Starting phenix.real_space_refine (version: dev) on Thu May 12 14:42:40 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9e_6240/05_2022/3j9e_6240.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9e_6240/05_2022/3j9e_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_6240/05_2022/3j9e_6240.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9e_6240/05_2022/3j9e_6240.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9e_6240/05_2022/3j9e_6240.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9e_6240/05_2022/3j9e_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 Convert atoms to be neutral 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-4597/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: 2.79, per 1000 atoms: 0.68 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: 1.71 Conformation dependent library (CDL) restraints added in 784.2 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: 0.20 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: 1.34 Time building geometry restraints manager: 1.85 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: 0.120 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: 0.910 Check model and map are aligned: 0.070 Convert atoms to be neutral: 0.040 Process input model: 16.150 Find NCS groups from input model: 0.120 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.230 ------------------------------------------------------------------------------- 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 : 21.30 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 : 0.566 Fit side-chains revert: symmetry clash outliers start: 106 outliers final: 47 residues processed: 167 average time/residue: 0.2208 time to fit residues: 43.2099 Evaluate side-chains 116 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 69 time to evaluate : 0.513 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 47 outliers final: 1 residues processed: 47 average time/residue: 0.0939 time to fit residues: 6.8197 ------------------------------------------------------------------------------- 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: 0.9980 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 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: 0.9782 ------------------------------------------------------------------------------- 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: 0.8642 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 4166 Z= 0.231 Angle : 0.955 25.848 5611 Z= 0.460 Chirality : 0.045 0.161 629 Planarity : 0.005 0.053 730 Dihedral : 7.374 50.457 560 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 1.36 % Allowed : 9.30 % Favored : 89.34 % Rotamer Outliers : 3.43 % 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: -1.24 (0.36), residues: 516 helix: 0.53 (0.30), residues: 281 sheet: -2.08 (0.80), residues: 34 loop : -2.62 (0.40), residues: 201 *********************** 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 97 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 0.503 Fit side-chains outliers start: 15 outliers final: 5 residues processed: 94 average time/residue: 0.1778 time to fit residues: 20.5315 Evaluate side-chains 66 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.467 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0418 time to fit residues: 1.0432 ------------------------------------------------------------------------------- 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: 0.0670 chunk 32 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 35 optimal weight: 0.4980 chunk 24 optimal weight: 9.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- 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 496 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 4166 Z= 0.192 Angle : 0.831 24.536 5611 Z= 0.392 Chirality : 0.043 0.157 629 Planarity : 0.004 0.050 730 Dihedral : 6.221 44.400 560 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 1.36 % Allowed : 8.14 % Favored : 90.50 % Rotamer Outliers : 2.29 % 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: -0.23 (0.38), residues: 516 helix: 1.56 (0.31), residues: 276 sheet: -1.43 (0.83), residues: 34 loop : -2.45 (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 83 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.495 Fit side-chains outliers start: 10 outliers final: 1 residues processed: 79 average time/residue: 0.1550 time to fit residues: 15.6618 Evaluate side-chains 61 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.501 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0417 time to fit residues: 0.7750 ------------------------------------------------------------------------------- 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: 30.0000 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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** D 465 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 4166 Z= 0.345 Angle : 0.864 24.268 5611 Z= 0.408 Chirality : 0.046 0.155 629 Planarity : 0.004 0.052 730 Dihedral : 6.125 34.563 560 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 1.36 % Allowed : 8.14 % Favored : 90.50 % Rotamer Outliers : 3.89 % 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: -0.07 (0.38), residues: 516 helix: 1.73 (0.31), residues: 281 sheet: -1.55 (0.82), residues: 34 loop : -2.50 (0.41), residues: 201 *********************** 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 73 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 56 time to evaluate : 0.514 Fit side-chains outliers start: 17 outliers final: 11 residues processed: 68 average time/residue: 0.1872 time to fit residues: 15.8421 Evaluate side-chains 62 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 0.506 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0862 time to fit residues: 2.0240 ------------------------------------------------------------------------------- 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: 0.7980 chunk 20 optimal weight: 0.8980 chunk 42 optimal weight: 0.2980 chunk 34 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 45 optimal weight: 0.0870 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 0.0050 overall best weight: 0.3772 ------------------------------------------------------------------------------- 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: 0.8578 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 4166 Z= 0.144 Angle : 0.760 24.448 5611 Z= 0.354 Chirality : 0.040 0.130 629 Planarity : 0.003 0.046 730 Dihedral : 5.472 25.681 560 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 1.16 % Allowed : 8.33 % Favored : 90.50 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.79 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.44 (0.39), residues: 516 helix: 2.27 (0.32), residues: 274 sheet: -1.22 (0.86), residues: 34 loop : -2.34 (0.41), residues: 208 *********************** 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 73 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 0.471 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 72 average time/residue: 0.1691 time to fit residues: 15.3449 Evaluate side-chains 59 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.513 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0487 time to fit residues: 0.9523 ------------------------------------------------------------------------------- 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: 3.9990 chunk 41 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 5 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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: 0.8659 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 4166 Z= 0.286 Angle : 0.808 24.773 5611 Z= 0.375 Chirality : 0.043 0.153 629 Planarity : 0.004 0.048 730 Dihedral : 5.501 31.822 560 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 1.16 % Allowed : 8.72 % Favored : 90.12 % Rotamer Outliers : 1.14 % 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: 0.43 (0.39), residues: 516 helix: 2.18 (0.32), residues: 276 sheet: -1.30 (0.84), residues: 34 loop : -2.23 (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 64 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.561 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 60 average time/residue: 0.1889 time to fit residues: 15.5082 Evaluate side-chains 57 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.664 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0752 time to fit residues: 1.5580 ------------------------------------------------------------------------------- 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: 0.9990 chunk 42 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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: 0.8653 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 4166 Z= 0.259 Angle : 0.795 24.930 5611 Z= 0.370 Chirality : 0.042 0.146 629 Planarity : 0.004 0.047 730 Dihedral : 5.430 30.432 560 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 1.16 % Allowed : 8.33 % Favored : 90.50 % 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: 0.48 (0.39), residues: 516 helix: 2.22 (0.32), residues: 276 sheet: -1.37 (0.84), residues: 34 loop : -2.21 (0.42), residues: 206 *********************** 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 : 0.467 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 58 average time/residue: 0.1515 time to fit residues: 11.6868 Evaluate side-chains 57 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.509 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0679 time to fit residues: 0.8105 ------------------------------------------------------------------------------- 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: 9.9990 chunk 4 optimal weight: 40.0000 chunk 39 optimal weight: 0.0370 chunk 45 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 14 optimal weight: 5.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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: 0.8573 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 4166 Z= 0.146 Angle : 0.746 25.241 5611 Z= 0.343 Chirality : 0.040 0.171 629 Planarity : 0.003 0.045 730 Dihedral : 5.021 24.786 560 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 1.16 % Allowed : 8.14 % Favored : 90.70 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.79 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.79 (0.40), residues: 516 helix: 2.50 (0.32), residues: 276 sheet: -0.93 (0.78), residues: 44 loop : -2.20 (0.44), 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 69 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.512 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 67 average time/residue: 0.1498 time to fit residues: 13.0456 Evaluate side-chains 56 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.501 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0413 time to fit residues: 0.9359 ------------------------------------------------------------------------------- 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: 3.9990 chunk 44 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 4166 Z= 0.162 Angle : 0.757 25.439 5611 Z= 0.348 Chirality : 0.041 0.196 629 Planarity : 0.003 0.045 730 Dihedral : 4.961 23.846 560 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.97 % Allowed : 7.95 % Favored : 91.09 % 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: 2.60 (0.32), residues: 276 sheet: -0.93 (0.78), residues: 44 loop : -2.20 (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 62 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.529 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 60 average time/residue: 0.1523 time to fit residues: 11.9972 Evaluate side-chains 56 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.508 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0436 time to fit residues: 0.7825 ------------------------------------------------------------------------------- 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: 0.5980 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 0.0170 chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 135 ASN ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8581 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 4166 Z= 0.171 Angle : 0.755 25.657 5611 Z= 0.348 Chirality : 0.041 0.231 629 Planarity : 0.003 0.045 730 Dihedral : 4.919 24.325 560 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.34 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: 0.90 (0.40), residues: 516 helix: 2.58 (0.32), residues: 277 sheet: -0.94 (0.78), residues: 44 loop : -2.15 (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 60 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.515 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 58 average time/residue: 0.1504 time to fit residues: 11.7150 Evaluate side-chains 60 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.580 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0485 time to fit residues: 0.9814 ------------------------------------------------------------------------------- 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: 30.0000 chunk 7 optimal weight: 5.9990 chunk 36 optimal weight: 0.0050 chunk 2 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 27 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 chunk 1 optimal weight: 0.2980 chunk 33 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 135 ASN ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3753 r_free = 0.3753 target = 0.158292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.117672 restraints weight = 4663.077| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.28 r_work: 0.3301 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work: 0.3267 rms_B_bonded: 2.10 restraints_weight: 0.1250 r_work: 0.3247 rms_B_bonded: 2.22 restraints_weight: 0.0625 r_work: 0.3224 rms_B_bonded: 2.41 restraints_weight: 0.0312 r_work: 0.3197 rms_B_bonded: 2.68 restraints_weight: 0.0156 r_work: 0.3165 rms_B_bonded: 3.05 restraints_weight: 0.0078 r_work: 0.3127 rms_B_bonded: 3.54 restraints_weight: 0.0039 r_work: 0.3082 rms_B_bonded: 4.18 restraints_weight: 0.0020 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.5061 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= 0.159 Angle : 0.748 25.783 5611 Z= 0.339 Chirality : 0.040 0.138 629 Planarity : 0.003 0.045 730 Dihedral : 4.825 21.433 560 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.97 % Allowed : 7.75 % Favored : 91.28 % 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: 0.98 (0.40), residues: 516 helix: 2.59 (0.32), residues: 282 sheet: -0.92 (0.79), residues: 44 loop : -2.14 (0.45), residues: 190 =============================================================================== Job complete usr+sys time: 1172.92 seconds wall clock time: 22 minutes 2.01 seconds (1322.01 seconds total)