Starting phenix.real_space_refine on Thu Dec 7 19:46:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9e_6240/12_2023/3j9e_6240.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9e_6240/12_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_6240/12_2023/3j9e_6240.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9e_6240/12_2023/3j9e_6240.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9e_6240/12_2023/3j9e_6240.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9e_6240/12_2023/3j9e_6240.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 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. 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-1.21rc1-5172/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: 2.71, per 1000 atoms: 0.66 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: 1.74 Conformation dependent library (CDL) restraints added in 788.3 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: 0.40 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: 0.97 Time building geometry restraints manager: 1.90 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 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: 0.080 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: 0.710 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.600 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 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 : 3.283 102.017 5611 Z= 2.334 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 % Allowed : 14.42 % Favored : 61.33 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.006 TRP D 371 HIS 0.014 0.004 HIS D 365 PHE 0.024 0.005 PHE D 133 TYR 0.032 0.005 TYR D 256 ARG 0.009 0.001 ARG D 430 *********************** 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 : 0.481 Fit side-chains revert: symmetry clash outliers start: 106 outliers final: 49 residues processed: 167 average time/residue: 0.2300 time to fit residues: 44.8068 Evaluate side-chains 118 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 69 time to evaluate : 0.488 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 49 outliers final: 2 residues processed: 49 average time/residue: 0.0861 time to fit residues: 6.4330 ------------------------------------------------------------------------------- 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: 1.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 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: 2.9990 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 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: 0.8450 moved from start: 0.3403 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= 0.223 Angle : 0.872 15.142 5611 Z= 0.462 Chirality : 0.046 0.161 629 Planarity : 0.005 0.051 730 Dihedral : 7.458 50.242 560 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 1.36 % Allowed : 9.11 % Favored : 89.53 % Rotamer: Outliers : 3.43 % Allowed : 21.28 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.59 % Twisted Proline : 0.00 % Twisted General : 0.80 % 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: -1.14 (0.35), residues: 516 helix: 0.69 (0.30), residues: 274 sheet: -2.06 (0.81), residues: 34 loop : -2.57 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 371 HIS 0.006 0.001 HIS D 457 PHE 0.024 0.002 PHE D 378 TYR 0.029 0.002 TYR D 429 ARG 0.004 0.001 ARG D 170 *********************** 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: 15 poor density : 83 time to evaluate : 0.464 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 96 average time/residue: 0.1902 time to fit residues: 22.3227 Evaluate side-chains 70 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.397 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0420 time to fit residues: 0.9955 ------------------------------------------------------------------------------- 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: 0.8980 chunk 47 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8419 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4166 Z= 0.193 Angle : 0.741 15.260 5611 Z= 0.397 Chirality : 0.043 0.153 629 Planarity : 0.004 0.048 730 Dihedral : 6.272 42.932 560 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.97 % Allowed : 8.14 % Favored : 90.89 % Rotamer: Outliers : 3.20 % Allowed : 21.28 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.59 % 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: -0.14 (0.37), residues: 516 helix: 1.67 (0.31), residues: 274 sheet: -1.38 (0.84), residues: 34 loop : -2.43 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 371 HIS 0.005 0.001 HIS D 496 PHE 0.023 0.002 PHE D 378 TYR 0.025 0.002 TYR D 429 ARG 0.003 0.000 ARG D 290 *********************** 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: 14 poor density : 70 time to evaluate : 0.464 Fit side-chains outliers start: 14 outliers final: 2 residues processed: 79 average time/residue: 0.1751 time to fit residues: 17.2903 Evaluate side-chains 59 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.479 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0525 time to fit residues: 0.8481 ------------------------------------------------------------------------------- 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: 9.9990 chunk 22 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 44 optimal weight: 9.9990 chunk 13 optimal weight: 0.0000 chunk 41 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- 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: 0.8439 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4166 Z= 0.223 Angle : 0.725 14.788 5611 Z= 0.385 Chirality : 0.043 0.143 629 Planarity : 0.004 0.047 730 Dihedral : 5.892 31.941 560 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 1.16 % Allowed : 7.17 % Favored : 91.67 % Rotamer: Outliers : 2.52 % Allowed : 23.34 % Favored : 74.14 % 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: 0.26 (0.38), residues: 516 helix: 2.11 (0.32), residues: 274 sheet: -1.25 (0.83), residues: 34 loop : -2.41 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 371 HIS 0.005 0.001 HIS D 403 PHE 0.024 0.002 PHE D 378 TYR 0.024 0.002 TYR D 429 ARG 0.003 0.000 ARG D 290 *********************** 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: 11 poor density : 62 time to evaluate : 0.426 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 70 average time/residue: 0.1954 time to fit residues: 16.7882 Evaluate side-chains 65 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.508 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1086 time to fit residues: 1.6885 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.9990 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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: 0.8437 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4166 Z= 0.233 Angle : 0.699 14.643 5611 Z= 0.374 Chirality : 0.042 0.144 629 Planarity : 0.004 0.046 730 Dihedral : 5.677 28.015 560 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.97 % Allowed : 7.95 % Favored : 91.09 % Rotamer: Outliers : 1.60 % Allowed : 24.71 % Favored : 73.68 % 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: 0.49 (0.39), residues: 516 helix: 2.27 (0.32), residues: 274 sheet: -1.18 (0.85), residues: 34 loop : -2.24 (0.41), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 411 HIS 0.005 0.001 HIS D 403 PHE 0.022 0.002 PHE D 378 TYR 0.023 0.002 TYR D 429 ARG 0.003 0.000 ARG D 290 *********************** 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 67 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.505 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 65 average time/residue: 0.1960 time to fit residues: 15.9400 Evaluate side-chains 56 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.478 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0644 time to fit residues: 0.7995 ------------------------------------------------------------------------------- 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: 1.9990 chunk 50 optimal weight: 1.9990 chunk 41 optimal weight: 0.1980 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 50.0000 chunk 16 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 5 optimal weight: 50.0000 chunk 28 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 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 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4166 Z= 0.170 Angle : 0.676 14.455 5611 Z= 0.357 Chirality : 0.041 0.141 629 Planarity : 0.003 0.043 730 Dihedral : 5.397 25.829 560 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.97 % Allowed : 8.14 % Favored : 90.89 % Rotamer: Outliers : 1.14 % Allowed : 25.17 % Favored : 73.68 % 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: 0.65 (0.39), residues: 516 helix: 2.37 (0.32), residues: 275 sheet: -0.84 (0.77), residues: 44 loop : -2.25 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 411 HIS 0.005 0.001 HIS D 403 PHE 0.022 0.002 PHE D 378 TYR 0.021 0.001 TYR D 429 ARG 0.002 0.000 ARG D 479 *********************** 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 70 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.390 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 68 average time/residue: 0.1755 time to fit residues: 15.0351 Evaluate side-chains 61 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.486 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0438 time to fit residues: 0.9379 ------------------------------------------------------------------------------- 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: 1.9990 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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: 0.8406 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4166 Z= 0.202 Angle : 0.687 14.328 5611 Z= 0.365 Chirality : 0.042 0.175 629 Planarity : 0.004 0.043 730 Dihedral : 5.348 26.239 560 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.78 % Allowed : 8.33 % Favored : 90.89 % Rotamer: Outliers : 1.14 % Allowed : 25.40 % Favored : 73.46 % 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: 0.69 (0.39), residues: 516 helix: 2.37 (0.32), residues: 276 sheet: -0.94 (0.75), residues: 44 loop : -2.16 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 411 HIS 0.006 0.001 HIS D 403 PHE 0.022 0.002 PHE D 378 TYR 0.021 0.001 TYR D 429 ARG 0.006 0.001 ARG D 479 *********************** 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 63 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 0.469 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 61 average time/residue: 0.1465 time to fit residues: 11.7765 Evaluate side-chains 54 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.471 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1384 time to fit residues: 1.0192 ------------------------------------------------------------------------------- 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: 10.0000 chunk 4 optimal weight: 30.0000 chunk 39 optimal weight: 3.9990 chunk 45 optimal weight: 0.0030 chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- 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: 0.8406 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4166 Z= 0.199 Angle : 0.670 14.089 5611 Z= 0.356 Chirality : 0.042 0.178 629 Planarity : 0.004 0.043 730 Dihedral : 5.267 26.810 560 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.78 % Allowed : 8.14 % Favored : 91.09 % Rotamer: Outliers : 1.14 % Allowed : 25.63 % Favored : 73.23 % 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 (0.39), residues: 516 helix: 2.43 (0.32), residues: 276 sheet: -0.97 (0.75), residues: 44 loop : -2.14 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 411 HIS 0.005 0.001 HIS D 403 PHE 0.022 0.002 PHE D 378 TYR 0.021 0.001 TYR D 429 ARG 0.005 0.000 ARG D 479 *********************** 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 60 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.471 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 56 average time/residue: 0.1459 time to fit residues: 10.8279 Evaluate side-chains 57 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.473 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0606 time to fit residues: 1.1896 ------------------------------------------------------------------------------- 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: 1.9990 chunk 44 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 41 optimal weight: 0.0870 chunk 4 optimal weight: 30.0000 overall best weight: 0.8760 ------------------------------------------------------------------------------- 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: 0.8384 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4166 Z= 0.179 Angle : 0.656 13.826 5611 Z= 0.351 Chirality : 0.041 0.226 629 Planarity : 0.003 0.042 730 Dihedral : 5.134 26.837 560 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.33 % Favored : 91.09 % Rotamer: Outliers : 0.46 % Allowed : 25.86 % Favored : 73.68 % 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: 0.83 (0.40), residues: 516 helix: 2.51 (0.32), residues: 276 sheet: -0.94 (0.76), residues: 44 loop : -2.12 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 411 HIS 0.005 0.001 HIS D 403 PHE 0.021 0.002 PHE D 378 TYR 0.021 0.001 TYR D 429 ARG 0.005 0.000 ARG D 479 *********************** 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: 2 poor density : 57 time to evaluate : 0.340 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 59 average time/residue: 0.1099 time to fit residues: 8.7375 Evaluate side-chains 55 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.331 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0353 time to fit residues: 0.5316 ------------------------------------------------------------------------------- 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: 0.9980 chunk 25 optimal weight: 0.1980 chunk 32 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8381 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4166 Z= 0.176 Angle : 0.650 13.655 5611 Z= 0.347 Chirality : 0.041 0.227 629 Planarity : 0.003 0.042 730 Dihedral : 5.039 26.797 560 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.95 % Favored : 91.47 % Rotamer: Outliers : 0.46 % Allowed : 26.54 % Favored : 73.00 % 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: 0.87 (0.39), residues: 516 helix: 2.53 (0.32), residues: 276 sheet: -0.94 (0.77), residues: 44 loop : -2.10 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 411 HIS 0.005 0.001 HIS D 403 PHE 0.021 0.002 PHE D 378 TYR 0.020 0.001 TYR D 429 ARG 0.005 0.000 ARG D 479 ********************** 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 56 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.464 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 55 average time/residue: 0.1424 time to fit residues: 10.7298 Evaluate side-chains 53 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.450 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0637 time to fit residues: 0.7416 ------------------------------------------------------------------------------- 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: 5.9990 chunk 2 optimal weight: 50.0000 chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.158957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.117741 restraints weight = 4648.185| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.29 r_work: 0.2822 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4166 Z= 0.237 Angle : 0.687 13.535 5611 Z= 0.363 Chirality : 0.043 0.248 629 Planarity : 0.004 0.043 730 Dihedral : 5.204 27.411 560 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.95 % Favored : 91.47 % Rotamer: Outliers : 0.46 % Allowed : 25.86 % Favored : 73.68 % 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 (0.39), residues: 516 helix: 2.50 (0.32), residues: 275 sheet: -1.03 (0.76), residues: 44 loop : -2.13 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 411 HIS 0.006 0.001 HIS D 403 PHE 0.021 0.002 PHE D 378 TYR 0.021 0.001 TYR D 429 ARG 0.005 0.000 ARG D 479 =============================================================================== Job complete usr+sys time: 1229.02 seconds wall clock time: 27 minutes 44.39 seconds (1664.39 seconds total)