Starting phenix.real_space_refine (version: dev) on Fri Feb 17 08:27:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9e_6240/02_2023/3j9e_6240.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9e_6240/02_2023/3j9e_6240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9e_6240/02_2023/3j9e_6240.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9e_6240/02_2023/3j9e_6240.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9e_6240/02_2023/3j9e_6240.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9e_6240/02_2023/3j9e_6240.pdb" } resolution = 3.3 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= 0.008 sd= 0.212 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "D GLU 40": "OE1" <-> "OE2" Residue "D GLU 63": "OE1" <-> "OE2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D GLU 143": "OE1" <-> "OE2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D GLU 165": "OE1" <-> "OE2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "D GLU 206": "OE1" <-> "OE2" Residue "D GLU 208": "OE1" <-> "OE2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D GLU 293": "OE1" <-> "OE2" Residue "D GLU 316": "OE1" <-> "OE2" Residue "D GLU 323": "OE1" <-> "OE2" Residue "D GLU 334": "OE1" <-> "OE2" Residue "D GLU 335": "OE1" <-> "OE2" Residue "D GLU 337": "OE1" <-> "OE2" Residue "D ARG 423": "NH1" <-> "NH2" Residue "D GLU 431": "OE1" <-> "OE2" Residue "D ARG 474": "NH1" <-> "NH2" Residue "D ARG 500": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 4098 Number of models: 1 Model: "" Number of chains: 1 Chain: "D" Number of atoms: 4098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4098 Classifications: {'peptide': 520} Link IDs: {'CIS': 9, 'PTRANS': 15, 'TRANS': 495} Chain breaks: 1 Time building chain proxies: 2.86, per 1000 atoms: 0.70 Number of scatterers: 4098 At special positions: 0 Unit cell: (63.63, 87.87, 99.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 777 8.00 N 722 7.00 C 2584 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: 1.57 Conformation dependent library (CDL) restraints added in 736.6 milliseconds 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 2 sheets defined 60.0% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'D' and resid 22 through 39 Processing helix chain 'D' and resid 41 through 46 removed outlier: 3.544A pdb=" N SER D 45 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ALA D 46 " --> pdb=" O ILE D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 66 removed outlier: 3.896A pdb=" N LEU D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR D 65 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY D 66 " --> pdb=" O GLY D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 115 removed outlier: 3.717A pdb=" N LYS D 98 " --> pdb=" O GLY D 94 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU D 110 " --> pdb=" O GLN D 106 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 123 removed outlier: 3.610A pdb=" N LYS D 122 " --> pdb=" O LYS D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 134 removed outlier: 4.063A pdb=" N GLU D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU D 129 " --> pdb=" O LYS D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 179 removed outlier: 4.285A pdb=" N GLU D 179 " --> pdb=" O ALA D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 210 Processing helix chain 'D' and resid 224 through 231 removed outlier: 3.689A pdb=" N ALA D 230 " --> pdb=" O ASP D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 256 removed outlier: 3.526A pdb=" N TYR D 256 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 266 Processing helix chain 'D' and resid 279 through 289 Processing helix chain 'D' and resid 295 through 324 removed outlier: 3.893A pdb=" N ALA D 309 " --> pdb=" O SER D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 340 Processing helix chain 'D' and resid 347 through 354 removed outlier: 3.507A pdb=" N MET D 351 " --> pdb=" O HIS D 347 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE D 354 " --> pdb=" O VAL D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 361 Processing helix chain 'D' and resid 384 through 388 removed outlier: 3.642A pdb=" N ASN D 388 " --> pdb=" O HIS D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 439 Processing helix chain 'D' and resid 449 through 453 removed outlier: 3.895A pdb=" N SER D 453 " --> pdb=" O LEU D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 483 Processing helix chain 'D' and resid 483 through 491 Processing helix chain 'D' and resid 494 through 508 Processing sheet with id= A, first strand: chain 'D' and resid 217 through 219 removed outlier: 3.694A pdb=" N GLN D 218 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 401 through 406 removed outlier: 6.313A pdb=" N ILE D 364 " --> pdb=" O SER D 463 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER D 463 " --> pdb=" O ILE D 364 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL D 366 " --> pdb=" O LEU D 461 " (cutoff:3.500A) 231 hydrogen bonds defined for protein. 669 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: 1.09 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.74 - 1.10: 2 1.10 - 1.47: 2183 1.47 - 1.83: 1978 1.83 - 2.19: 2 2.19 - 2.55: 1 Bond restraints: 4166 Sorted by residual: bond pdb=" C LYS D 454 " pdb=" N THR D 455 " ideal model delta sigma weight residual 1.332 2.549 -1.217 1.40e-02 5.10e+03 7.55e+03 bond pdb=" C GLY D 442 " pdb=" N THR D 443 " ideal model delta sigma weight residual 1.331 2.157 -0.826 1.29e-02 6.01e+03 4.10e+03 bond pdb=" C GLU D 67 " pdb=" N SER D 68 " ideal model delta sigma weight residual 1.332 0.743 0.589 1.40e-02 5.10e+03 1.77e+03 bond pdb=" C LYS D 13 " pdb=" N LYS D 14 " ideal model delta sigma weight residual 1.332 0.842 0.491 1.38e-02 5.25e+03 1.26e+03 bond pdb=" C LEU D 513 " pdb=" N GLY D 514 " ideal model delta sigma weight residual 1.328 1.521 -0.193 1.24e-02 6.50e+03 2.42e+02 ... (remaining 4161 not shown) Histogram of bond angle deviations from ideal: 20.68 - 45.11: 4 45.11 - 69.53: 0 69.53 - 93.95: 4 93.95 - 118.38: 3335 118.38 - 142.80: 2268 Bond angle restraints: 5611 Sorted by residual: angle pdb=" O GLY D 442 " pdb=" C GLY D 442 " pdb=" N THR D 443 " ideal model delta sigma weight residual 122.70 20.68 102.02 1.30e+00 5.92e-01 6.16e+03 angle pdb=" O ALA D 138 " pdb=" C ALA D 138 " pdb=" N ASN D 139 " ideal model delta sigma weight residual 122.96 38.51 84.45 1.13e+00 7.83e-01 5.59e+03 angle pdb=" O LEU D 513 " pdb=" C LEU D 513 " pdb=" N GLY D 514 " ideal model delta sigma weight residual 123.10 42.69 80.41 1.29e+00 6.01e-01 3.88e+03 angle pdb=" O LYS D 13 " pdb=" C LYS D 13 " pdb=" N LYS D 14 " ideal model delta sigma weight residual 122.92 70.70 52.22 1.17e+00 7.31e-01 1.99e+03 angle pdb=" C LYS D 454 " pdb=" N THR D 455 " pdb=" CA THR D 455 " ideal model delta sigma weight residual 121.54 44.01 77.53 1.91e+00 2.74e-01 1.65e+03 ... (remaining 5606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 2081 17.93 - 35.87: 290 35.87 - 53.80: 128 53.80 - 71.73: 44 71.73 - 89.67: 8 Dihedral angle restraints: 2551 sinusoidal: 1047 harmonic: 1504 Sorted by residual: dihedral pdb=" CA PHE D 123 " pdb=" C PHE D 123 " pdb=" N GLY D 124 " pdb=" CA GLY D 124 " ideal model delta harmonic sigma weight residual -180.00 -132.64 -47.36 0 5.00e+00 4.00e-02 8.97e+01 dihedral pdb=" CA LYS D 454 " pdb=" C LYS D 454 " pdb=" N THR D 455 " pdb=" CA THR D 455 " ideal model delta harmonic sigma weight residual -180.00 -138.13 -41.87 0 5.00e+00 4.00e-02 7.01e+01 dihedral pdb=" CA ALA D 138 " pdb=" C ALA D 138 " pdb=" N ASN D 139 " pdb=" CA ASN D 139 " ideal model delta harmonic sigma weight residual 0.00 40.93 -40.93 0 5.00e+00 4.00e-02 6.70e+01 ... (remaining 2548 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 447 0.087 - 0.173: 153 0.173 - 0.260: 23 0.260 - 0.347: 5 0.347 - 0.434: 1 Chirality restraints: 629 Sorted by residual: chirality pdb=" CA ARG D 492 " pdb=" N ARG D 492 " pdb=" C ARG D 492 " pdb=" CB ARG D 492 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.70e+00 chirality pdb=" CA GLU D 83 " pdb=" N GLU D 83 " pdb=" C GLU D 83 " pdb=" CB GLU D 83 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA LEU D 401 " pdb=" N LEU D 401 " pdb=" C LEU D 401 " pdb=" CB LEU D 401 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 626 not shown) Planarity restraints: 730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 13 " 0.145 2.00e-02 2.50e+03 2.70e-01 7.28e+02 pdb=" C LYS D 13 " -0.467 2.00e-02 2.50e+03 pdb=" O LYS D 13 " 0.183 2.00e-02 2.50e+03 pdb=" N LYS D 14 " 0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 513 " -0.142 2.00e-02 2.50e+03 2.36e-01 5.57e+02 pdb=" C LEU D 513 " 0.308 2.00e-02 2.50e+03 pdb=" O LEU D 513 " -0.300 2.00e-02 2.50e+03 pdb=" N GLY D 514 " 0.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 138 " -0.117 2.00e-02 2.50e+03 1.71e-01 2.92e+02 pdb=" C ALA D 138 " 0.249 2.00e-02 2.50e+03 pdb=" O ALA D 138 " 0.062 2.00e-02 2.50e+03 pdb=" N ASN D 139 " -0.193 2.00e-02 2.50e+03 ... (remaining 727 not shown) Histogram of nonbonded interaction distances: 1.22 - 1.96: 12 1.96 - 2.69: 371 2.69 - 3.43: 5801 3.43 - 4.16: 9728 4.16 - 4.90: 16842 Nonbonded interactions: 32754 Sorted by model distance: nonbonded pdb=" N LYS D 454 " pdb=" OG1 THR D 455 " model vdw 1.223 2.520 nonbonded pdb=" CA LYS D 454 " pdb=" OG1 THR D 455 " model vdw 1.275 3.470 nonbonded pdb=" O LYS D 13 " pdb=" CA LYS D 14 " model vdw 1.312 2.776 nonbonded pdb=" O LYS D 13 " pdb=" CB LYS D 14 " model vdw 1.397 3.440 nonbonded pdb=" O LEU D 513 " pdb=" CA GLY D 514 " model vdw 1.510 2.752 ... (remaining 32749 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: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2584 2.51 5 N 722 2.21 5 O 777 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: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.850 Check model and map are aligned: 0.070 Process input model: 15.750 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 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 : 0.032 1.217 4166 Z= 1.737 Angle : 3.281 102.017 5611 Z= 2.330 Chirality : 0.085 0.434 629 Planarity : 0.018 0.270 730 Dihedral : 21.306 89.665 1579 Min Nonbonded Distance : 1.223 Molprobity Statistics. All-atom Clashscore : 20.81 Ramachandran Plot: Outliers : 2.93 % Allowed : 9.77 % Favored : 87.30 % Rotamer Outliers : 24.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.60 % Twisted Proline : 0.00 % Twisted General : 1.20 % 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: -3.41 (0.31), residues: 512 helix: -2.02 (0.24), residues: 273 sheet: -3.20 (0.71), residues: 40 loop : -2.15 (0.42), residues: 199 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 85 time to evaluate : 0.545 Fit side-chains revert: symmetry clash outliers start: 106 outliers final: 49 residues processed: 167 average time/residue: 0.2563 time to fit residues: 49.9032 Evaluate side-chains 118 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 69 time to evaluate : 0.500 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 49 outliers final: 2 residues processed: 49 average time/residue: 0.0879 time to fit residues: 6.7673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 GLN D 96 GLN D 307 ASN ** D 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 496 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4166 Z= 0.212 Angle : 0.941 25.778 5611 Z= 0.453 Chirality : 0.045 0.162 629 Planarity : 0.005 0.051 730 Dihedral : 7.298 49.974 560 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 1.16 % Allowed : 9.11 % Favored : 89.73 % Rotamer Outliers : 3.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.79 % Twisted Proline : 0.00 % Twisted General : 0.60 % 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: -1.08 (0.36), residues: 516 helix: 0.72 (0.30), residues: 274 sheet: -2.04 (0.81), residues: 34 loop : -2.50 (0.40), residues: 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 84 time to evaluate : 0.468 Fit side-chains outliers start: 14 outliers final: 5 residues processed: 96 average time/residue: 0.1972 time to fit residues: 23.1469 Evaluate side-chains 67 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.498 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0460 time to fit residues: 1.1253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 13 optimal weight: 0.3980 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 chunk 24 optimal weight: 9.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 363 GLN ** D 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 HIS D 496 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 4166 Z= 0.218 Angle : 0.836 24.350 5611 Z= 0.394 Chirality : 0.043 0.151 629 Planarity : 0.004 0.049 730 Dihedral : 6.214 42.511 560 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 1.36 % Allowed : 8.72 % Favored : 89.92 % Rotamer Outliers : 3.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.79 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -0.18 (0.38), residues: 516 helix: 1.62 (0.31), residues: 276 sheet: -1.42 (0.83), residues: 34 loop : -2.44 (0.41), residues: 206 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 68 time to evaluate : 0.457 Fit side-chains outliers start: 16 outliers final: 4 residues processed: 80 average time/residue: 0.1743 time to fit residues: 17.7459 Evaluate side-chains 60 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.474 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0545 time to fit residues: 1.1085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 40.0000 chunk 22 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 44 optimal weight: 9.9990 chunk 13 optimal weight: 0.0570 chunk 41 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 overall best weight: 1.2500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 4166 Z= 0.212 Angle : 0.798 24.257 5611 Z= 0.375 Chirality : 0.042 0.143 629 Planarity : 0.004 0.048 730 Dihedral : 5.766 30.855 560 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 1.36 % Allowed : 7.36 % Favored : 91.28 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.79 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.26 (0.39), residues: 516 helix: 2.10 (0.32), residues: 275 sheet: -1.31 (0.84), residues: 34 loop : -2.39 (0.40), residues: 207 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 62 time to evaluate : 0.460 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 67 average time/residue: 0.1813 time to fit residues: 15.3540 Evaluate side-chains 62 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.520 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1158 time to fit residues: 1.6277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 4166 Z= 0.241 Angle : 0.785 24.429 5611 Z= 0.369 Chirality : 0.042 0.146 629 Planarity : 0.004 0.047 730 Dihedral : 5.567 30.565 560 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 1.16 % Allowed : 8.14 % Favored : 90.70 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.79 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.44 (0.39), residues: 516 helix: 2.22 (0.32), residues: 275 sheet: -1.34 (0.85), residues: 34 loop : -2.25 (0.42), residues: 207 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.538 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 61 average time/residue: 0.1930 time to fit residues: 14.7885 Evaluate side-chains 57 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.532 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0647 time to fit residues: 0.9693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 4 optimal weight: 50.0000 chunk 16 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 5 optimal weight: 50.0000 chunk 28 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 4166 Z= 0.232 Angle : 0.779 24.699 5611 Z= 0.361 Chirality : 0.042 0.145 629 Planarity : 0.004 0.046 730 Dihedral : 5.450 30.432 560 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 1.16 % Allowed : 7.95 % Favored : 90.89 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.79 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.46 (0.39), residues: 516 helix: 2.21 (0.32), residues: 276 sheet: -1.44 (0.84), residues: 34 loop : -2.19 (0.42), residues: 206 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.473 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 62 average time/residue: 0.1671 time to fit residues: 13.3371 Evaluate side-chains 60 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.505 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0510 time to fit residues: 1.3031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 4166 Z= 0.342 Angle : 0.828 24.954 5611 Z= 0.388 Chirality : 0.044 0.156 629 Planarity : 0.004 0.048 730 Dihedral : 5.659 34.965 560 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 1.16 % Allowed : 7.95 % Favored : 90.89 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.79 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.32 (0.39), residues: 516 helix: 2.06 (0.32), residues: 277 sheet: -1.56 (0.81), residues: 34 loop : -2.22 (0.42), residues: 205 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.494 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 58 average time/residue: 0.1462 time to fit residues: 11.3263 Evaluate side-chains 55 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.472 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0463 time to fit residues: 0.9088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 4.9990 chunk 4 optimal weight: 50.0000 chunk 39 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 4166 Z= 0.173 Angle : 0.754 25.203 5611 Z= 0.346 Chirality : 0.041 0.134 629 Planarity : 0.003 0.045 730 Dihedral : 5.206 28.400 560 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 1.16 % Allowed : 8.14 % Favored : 90.70 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.79 % 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: 0.60 (0.39), residues: 516 helix: 2.35 (0.32), residues: 276 sheet: -1.10 (0.77), residues: 44 loop : -2.27 (0.43), residues: 196 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.518 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 65 average time/residue: 0.1826 time to fit residues: 14.9381 Evaluate side-chains 53 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.503 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0412 time to fit residues: 0.6999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 0.0670 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 4 optimal weight: 30.0000 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 135 ASN ** D 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4166 Z= 0.171 Angle : 0.756 25.430 5611 Z= 0.350 Chirality : 0.041 0.208 629 Planarity : 0.003 0.045 730 Dihedral : 5.032 28.861 560 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.97 % Allowed : 7.75 % Favored : 91.28 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.79 % 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: 0.75 (0.40), residues: 516 helix: 2.48 (0.32), residues: 276 sheet: -0.96 (0.79), residues: 44 loop : -2.23 (0.43), residues: 196 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.500 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 57 average time/residue: 0.1713 time to fit residues: 12.6577 Evaluate side-chains 56 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.546 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0588 time to fit residues: 0.9486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 135 ASN ** D 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 4166 Z= 0.181 Angle : 0.759 25.636 5611 Z= 0.351 Chirality : 0.041 0.218 629 Planarity : 0.003 0.045 730 Dihedral : 4.930 26.211 560 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.97 % Allowed : 7.95 % Favored : 91.09 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.79 % 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: 0.78 (0.40), residues: 516 helix: 2.47 (0.32), residues: 277 sheet: -0.94 (0.80), residues: 44 loop : -2.20 (0.43), residues: 195 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.500 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 58 average time/residue: 0.1384 time to fit residues: 10.8113 Evaluate side-chains 55 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.448 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0416 time to fit residues: 0.7046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 50.0000 chunk 7 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 2 optimal weight: 30.0000 chunk 29 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 1 optimal weight: 0.3980 chunk 33 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 135 ASN ** D 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.163387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.121734 restraints weight = 4616.434| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.37 r_work: 0.3163 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 4166 Z= 0.158 Angle : 0.745 25.758 5611 Z= 0.342 Chirality : 0.041 0.212 629 Planarity : 0.003 0.044 730 Dihedral : 4.814 26.464 560 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.97 % Allowed : 7.36 % Favored : 91.67 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.79 % 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: 0.88 (0.40), residues: 516 helix: 2.55 (0.32), residues: 277 sheet: -0.90 (0.80), residues: 44 loop : -2.13 (0.44), residues: 195 =============================================================================== Job complete usr+sys time: 1222.70 seconds wall clock time: 22 minutes 54.90 seconds (1374.90 seconds total)