 time to fit residues: 23.5991 Evaluate side-chains 43 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.284 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.0060 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 192 HIS p 189 GLN p 192 HIS s 12 GLN s 36 ASN s 63 GLN ** s 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 36 ASN ** t 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 2168 Z= 0.236 Angle : 0.814 11.162 2925 Z= 0.409 Chirality : 0.050 0.155 346 Planarity : 0.006 0.038 377 Dihedral : 6.195 24.047 279 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 29.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer Outliers : 2.44 % 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: -2.97 (0.45), residues: 257 helix: -1.02 (0.41), residues: 117 sheet: -0.88 (0.80), residues: 40 loop : -3.61 (0.47), residues: 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 59 average time/residue: 0.2163 time to fit residues: 14.2496 Evaluate side-chains 41 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.280 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0290 time to fit residues: 0.5158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 0.1980 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 192 HIS ** s 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.6200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 2168 Z= 0.225 Angle : 0.781 10.636 2925 Z= 0.387 Chirality : 0.048 0.149 346 Planarity : 0.005 0.033 377 Dihedral : 6.018 20.219 279 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 28.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.47), residues: 257 helix: -0.19 (0.47), residues: 110 sheet: -0.81 (0.84), residues: 40 loop : -3.25 (0.45), residues: 107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 52 average time/residue: 0.1908 time to fit residues: 11.2413 Evaluate side-chains 42 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.281 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1386 time to fit residues: 1.3073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 0.0870 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 0.2980 chunk 9 optimal weight: 0.2980 chunk 16 optimal weight: 0.8980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 192 HIS ** s 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.6671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 2168 Z= 0.191 Angle : 0.773 10.679 2925 Z= 0.374 Chirality : 0.048 0.180 346 Planarity : 0.005 0.035 377 Dihedral : 5.637 17.050 279 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 25.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.49), residues: 257 helix: 0.08 (0.48), residues: 111 sheet: -0.56 (0.86), residues: 40 loop : -3.07 (0.47), residues: 106 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 50 average time/residue: 0.1821 time to fit residues: 10.4664 Evaluate side-chains 39 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.322 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0332 time to fit residues: 0.5374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 0.1980 chunk 8 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 14 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 192 HIS ** s 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.7175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 2168 Z= 0.192 Angle : 0.739 10.262 2925 Z= 0.364 Chirality : 0.048 0.210 346 Planarity : 0.005 0.037 377 Dihedral : 5.613 17.048 279 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 24.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer Outliers : 3.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.50), residues: 257 helix: 0.32 (0.48), residues: 112 sheet: -0.22 (0.86), residues: 40 loop : -2.74 (0.49), residues: 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 51 average time/residue: 0.1705 time to fit residues: 10.0517 Evaluate side-chains 43 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.289 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0307 time to fit residues: 0.6309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 192 HIS ** t 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.7503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 2168 Z= 0.217 Angle : 0.777 9.595 2925 Z= 0.386 Chirality : 0.049 0.173 346 Planarity : 0.005 0.038 377 Dihedral : 5.716 18.059 279 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 28.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.50), residues: 257 helix: 0.28 (0.48), residues: 112 sheet: -0.39 (0.81), residues: 40 loop : -2.67 (0.52), residues: 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 44 average time/residue: 0.1690 time to fit residues: 8.6438 Evaluate side-chains 41 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.277 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0269 time to fit residues: 0.5455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 0.0170 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 192 HIS ** s 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.7705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 2168 Z= 0.205 Angle : 0.815 16.147 2925 Z= 0.388 Chirality : 0.049 0.167 346 Planarity : 0.005 0.037 377 Dihedral : 5.614 16.997 279 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 28.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.50), residues: 257 helix: 0.30 (0.48), residues: 111 sheet: -0.37 (0.78), residues: 39 loop : -2.61 (0.54), residues: 107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 44 average time/residue: 0.1832 time to fit residues: 9.2784 Evaluate side-chains 37 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.274 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0376 time to fit residues: 0.4953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 0.0670 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 0.0570 chunk 6 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 192 HIS ** s 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.7910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 2168 Z= 0.208 Angle : 0.880 15.912 2925 Z= 0.410 Chirality : 0.050 0.168 346 Planarity : 0.005 0.046 377 Dihedral : 5.559 16.091 279 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 28.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.50), residues: 257 helix: 0.27 (0.48), residues: 113 sheet: -1.51 (0.68), residues: 47 loop : -2.14 (0.59), residues: 97 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 41 average time/residue: 0.1822 time to fit residues: 8.6511 Evaluate side-chains 38 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.244 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0287 time to fit residues: 0.4592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 24 optimal weight: 0.3980 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 0.0980 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 21 optimal weight: 0.0980 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 192 HIS ** s 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.8176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 2168 Z= 0.198 Angle : 0.896 16.184 2925 Z= 0.419 Chirality : 0.050 0.171 346 Planarity : 0.005 0.042 377 Dihedral : 5.545 17.258 279 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 27.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.51), residues: 257 helix: 0.44 (0.49), residues: 113 sheet: -1.57 (0.69), residues: 47 loop : -2.11 (0.58), residues: 97 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 44 average time/residue: 0.1573 time to fit residues: 8.0616 Evaluate side-chains 42 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 37 time to evaluate : 0.260 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0306 time to fit residues: 0.6367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 20 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** s 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.8349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 2168 Z= 0.230 Angle : 0.930 16.689 2925 Z= 0.445 Chirality : 0.052 0.164 346 Planarity : 0.005 0.038 377 Dihedral : 5.707 17.080 279 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 30.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.50), residues: 257 helix: 0.17 (0.48), residues: 112 sheet: -1.64 (0.70), residues: 47 loop : -2.07 (0.59), residues: 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 40 average time/residue: 0.1590 time to fit residues: 7.5078 Evaluate side-chains 38 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.284 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0349 time to fit residues: 0.4403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 9 optimal weight: 0.0370 chunk 24 optimal weight: 0.2980 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 192 HIS ** s 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 24 ASN ** s 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.060949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.055474 restraints weight = 18373.968| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 5.64 r_work: 0.3854 rms_B_bonded: 5.40 restraints_weight: 2.0000 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.8562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 2168 Z= 0.215 Angle : 0.961 17.908 2925 Z= 0.449 Chirality : 0.051 0.160 346 Planarity : 0.005 0.041 377 Dihedral : 5.801 18.993 279 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 24.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.51), residues: 257 helix: 0.18 (0.48), residues: 113 sheet: -0.70 (0.75), residues: 39 loop : -2.18 (0.58), residues: 105 =============================================================================== Job complete usr+sys time: 1454.12 seconds wall clock time: 26 minutes 38.89 seconds (1598.89 seconds total)