Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:36:13 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vu8_32126/11_2022/7vu8_32126_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vu8_32126/11_2022/7vu8_32126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vu8_32126/11_2022/7vu8_32126.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vu8_32126/11_2022/7vu8_32126.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vu8_32126/11_2022/7vu8_32126_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vu8_32126/11_2022/7vu8_32126_updated.pdb" } resolution = 3.0 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= 0.001 sd= 0.006 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 "B ASP 62": "OD1" <-> "OD2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 99": "NH1" <-> "NH2" Residue "B TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 1433 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1433 Unusual residues: {'ACK': 1} Classifications: {'peptide': 170, 'undetermined': 1} Link IDs: {'PTRANS': 6, 'TRANS': 163, None: 1} Not linked: pdbres="GLU B 228 " pdbres="ACK B 301 " Time building chain proxies: 1.47, per 1000 atoms: 1.03 Number of scatterers: 1433 At special positions: 0 Unit cell: (66.066, 54.054, 48.048, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 5 16.00 P 1 15.00 O 262 8.00 N 251 7.00 C 914 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: 0.63 Conformation dependent library (CDL) restraints added in 190.5 milliseconds 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 320 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 7 helices and 1 sheets defined 44.7% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'B' and resid 69 through 72 No H-bonds generated for 'chain 'B' and resid 69 through 72' Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.620A pdb=" N PHE B 83 " --> pdb=" O PHE B 79 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR B 86 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR B 87 " --> pdb=" O PHE B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 114 Processing helix chain 'B' and resid 130 through 145 removed outlier: 4.346A pdb=" N MET B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU B 138 " --> pdb=" O MET B 134 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 179 removed outlier: 3.683A pdb=" N LYS B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA B 178 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASN B 179 " --> pdb=" O ARG B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 198 removed outlier: 4.061A pdb=" N LYS B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP B 198 " --> pdb=" O LYS B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 226 removed outlier: 3.817A pdb=" N HIS B 224 " --> pdb=" O ASP B 220 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 63 through 66 removed outlier: 6.384A pdb=" N ILE B 117 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N SER B 66 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL B 119 " --> pdb=" O SER B 66 " (cutoff:3.500A) No H-bonds generated for sheet with id= A 33 hydrogen bonds defined for protein. 99 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: 0.27 Time building geometry restraints manager: 0.66 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: 341 1.33 - 1.45: 326 1.45 - 1.57: 796 1.57 - 1.69: 2 1.69 - 1.81: 7 Bond restraints: 1472 Sorted by residual: bond pdb=" O3P ACK B 301 " pdb=" P ACK B 301 " ideal model delta sigma weight residual 1.588 1.480 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" C PHE B 76 " pdb=" O PHE B 76 " ideal model delta sigma weight residual 1.235 1.288 -0.054 1.23e-02 6.61e+03 1.89e+01 bond pdb=" C THR B 77 " pdb=" O THR B 77 " ideal model delta sigma weight residual 1.236 1.284 -0.047 1.25e-02 6.40e+03 1.43e+01 bond pdb=" N ILE B 89 " pdb=" CA ILE B 89 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.15e-02 7.56e+03 1.27e+01 bond pdb=" N THR B 72 " pdb=" CA THR B 72 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.22e-02 6.72e+03 1.06e+01 ... (remaining 1467 not shown) Histogram of bond angle deviations from ideal: 92.92 - 101.14: 3 101.14 - 109.35: 125 109.35 - 117.56: 939 117.56 - 125.77: 887 125.77 - 133.98: 33 Bond angle restraints: 1987 Sorted by residual: angle pdb=" N ASP B 198 " pdb=" CA ASP B 198 " pdb=" C ASP B 198 " ideal model delta sigma weight residual 114.56 107.84 6.72 1.27e+00 6.20e-01 2.80e+01 angle pdb=" N TYR B 87 " pdb=" CA TYR B 87 " pdb=" C TYR B 87 " ideal model delta sigma weight residual 113.02 107.90 5.12 1.20e+00 6.94e-01 1.82e+01 angle pdb=" C LEU B 98 " pdb=" CA LEU B 98 " pdb=" CB LEU B 98 " ideal model delta sigma weight residual 117.23 112.07 5.16 1.36e+00 5.41e-01 1.44e+01 angle pdb=" CA VAL B 63 " pdb=" C VAL B 63 " pdb=" O VAL B 63 " ideal model delta sigma weight residual 121.49 117.79 3.70 1.01e+00 9.80e-01 1.34e+01 angle pdb=" N ASP B 95 " pdb=" CA ASP B 95 " pdb=" C ASP B 95 " ideal model delta sigma weight residual 114.39 109.10 5.29 1.45e+00 4.76e-01 1.33e+01 ... (remaining 1982 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.50: 736 10.50 - 21.01: 81 21.01 - 31.51: 27 31.51 - 42.01: 16 42.01 - 52.51: 5 Dihedral angle restraints: 865 sinusoidal: 368 harmonic: 497 Sorted by residual: dihedral pdb=" N LYS B 227 " pdb=" CA LYS B 227 " pdb=" CB LYS B 227 " pdb=" CG LYS B 227 " ideal model delta sinusoidal sigma weight residual -180.00 -127.49 -52.51 3 1.50e+01 4.44e-03 9.12e+00 dihedral pdb=" N PHE B 79 " pdb=" CA PHE B 79 " pdb=" CB PHE B 79 " pdb=" CG PHE B 79 " ideal model delta sinusoidal sigma weight residual 180.00 -130.34 -49.66 3 1.50e+01 4.44e-03 8.80e+00 dihedral pdb=" CA ARG B 110 " pdb=" CB ARG B 110 " pdb=" CG ARG B 110 " pdb=" CD ARG B 110 " ideal model delta sinusoidal sigma weight residual -180.00 -133.44 -46.56 3 1.50e+01 4.44e-03 8.36e+00 ... (remaining 862 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 124 0.047 - 0.094: 51 0.094 - 0.141: 18 0.141 - 0.188: 5 0.188 - 0.236: 6 Chirality restraints: 204 Sorted by residual: chirality pdb=" CA LYS B 100 " pdb=" N LYS B 100 " pdb=" C LYS B 100 " pdb=" CB LYS B 100 " 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=" CB ILE B 104 " pdb=" CA ILE B 104 " pdb=" CG1 ILE B 104 " pdb=" CG2 ILE B 104 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA ILE B 151 " pdb=" N ILE B 151 " pdb=" C ILE B 151 " pdb=" CB ILE B 151 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 201 not shown) Planarity restraints: 251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 70 " -0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C PRO B 70 " 0.057 2.00e-02 2.50e+03 pdb=" O PRO B 70 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP B 71 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 71 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.19e+00 pdb=" C ASP B 71 " 0.035 2.00e-02 2.50e+03 pdb=" O ASP B 71 " -0.013 2.00e-02 2.50e+03 pdb=" N THR B 72 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 86 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.59e+00 pdb=" C TYR B 86 " 0.033 2.00e-02 2.50e+03 pdb=" O TYR B 86 " -0.012 2.00e-02 2.50e+03 pdb=" N TYR B 87 " -0.011 2.00e-02 2.50e+03 ... (remaining 248 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 407 2.83 - 3.34: 1297 3.34 - 3.86: 2131 3.86 - 4.38: 2513 4.38 - 4.90: 3977 Nonbonded interactions: 10325 Sorted by model distance: nonbonded pdb=" OD1 ASP B 182 " pdb=" N GLY B 183 " model vdw 2.308 2.520 nonbonded pdb=" OE2 GLU B 138 " pdb=" NH2 ARG B 141 " model vdw 2.308 2.520 nonbonded pdb=" CD2 LEU B 98 " pdb=" N ARG B 99 " model vdw 2.426 3.540 nonbonded pdb=" NE ARG B 164 " pdb=" O GLY B 197 " model vdw 2.428 2.520 nonbonded pdb=" O ALA B 219 " pdb=" OG SER B 223 " model vdw 2.436 2.440 ... (remaining 10320 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 5 5.16 5 C 914 2.51 5 N 251 2.21 5 O 262 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: 0.660 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: 3.490 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.040 Process input model: 10.080 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 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 : 0.009 0.108 1472 Z= 0.624 Angle : 1.189 10.589 1987 Z= 0.809 Chirality : 0.069 0.236 204 Planarity : 0.005 0.033 251 Dihedral : 11.958 52.515 545 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer Outliers : 4.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.27 (0.46), residues: 168 helix: -3.13 (0.41), residues: 66 sheet: -5.55 (0.71), residues: 19 loop : -3.25 (0.52), residues: 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.188 Fit side-chains outliers start: 7 outliers final: 0 residues processed: 49 average time/residue: 0.7571 time to fit residues: 37.9789 Evaluate side-chains 21 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.180 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 14 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 0.0770 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 1472 Z= 0.137 Angle : 0.567 5.023 1987 Z= 0.285 Chirality : 0.045 0.127 204 Planarity : 0.003 0.024 251 Dihedral : 3.814 12.225 188 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 5.96 % 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: -3.40 (0.57), residues: 168 helix: -1.08 (0.55), residues: 71 sheet: -4.63 (0.91), residues: 19 loop : -2.72 (0.60), residues: 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 30 time to evaluate : 0.178 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 34 average time/residue: 0.6159 time to fit residues: 21.6297 Evaluate side-chains 25 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.179 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.2486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 4 optimal weight: 0.0270 chunk 15 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 0.0040 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 overall best weight: 1.2054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 1472 Z= 0.122 Angle : 0.522 8.354 1987 Z= 0.256 Chirality : 0.044 0.128 204 Planarity : 0.004 0.058 251 Dihedral : 3.551 11.694 188 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 7.95 % 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: -2.45 (0.64), residues: 168 helix: -0.06 (0.60), residues: 73 sheet: -4.50 (0.91), residues: 21 loop : -2.31 (0.70), residues: 74 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 24 time to evaluate : 0.186 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 33 average time/residue: 0.6969 time to fit residues: 23.6961 Evaluate side-chains 27 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 20 time to evaluate : 0.179 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.0190 time to fit residues: 0.2768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 15 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 14 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.023 1472 Z= 0.227 Angle : 0.588 6.937 1987 Z= 0.296 Chirality : 0.046 0.129 204 Planarity : 0.004 0.050 251 Dihedral : 4.073 11.218 188 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 9.93 % 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: -2.19 (0.64), residues: 168 helix: 0.34 (0.63), residues: 73 sheet: -4.33 (0.98), residues: 19 loop : -2.48 (0.64), residues: 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 23 time to evaluate : 0.206 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 33 average time/residue: 0.6508 time to fit residues: 22.1651 Evaluate side-chains 30 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 19 time to evaluate : 0.184 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 3 average time/residue: 0.0672 time to fit residues: 0.4867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 0 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 1472 Z= 0.193 Angle : 0.554 5.961 1987 Z= 0.280 Chirality : 0.045 0.140 204 Planarity : 0.004 0.043 251 Dihedral : 4.072 10.704 188 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer Outliers : 9.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.63), residues: 168 helix: 0.51 (0.63), residues: 73 sheet: -4.25 (0.98), residues: 19 loop : -2.50 (0.61), residues: 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 23 time to evaluate : 0.190 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 35 average time/residue: 0.5618 time to fit residues: 20.3675 Evaluate side-chains 32 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 21 time to evaluate : 0.198 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 2 average time/residue: 0.0886 time to fit residues: 0.4595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 10 optimal weight: 0.0570 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.6702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 1472 Z= 0.113 Angle : 0.523 6.240 1987 Z= 0.251 Chirality : 0.043 0.134 204 Planarity : 0.003 0.040 251 Dihedral : 3.582 10.796 188 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer Outliers : 5.96 % 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: -1.77 (0.63), residues: 168 helix: 0.88 (0.62), residues: 72 sheet: -3.81 (1.03), residues: 19 loop : -2.54 (0.60), residues: 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 17 time to evaluate : 0.187 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 26 average time/residue: 0.5905 time to fit residues: 15.9382 Evaluate side-chains 26 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 17 time to evaluate : 0.179 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 1 average time/residue: 0.1590 time to fit residues: 0.4130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 9 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 12 optimal weight: 0.0980 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.016 1472 Z= 0.114 Angle : 0.514 5.512 1987 Z= 0.253 Chirality : 0.043 0.137 204 Planarity : 0.003 0.036 251 Dihedral : 3.526 10.893 188 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 5.30 % 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: -1.64 (0.63), residues: 168 helix: 1.08 (0.63), residues: 72 sheet: -3.77 (1.00), residues: 19 loop : -2.57 (0.58), residues: 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 17 time to evaluate : 0.185 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 25 average time/residue: 0.5949 time to fit residues: 15.4452 Evaluate side-chains 24 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 16 time to evaluate : 0.173 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 0.2469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 1472 Z= 0.185 Angle : 0.561 5.257 1987 Z= 0.281 Chirality : 0.045 0.138 204 Planarity : 0.003 0.037 251 Dihedral : 3.781 11.435 188 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer Outliers : 5.96 % 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: -1.68 (0.62), residues: 168 helix: 1.07 (0.64), residues: 71 sheet: -3.91 (0.95), residues: 19 loop : -2.54 (0.57), residues: 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 19 time to evaluate : 0.179 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 27 average time/residue: 0.5668 time to fit residues: 15.9169 Evaluate side-chains 22 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 14 time to evaluate : 0.177 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 0.2479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 10 optimal weight: 0.4980 chunk 14 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 0.0050 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 1472 Z= 0.137 Angle : 0.582 7.138 1987 Z= 0.283 Chirality : 0.043 0.136 204 Planarity : 0.004 0.035 251 Dihedral : 3.592 11.521 188 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer Outliers : 6.62 % 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: -1.51 (0.62), residues: 168 helix: 1.25 (0.63), residues: 72 sheet: -3.69 (1.00), residues: 18 loop : -2.61 (0.56), residues: 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 18 time to evaluate : 0.181 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 26 average time/residue: 0.4569 time to fit residues: 12.4848 Evaluate side-chains 23 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 15 time to evaluate : 0.182 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.0177 time to fit residues: 0.2604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 9 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 1472 Z= 0.176 Angle : 0.619 5.447 1987 Z= 0.315 Chirality : 0.044 0.136 204 Planarity : 0.003 0.035 251 Dihedral : 3.604 13.089 188 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 4.64 % 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: -1.55 (0.61), residues: 168 helix: 1.20 (0.62), residues: 71 sheet: -3.53 (0.98), residues: 18 loop : -2.61 (0.55), residues: 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 15 time to evaluate : 0.217 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 22 average time/residue: 0.4387 time to fit residues: 10.2174 Evaluate side-chains 22 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 15 time to evaluate : 0.174 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 0.2420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 1 optimal weight: 0.5980 chunk 4 optimal weight: 0.0970 chunk 3 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 0 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.144594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.115905 restraints weight = 2304.928| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 4.79 r_work: 0.3658 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work: 0.3643 rms_B_bonded: 4.52 restraints_weight: 0.1250 r_work: 0.3634 rms_B_bonded: 4.55 restraints_weight: 0.0625 r_work: 0.3626 rms_B_bonded: 4.61 restraints_weight: 0.0312 r_work: 0.3617 rms_B_bonded: 4.69 restraints_weight: 0.0156 r_work: 0.3608 rms_B_bonded: 4.78 restraints_weight: 0.0078 r_work: 0.3600 rms_B_bonded: 4.88 restraints_weight: 0.0039 r_work: 0.3591 rms_B_bonded: 5.00 restraints_weight: 0.0020 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 1472 Z= 0.154 Angle : 0.587 5.248 1987 Z= 0.297 Chirality : 0.043 0.135 204 Planarity : 0.004 0.034 251 Dihedral : 3.485 13.637 188 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 5.30 % 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: -1.41 (0.61), residues: 168 helix: 1.27 (0.62), residues: 71 sheet: -3.20 (1.01), residues: 18 loop : -2.56 (0.54), residues: 79 =============================================================================== Job complete usr+sys time: 1009.83 seconds wall clock time: 18 minutes 28.04 seconds (1108.04 seconds total)