Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:04:20 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v5v_21054/11_2022/6v5v_21054_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v5v_21054/11_2022/6v5v_21054.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v5v_21054/11_2022/6v5v_21054.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v5v_21054/11_2022/6v5v_21054.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v5v_21054/11_2022/6v5v_21054_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v5v_21054/11_2022/6v5v_21054_updated.pdb" } resolution = 3.8 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= 0.001 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 "g ARG 3": "NH1" <-> "NH2" Residue "g GLU 116": "OE1" <-> "OE2" Residue "g ARG 343": "NH1" <-> "NH2" Residue "g ARG 362": "NH1" <-> "NH2" Residue "g ARG 393": "NH1" <-> "NH2" Residue "g ASP 422": "OD1" <-> "OD2" Residue "g ARG 440": "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: 2979 Number of models: 1 Model: "" Number of chains: 1 Chain: "g" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2979 Unusual residues: {'GDP': 1} Classifications: {'peptide': 369, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 352, None: 1} Not linked: pdbres="SER g 445 " pdbres="GDP g 501 " Chain breaks: 11 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 2.27, per 1000 atoms: 0.76 Number of scatterers: 2979 At special positions: 0 Unit cell: (72.09, 65.415, 73.425, 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 14 16.00 P 2 15.00 O 558 8.00 N 522 7.00 C 1883 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: 1.20 Conformation dependent library (CDL) restraints added in 415.5 milliseconds 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 700 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 15 helices and 2 sheets defined 46.9% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'g' and resid 11 through 28 Processing helix chain 'g' and resid 73 through 79 Processing helix chain 'g' and resid 83 through 85 No H-bonds generated for 'chain 'g' and resid 83 through 85' Processing helix chain 'g' and resid 104 through 113 Processing helix chain 'g' and resid 115 through 127 removed outlier: 3.879A pdb=" N ILE g 121 " --> pdb=" O ASP g 117 " (cutoff:3.500A) Processing helix chain 'g' and resid 145 through 160 Processing helix chain 'g' and resid 184 through 195 Processing helix chain 'g' and resid 207 through 217 Processing helix chain 'g' and resid 225 through 239 removed outlier: 4.331A pdb=" N GLN g 230 " --> pdb=" O SER g 226 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU g 231 " --> pdb=" O GLN g 227 " (cutoff:3.500A) Processing helix chain 'g' and resid 241 through 244 No H-bonds generated for 'chain 'g' and resid 241 through 244' Processing helix chain 'g' and resid 253 through 260 removed outlier: 4.220A pdb=" N SER g 259 " --> pdb=" O GLY g 255 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU g 260 " --> pdb=" O LEU g 256 " (cutoff:3.500A) Processing helix chain 'g' and resid 290 through 297 Processing helix chain 'g' and resid 333 through 343 Processing helix chain 'g' and resid 382 through 399 removed outlier: 3.553A pdb=" N SER g 385 " --> pdb=" O THR g 382 " (cutoff:3.500A) Processing helix chain 'g' and resid 420 through 438 Processing sheet with id= A, first strand: chain 'g' and resid 64 through 66 removed outlier: 8.953A pdb=" N VAL g 65 " --> pdb=" O ILE g 5 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N THR g 7 " --> pdb=" O VAL g 65 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ILE g 6 " --> pdb=" O GLU g 133 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE g 135 " --> pdb=" O ILE g 6 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU g 8 " --> pdb=" O PHE g 135 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU g 137 " --> pdb=" O LEU g 8 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'g' and resid 270 through 273 removed outlier: 3.886A pdb=" N ALA g 319 " --> pdb=" O ASN g 380 " (cutoff:3.500A) 123 hydrogen bonds defined for protein. 324 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: 0.67 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 970 1.34 - 1.46: 572 1.46 - 1.57: 1464 1.57 - 1.69: 3 1.69 - 1.81: 22 Bond restraints: 3031 Sorted by residual: bond pdb=" C5 GDP g 501 " pdb=" C4 GDP g 501 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.15e+00 bond pdb=" C THR g 274 " pdb=" N PRO g 275 " ideal model delta sigma weight residual 1.334 1.354 -0.020 2.34e-02 1.83e+03 7.43e-01 bond pdb=" CA THR g 274 " pdb=" C THR g 274 " ideal model delta sigma weight residual 1.524 1.533 -0.010 1.26e-02 6.30e+03 5.70e-01 bond pdb=" C GLN g 184 " pdb=" N PRO g 185 " ideal model delta sigma weight residual 1.335 1.344 -0.009 1.36e-02 5.41e+03 3.94e-01 bond pdb=" C3' GDP g 501 " pdb=" C2' GDP g 501 " ideal model delta sigma weight residual 1.524 1.513 0.011 2.00e-02 2.50e+03 3.16e-01 ... (remaining 3026 not shown) Histogram of bond angle deviations from ideal: 100.50 - 107.61: 110 107.61 - 114.71: 1827 114.71 - 121.82: 1559 121.82 - 128.93: 583 128.93 - 136.04: 20 Bond angle restraints: 4099 Sorted by residual: angle pdb=" N THR g 274 " pdb=" CA THR g 274 " pdb=" C THR g 274 " ideal model delta sigma weight residual 109.81 115.82 -6.01 2.21e+00 2.05e-01 7.39e+00 angle pdb=" CA THR g 274 " pdb=" C THR g 274 " pdb=" N PRO g 275 " ideal model delta sigma weight residual 118.44 121.90 -3.46 1.59e+00 3.96e-01 4.73e+00 angle pdb=" C LEU g 266 " pdb=" N HIS g 267 " pdb=" CA HIS g 267 " ideal model delta sigma weight residual 123.25 120.27 2.98 1.69e+00 3.50e-01 3.10e+00 angle pdb=" C THR g 274 " pdb=" N PRO g 275 " pdb=" CA PRO g 275 " ideal model delta sigma weight residual 120.79 118.51 2.28 1.30e+00 5.92e-01 3.08e+00 angle pdb=" C3' GDP g 501 " pdb=" C2' GDP g 501 " pdb=" C1' GDP g 501 " ideal model delta sigma weight residual 111.00 105.84 5.16 3.00e+00 1.11e-01 2.96e+00 ... (remaining 4094 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.07: 1712 22.07 - 44.14: 104 44.14 - 66.22: 5 66.22 - 88.29: 2 88.29 - 110.36: 2 Dihedral angle restraints: 1825 sinusoidal: 752 harmonic: 1073 Sorted by residual: dihedral pdb=" O2B GDP g 501 " pdb=" O3A GDP g 501 " pdb=" PB GDP g 501 " pdb=" PA GDP g 501 " ideal model delta sinusoidal sigma weight residual 180.00 69.64 110.36 1 2.00e+01 2.50e-03 3.24e+01 dihedral pdb=" CB GLU g 112 " pdb=" CG GLU g 112 " pdb=" CD GLU g 112 " pdb=" OE1 GLU g 112 " ideal model delta sinusoidal sigma weight residual 0.00 88.90 -88.90 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CA LYS g 193 " pdb=" CB LYS g 193 " pdb=" CG LYS g 193 " pdb=" CD LYS g 193 " ideal model delta sinusoidal sigma weight residual -60.00 -113.08 53.08 3 1.50e+01 4.44e-03 9.17e+00 ... (remaining 1822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 311 0.034 - 0.068: 109 0.068 - 0.102: 34 0.102 - 0.136: 13 0.136 - 0.170: 1 Chirality restraints: 468 Sorted by residual: chirality pdb=" CA THR g 274 " pdb=" N THR g 274 " pdb=" C THR g 274 " pdb=" CB THR g 274 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CA ILE g 320 " pdb=" N ILE g 320 " pdb=" C ILE g 320 " pdb=" CB ILE g 320 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA ILE g 323 " pdb=" N ILE g 323 " pdb=" C ILE g 323 " pdb=" CB ILE g 323 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.50e-01 ... (remaining 465 not shown) Planarity restraints: 516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER g 32 " -0.025 5.00e-02 4.00e+02 3.76e-02 2.27e+00 pdb=" N PRO g 33 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO g 33 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO g 33 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER g 80 " 0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO g 81 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO g 81 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO g 81 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE g 349 " -0.018 5.00e-02 4.00e+02 2.70e-02 1.17e+00 pdb=" N PRO g 350 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO g 350 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO g 350 " -0.015 5.00e-02 4.00e+02 ... (remaining 513 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 357 2.75 - 3.29: 3045 3.29 - 3.82: 4690 3.82 - 4.36: 5481 4.36 - 4.90: 9307 Nonbonded interactions: 22880 Sorted by model distance: nonbonded pdb=" O GLU g 28 " pdb=" OG SER g 364 " model vdw 2.212 2.440 nonbonded pdb=" OE2 GLU g 28 " pdb=" OG SER g 237 " model vdw 2.285 2.440 nonbonded pdb=" OE2 GLU g 112 " pdb=" OH TYR g 152 " model vdw 2.303 2.440 nonbonded pdb=" OD1 ASP g 123 " pdb=" OH TYR g 161 " model vdw 2.304 2.440 nonbonded pdb=" O SER g 226 " pdb=" NE2 GLN g 230 " model vdw 2.330 2.520 ... (remaining 22875 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 2 5.49 5 S 14 5.16 5 C 1883 2.51 5 N 522 2.21 5 O 558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.720 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.030 Process input model: 13.900 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 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 : 0.003 0.021 3031 Z= 0.172 Angle : 0.507 6.008 4099 Z= 0.283 Chirality : 0.041 0.170 468 Planarity : 0.004 0.038 516 Dihedral : 13.582 110.360 1125 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.42), residues: 345 helix: -0.49 (0.37), residues: 177 sheet: -1.74 (0.58), residues: 63 loop : -2.35 (0.58), residues: 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.375 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1792 time to fit residues: 7.3276 Evaluate side-chains 21 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.370 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 chunk 14 optimal weight: 0.0170 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 21 optimal weight: 0.0040 chunk 33 optimal weight: 2.9990 overall best weight: 0.3630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 110 GLN g 227 GLN g 430 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 3031 Z= 0.142 Angle : 0.489 5.812 4099 Z= 0.231 Chirality : 0.041 0.162 468 Planarity : 0.004 0.042 516 Dihedral : 5.421 76.855 409 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 0.61 % 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: -0.80 (0.45), residues: 345 helix: 0.49 (0.39), residues: 176 sheet: -1.21 (0.61), residues: 63 loop : -1.68 (0.61), residues: 106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 27 time to evaluate : 0.476 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 27 average time/residue: 0.1668 time to fit residues: 5.8011 Evaluate side-chains 23 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 21 time to evaluate : 0.386 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0347 time to fit residues: 0.5982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.8261 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 3031 Z= 0.208 Angle : 0.514 6.157 4099 Z= 0.252 Chirality : 0.042 0.172 468 Planarity : 0.004 0.044 516 Dihedral : 5.022 61.017 409 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer Outliers : 2.13 % 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: -0.35 (0.47), residues: 345 helix: 0.83 (0.40), residues: 176 sheet: -1.19 (0.61), residues: 61 loop : -1.29 (0.65), residues: 108 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 21 time to evaluate : 0.374 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 27 average time/residue: 0.1307 time to fit residues: 4.7742 Evaluate side-chains 25 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.360 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0387 time to fit residues: 0.6365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8252 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 3031 Z= 0.187 Angle : 0.511 6.047 4099 Z= 0.253 Chirality : 0.042 0.167 468 Planarity : 0.004 0.044 516 Dihedral : 4.781 50.985 409 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 0.91 % 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: -0.20 (0.47), residues: 345 helix: 0.94 (0.40), residues: 180 sheet: -1.03 (0.61), residues: 63 loop : -1.32 (0.68), residues: 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.394 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 25 average time/residue: 0.1215 time to fit residues: 4.1679 Evaluate side-chains 23 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 21 time to evaluate : 0.369 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0278 time to fit residues: 0.5149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.3980 chunk 14 optimal weight: 0.0050 chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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: 0.8232 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 3031 Z= 0.151 Angle : 0.494 6.291 4099 Z= 0.244 Chirality : 0.041 0.161 468 Planarity : 0.004 0.044 516 Dihedral : 4.520 40.472 409 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer Outliers : 0.30 % 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: 0.02 (0.48), residues: 345 helix: 1.13 (0.41), residues: 180 sheet: -0.90 (0.61), residues: 63 loop : -1.27 (0.68), residues: 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.390 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 24 average time/residue: 0.1341 time to fit residues: 4.3983 Evaluate side-chains 24 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.380 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0337 time to fit residues: 0.5793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 3031 Z= 0.177 Angle : 0.508 5.937 4099 Z= 0.250 Chirality : 0.041 0.164 468 Planarity : 0.004 0.044 516 Dihedral : 4.507 35.983 409 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 1.52 % 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: 0.09 (0.48), residues: 345 helix: 1.12 (0.41), residues: 180 sheet: -0.80 (0.62), residues: 63 loop : -1.17 (0.69), residues: 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 0.368 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 25 average time/residue: 0.1274 time to fit residues: 4.4081 Evaluate side-chains 23 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 21 time to evaluate : 0.384 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0441 time to fit residues: 0.6249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 0.0670 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 0.0000 chunk 6 optimal weight: 2.9990 overall best weight: 0.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 325 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 3031 Z= 0.142 Angle : 0.491 5.770 4099 Z= 0.240 Chirality : 0.041 0.157 468 Planarity : 0.004 0.044 516 Dihedral : 4.378 30.231 409 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 0.30 % 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: 0.20 (0.48), residues: 345 helix: 1.21 (0.41), residues: 180 sheet: -0.65 (0.64), residues: 62 loop : -1.19 (0.68), residues: 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.366 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 24 average time/residue: 0.1329 time to fit residues: 4.3560 Evaluate side-chains 21 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.377 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 32 optimal weight: 0.3980 chunk 34 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 0.0000 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 325 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 3031 Z= 0.154 Angle : 0.515 5.801 4099 Z= 0.254 Chirality : 0.041 0.159 468 Planarity : 0.004 0.044 516 Dihedral : 4.324 31.014 409 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 0.91 % 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: 0.25 (0.48), residues: 345 helix: 1.23 (0.41), residues: 179 sheet: -0.54 (0.64), residues: 63 loop : -1.17 (0.69), residues: 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.371 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 25 average time/residue: 0.0927 time to fit residues: 3.5039 Evaluate side-chains 24 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.372 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0467 time to fit residues: 0.6422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 0.0040 chunk 31 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.0020 overall best weight: 0.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 325 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 3031 Z= 0.135 Angle : 0.504 5.775 4099 Z= 0.245 Chirality : 0.041 0.157 468 Planarity : 0.004 0.044 516 Dihedral : 4.251 30.279 409 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 0.61 % 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: 0.30 (0.48), residues: 345 helix: 1.26 (0.41), residues: 179 sheet: -0.48 (0.65), residues: 63 loop : -1.13 (0.69), residues: 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.353 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 25 average time/residue: 0.0945 time to fit residues: 3.5790 Evaluate side-chains 26 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.394 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0333 time to fit residues: 0.6164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 23 optimal weight: 0.0570 chunk 31 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 325 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 3031 Z= 0.176 Angle : 0.525 5.992 4099 Z= 0.257 Chirality : 0.042 0.164 468 Planarity : 0.004 0.044 516 Dihedral : 4.320 32.614 409 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 0.61 % 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: 0.27 (0.49), residues: 345 helix: 1.22 (0.41), residues: 179 sheet: -0.44 (0.67), residues: 63 loop : -1.14 (0.69), residues: 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 21 time to evaluate : 0.347 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 23 average time/residue: 0.0898 time to fit residues: 3.2133 Evaluate side-chains 22 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.349 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0331 time to fit residues: 0.5164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 0.0770 chunk 25 optimal weight: 0.0980 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 0.0570 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 0.0000 overall best weight: 0.1860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 325 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.074789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.066413 restraints weight = 10966.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.068020 restraints weight = 5634.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.069175 restraints weight = 3536.723| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 3031 Z= 0.129 Angle : 0.507 6.526 4099 Z= 0.245 Chirality : 0.041 0.152 468 Planarity : 0.004 0.044 516 Dihedral : 4.187 29.063 409 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.48), residues: 345 helix: 1.23 (0.40), residues: 179 sheet: -0.38 (0.69), residues: 62 loop : -1.22 (0.67), residues: 104 =============================================================================== Job complete usr+sys time: 1097.95 seconds wall clock time: 20 minutes 26.13 seconds (1226.13 seconds total)