Starting phenix.real_space_refine on Mon Mar 11 01:46:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sy2_25514/03_2024/7sy2_25514.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sy2_25514/03_2024/7sy2_25514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sy2_25514/03_2024/7sy2_25514.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sy2_25514/03_2024/7sy2_25514.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sy2_25514/03_2024/7sy2_25514.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sy2_25514/03_2024/7sy2_25514.pdb" } resolution = 3.11 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.032 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 37 5.16 5 C 4191 2.51 5 N 1077 2.21 5 O 1249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6554 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1594 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 4.50, per 1000 atoms: 0.69 Number of scatterers: 6554 At special positions: 0 Unit cell: (80, 83, 122, 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 37 16.00 O 1249 8.00 N 1077 7.00 C 4191 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.02 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 Links applied NAG-ASN " NAG B1301 " - " ASN B 343 " " NAG E 701 " - " ASN E 53 " " NAG E 702 " - " ASN E 90 " " NAG E 703 " - " ASN E 103 " " NAG E 704 " - " ASN E 322 " " NAG E 705 " - " ASN E 432 " " NAG E 706 " - " ASN E 546 " Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.3 seconds 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1500 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 7 sheets defined 57.2% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.502A pdb=" N LYS B 386 " --> pdb=" O SER B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.745A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.792A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 Processing helix chain 'E' and resid 82 through 83 No H-bonds generated for 'chain 'E' and resid 82 through 83' Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.751A pdb=" N GLU E 87 " --> pdb=" O PRO E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.994A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 146 through 155 removed outlier: 3.967A pdb=" N ILE E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 194 Proline residue: E 178 - end of helix removed outlier: 3.710A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 218 through 252 removed outlier: 3.659A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.801A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 300 Processing helix chain 'E' and resid 303 through 318 Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.583A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.685A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 388 No H-bonds generated for 'chain 'E' and resid 386 through 388' Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 397 through 413 removed outlier: 4.279A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.519A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.358A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 499 through 502 removed outlier: 3.734A pdb=" N SER E 502 " --> pdb=" O ASP E 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 499 through 502' Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 512 through 533 removed outlier: 4.434A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.902A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.981A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'E' and resid 131 through 132 removed outlier: 3.690A pdb=" N LEU E 142 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.005A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.335A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 915 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: 1.75 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2083 1.35 - 1.47: 1794 1.47 - 1.60: 2802 1.60 - 1.72: 0 1.72 - 1.85: 58 Bond restraints: 6737 Sorted by residual: bond pdb=" C1 NAG E 702 " pdb=" O5 NAG E 702 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.07e+00 bond pdb=" C1 NAG E 703 " pdb=" O5 NAG E 703 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 4.98e+00 bond pdb=" C1 NAG E 704 " pdb=" O5 NAG E 704 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.84e+00 bond pdb=" C1 NAG E 706 " pdb=" O5 NAG E 706 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.27e+00 bond pdb=" C1 NAG E 705 " pdb=" O5 NAG E 705 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.11e+00 ... (remaining 6732 not shown) Histogram of bond angle deviations from ideal: 98.13 - 105.32: 160 105.32 - 112.51: 3275 112.51 - 119.70: 2401 119.70 - 126.90: 3197 126.90 - 134.09: 123 Bond angle restraints: 9156 Sorted by residual: angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.82 128.95 -6.13 1.42e+00 4.96e-01 1.86e+01 angle pdb=" CA CYS E 141 " pdb=" CB CYS E 141 " pdb=" SG CYS E 141 " ideal model delta sigma weight residual 114.40 123.57 -9.17 2.30e+00 1.89e-01 1.59e+01 angle pdb=" CA ASN E 437 " pdb=" CB ASN E 437 " pdb=" CG ASN E 437 " ideal model delta sigma weight residual 112.60 115.98 -3.38 1.00e+00 1.00e+00 1.14e+01 angle pdb=" CB MET E 323 " pdb=" CG MET E 323 " pdb=" SD MET E 323 " ideal model delta sigma weight residual 112.70 122.83 -10.13 3.00e+00 1.11e-01 1.14e+01 angle pdb=" N TYR B 495 " pdb=" CA TYR B 495 " pdb=" C TYR B 495 " ideal model delta sigma weight residual 110.52 105.59 4.93 1.48e+00 4.57e-01 1.11e+01 ... (remaining 9151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 3687 17.13 - 34.25: 306 34.25 - 51.38: 48 51.38 - 68.51: 13 68.51 - 85.63: 12 Dihedral angle restraints: 4066 sinusoidal: 1727 harmonic: 2339 Sorted by residual: dihedral pdb=" CB CYS E 133 " pdb=" SG CYS E 133 " pdb=" SG CYS E 141 " pdb=" CB CYS E 141 " ideal model delta sinusoidal sigma weight residual -86.00 -43.43 -42.57 1 1.00e+01 1.00e-02 2.53e+01 dihedral pdb=" SG CYS B 391 " pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " pdb=" CA CYS B 525 " ideal model delta sinusoidal sigma weight residual 79.00 16.60 62.40 1 2.00e+01 2.50e-03 1.29e+01 dihedral pdb=" C ASN B 360 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " pdb=" CB ASN B 360 " ideal model delta harmonic sigma weight residual -122.60 -130.73 8.13 0 2.50e+00 1.60e-01 1.06e+01 ... (remaining 4063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 713 0.053 - 0.107: 200 0.107 - 0.160: 55 0.160 - 0.213: 8 0.213 - 0.267: 2 Chirality restraints: 978 Sorted by residual: chirality pdb=" CA ASN B 360 " pdb=" N ASN B 360 " pdb=" C ASN B 360 " pdb=" CB ASN B 360 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CB VAL E 581 " pdb=" CA VAL E 581 " pdb=" CG1 VAL E 581 " pdb=" CG2 VAL E 581 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ASN E 437 " pdb=" N ASN E 437 " pdb=" C ASN E 437 " pdb=" CB ASN E 437 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 975 not shown) Planarity restraints: 1184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 169 " 0.017 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C ARG E 169 " -0.058 2.00e-02 2.50e+03 pdb=" O ARG E 169 " 0.022 2.00e-02 2.50e+03 pdb=" N SER E 170 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP E 168 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.52e+00 pdb=" C TRP E 168 " -0.047 2.00e-02 2.50e+03 pdb=" O TRP E 168 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG E 169 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR E 41 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.87e+00 pdb=" C TYR E 41 " 0.045 2.00e-02 2.50e+03 pdb=" O TYR E 41 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN E 42 " -0.015 2.00e-02 2.50e+03 ... (remaining 1181 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1934 2.83 - 3.34: 5949 3.34 - 3.86: 11371 3.86 - 4.38: 12856 4.38 - 4.90: 22341 Nonbonded interactions: 54451 Sorted by model distance: nonbonded pdb=" OH TYR E 183 " pdb=" OD1 ASP E 509 " model vdw 2.307 2.440 nonbonded pdb=" O ASN E 117 " pdb=" ND2 ASN E 121 " model vdw 2.349 2.520 nonbonded pdb=" OE1 GLU B 406 " pdb=" OH TYR B 495 " model vdw 2.354 2.440 nonbonded pdb=" O MET E 152 " pdb=" NH1 ARG E 161 " model vdw 2.355 2.520 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.356 2.440 ... (remaining 54446 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: 4.820 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: 15.830 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 21.560 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 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 : 0.005 0.059 6737 Z= 0.322 Angle : 0.844 10.130 9156 Z= 0.460 Chirality : 0.055 0.267 978 Planarity : 0.007 0.065 1177 Dihedral : 13.461 85.634 2548 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.14 % Allowed : 1.86 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.26), residues: 793 helix: -0.05 (0.23), residues: 385 sheet: 0.55 (0.66), residues: 53 loop : -0.59 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 566 HIS 0.004 0.001 HIS E 34 PHE 0.031 0.002 PHE E 369 TYR 0.029 0.002 TYR E 385 ARG 0.007 0.001 ARG E 460 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8467 (m-30) cc_final: 0.8200 (m-30) REVERT: E 290 ASN cc_start: 0.8480 (t0) cc_final: 0.7701 (t0) REVERT: E 408 MET cc_start: 0.9425 (mmt) cc_final: 0.9219 (mmt) REVERT: E 474 MET cc_start: 0.8855 (mmt) cc_final: 0.8342 (mmm) REVERT: E 498 CYS cc_start: 0.7597 (t) cc_final: 0.6794 (t) outliers start: 1 outliers final: 0 residues processed: 96 average time/residue: 0.3144 time to fit residues: 36.5689 Evaluate side-chains 48 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 46 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 154 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6737 Z= 0.194 Angle : 0.529 8.577 9156 Z= 0.274 Chirality : 0.040 0.144 978 Planarity : 0.004 0.041 1177 Dihedral : 5.723 57.849 1013 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.86 % Allowed : 6.14 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.28), residues: 793 helix: 1.13 (0.25), residues: 402 sheet: 0.50 (0.67), residues: 52 loop : -0.13 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 165 HIS 0.005 0.001 HIS E 34 PHE 0.018 0.001 PHE E 369 TYR 0.011 0.001 TYR E 385 ARG 0.005 0.000 ARG E 306 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8415 (m-30) cc_final: 0.8158 (m-30) REVERT: B 406 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8539 (mt-10) REVERT: E 498 CYS cc_start: 0.7892 (t) cc_final: 0.7320 (t) outliers start: 6 outliers final: 3 residues processed: 55 average time/residue: 0.2318 time to fit residues: 17.3815 Evaluate side-chains 50 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 151 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN B 498 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6737 Z= 0.192 Angle : 0.503 8.055 9156 Z= 0.258 Chirality : 0.039 0.143 978 Planarity : 0.004 0.033 1177 Dihedral : 5.189 57.222 1013 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.29 % Allowed : 7.86 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.29), residues: 793 helix: 1.50 (0.25), residues: 410 sheet: 0.98 (0.73), residues: 42 loop : 0.12 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 PHE 0.016 0.001 PHE E 369 TYR 0.012 0.001 TYR E 385 ARG 0.003 0.000 ARG E 306 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8387 (m-30) cc_final: 0.8124 (m-30) REVERT: B 406 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8548 (mt-10) REVERT: E 249 MET cc_start: 0.8598 (ttp) cc_final: 0.8312 (ttp) REVERT: E 325 GLN cc_start: 0.8650 (tp-100) cc_final: 0.7981 (tp-100) REVERT: E 498 CYS cc_start: 0.7984 (t) cc_final: 0.7308 (t) outliers start: 9 outliers final: 3 residues processed: 60 average time/residue: 0.1844 time to fit residues: 15.2430 Evaluate side-chains 46 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 151 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 1 optimal weight: 0.0770 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN E 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6737 Z= 0.185 Angle : 0.477 5.939 9156 Z= 0.247 Chirality : 0.040 0.152 978 Planarity : 0.003 0.032 1177 Dihedral : 4.959 57.863 1013 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.29 % Allowed : 9.57 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.29), residues: 793 helix: 1.63 (0.25), residues: 410 sheet: 1.06 (0.73), residues: 41 loop : 0.24 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 PHE 0.015 0.001 PHE E 369 TYR 0.011 0.001 TYR E 385 ARG 0.003 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 386 LYS cc_start: 0.8888 (pttm) cc_final: 0.8480 (pttp) REVERT: B 405 ASP cc_start: 0.8396 (m-30) cc_final: 0.8114 (m-30) REVERT: B 406 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8461 (mt-10) REVERT: E 249 MET cc_start: 0.8587 (ttp) cc_final: 0.8186 (ttp) REVERT: E 325 GLN cc_start: 0.8639 (tp-100) cc_final: 0.7955 (tp-100) REVERT: E 498 CYS cc_start: 0.8037 (t) cc_final: 0.7251 (t) outliers start: 9 outliers final: 5 residues processed: 55 average time/residue: 0.2022 time to fit residues: 15.3204 Evaluate side-chains 50 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 330 ASN ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6737 Z= 0.175 Angle : 0.468 5.353 9156 Z= 0.243 Chirality : 0.039 0.134 978 Planarity : 0.003 0.034 1177 Dihedral : 4.750 57.790 1013 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.43 % Allowed : 10.14 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.29), residues: 793 helix: 1.70 (0.25), residues: 410 sheet: 0.93 (0.72), residues: 41 loop : 0.36 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 PHE 0.015 0.001 PHE E 523 TYR 0.010 0.001 TYR E 385 ARG 0.004 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: B 386 LYS cc_start: 0.8878 (pttm) cc_final: 0.8537 (pttp) REVERT: B 405 ASP cc_start: 0.8367 (m-30) cc_final: 0.8137 (m-30) REVERT: B 406 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8529 (mt-10) REVERT: E 325 GLN cc_start: 0.8627 (tp-100) cc_final: 0.8172 (tp40) REVERT: E 498 CYS cc_start: 0.8099 (t) cc_final: 0.7412 (t) outliers start: 10 outliers final: 6 residues processed: 54 average time/residue: 0.1926 time to fit residues: 14.4489 Evaluate side-chains 52 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 43 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 ASN ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6737 Z= 0.298 Angle : 0.546 6.763 9156 Z= 0.282 Chirality : 0.041 0.141 978 Planarity : 0.003 0.036 1177 Dihedral : 4.992 58.473 1013 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.14 % Allowed : 11.29 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.30), residues: 793 helix: 1.64 (0.25), residues: 413 sheet: 0.78 (0.74), residues: 41 loop : 0.51 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.005 0.001 HIS E 34 PHE 0.017 0.001 PHE E 523 TYR 0.014 0.001 TYR E 385 ARG 0.004 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: B 386 LYS cc_start: 0.8973 (pttm) cc_final: 0.8649 (pttp) REVERT: B 405 ASP cc_start: 0.8387 (m-30) cc_final: 0.8080 (m-30) REVERT: B 406 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8453 (mt-10) REVERT: E 190 MET cc_start: 0.8864 (tmm) cc_final: 0.8657 (ttt) REVERT: E 325 GLN cc_start: 0.8665 (tp-100) cc_final: 0.8182 (tp40) REVERT: E 360 MET cc_start: 0.8619 (ttm) cc_final: 0.8404 (ttm) REVERT: E 498 CYS cc_start: 0.8287 (t) cc_final: 0.7459 (t) outliers start: 8 outliers final: 8 residues processed: 49 average time/residue: 0.1923 time to fit residues: 13.3309 Evaluate side-chains 49 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.0010 chunk 64 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6737 Z= 0.165 Angle : 0.476 5.839 9156 Z= 0.246 Chirality : 0.039 0.129 978 Planarity : 0.003 0.037 1177 Dihedral : 4.667 58.176 1013 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.14 % Allowed : 12.29 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.30), residues: 793 helix: 1.72 (0.25), residues: 412 sheet: 0.73 (0.75), residues: 41 loop : 0.56 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 PHE 0.014 0.001 PHE E 523 TYR 0.009 0.001 TYR E 516 ARG 0.003 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: B 386 LYS cc_start: 0.8932 (pttm) cc_final: 0.8594 (pttp) REVERT: B 405 ASP cc_start: 0.8366 (m-30) cc_final: 0.8071 (m-30) REVERT: B 406 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8454 (mt-10) REVERT: E 325 GLN cc_start: 0.8631 (tp-100) cc_final: 0.8133 (tp40) REVERT: E 498 CYS cc_start: 0.8046 (t) cc_final: 0.7070 (t) outliers start: 8 outliers final: 8 residues processed: 53 average time/residue: 0.1736 time to fit residues: 13.2995 Evaluate side-chains 53 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 chunk 70 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6737 Z= 0.213 Angle : 0.494 5.835 9156 Z= 0.255 Chirality : 0.040 0.131 978 Planarity : 0.003 0.038 1177 Dihedral : 4.682 58.357 1013 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.29 % Allowed : 13.29 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.30), residues: 793 helix: 1.74 (0.25), residues: 412 sheet: 0.73 (0.74), residues: 41 loop : 0.60 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 PHE 0.016 0.001 PHE E 369 TYR 0.011 0.001 TYR E 385 ARG 0.003 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: B 386 LYS cc_start: 0.8956 (pttm) cc_final: 0.8633 (pttp) REVERT: B 405 ASP cc_start: 0.8378 (m-30) cc_final: 0.8072 (m-30) REVERT: B 406 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8481 (mt-10) REVERT: E 325 GLN cc_start: 0.8641 (tp-100) cc_final: 0.8150 (tp40) REVERT: E 498 CYS cc_start: 0.8148 (t) cc_final: 0.7170 (t) outliers start: 9 outliers final: 8 residues processed: 51 average time/residue: 0.1850 time to fit residues: 13.5344 Evaluate side-chains 52 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 0.0070 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6737 Z= 0.176 Angle : 0.478 5.438 9156 Z= 0.247 Chirality : 0.039 0.128 978 Planarity : 0.003 0.040 1177 Dihedral : 4.583 58.283 1013 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.14 % Allowed : 13.57 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.30), residues: 793 helix: 1.77 (0.25), residues: 411 sheet: 0.68 (0.74), residues: 41 loop : 0.64 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 PHE 0.014 0.001 PHE E 523 TYR 0.010 0.001 TYR E 385 ARG 0.004 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: B 386 LYS cc_start: 0.8955 (pttm) cc_final: 0.8606 (pttp) REVERT: B 405 ASP cc_start: 0.8365 (m-30) cc_final: 0.8122 (m-30) REVERT: B 406 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8516 (mt-10) REVERT: B 518 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7210 (tt) REVERT: E 325 GLN cc_start: 0.8632 (tp-100) cc_final: 0.8123 (tp40) REVERT: E 498 CYS cc_start: 0.8151 (t) cc_final: 0.7160 (t) outliers start: 8 outliers final: 7 residues processed: 51 average time/residue: 0.1846 time to fit residues: 13.5114 Evaluate side-chains 53 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 66 optimal weight: 0.0000 chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6737 Z= 0.173 Angle : 0.477 5.321 9156 Z= 0.247 Chirality : 0.040 0.148 978 Planarity : 0.003 0.040 1177 Dihedral : 4.535 58.404 1013 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.29 % Allowed : 13.57 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.30), residues: 793 helix: 1.80 (0.26), residues: 411 sheet: 0.65 (0.74), residues: 41 loop : 0.70 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 PHE 0.015 0.001 PHE E 523 TYR 0.010 0.001 TYR E 516 ARG 0.004 0.000 ARG B 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: B 386 LYS cc_start: 0.8931 (pttm) cc_final: 0.8581 (pttp) REVERT: B 405 ASP cc_start: 0.8372 (m-30) cc_final: 0.8127 (m-30) REVERT: B 406 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8521 (mt-10) REVERT: B 518 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7161 (tt) REVERT: E 325 GLN cc_start: 0.8626 (tp-100) cc_final: 0.8117 (tp40) REVERT: E 497 TYR cc_start: 0.8577 (m-80) cc_final: 0.8027 (m-80) REVERT: E 498 CYS cc_start: 0.8154 (t) cc_final: 0.7326 (t) outliers start: 9 outliers final: 8 residues processed: 52 average time/residue: 0.1963 time to fit residues: 14.7727 Evaluate side-chains 54 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 7 optimal weight: 0.0970 chunk 11 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 71 optimal weight: 0.0470 chunk 42 optimal weight: 1.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.063707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.049305 restraints weight = 21222.327| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 3.45 r_work: 0.2735 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6737 Z= 0.151 Angle : 0.465 5.258 9156 Z= 0.241 Chirality : 0.039 0.144 978 Planarity : 0.003 0.040 1177 Dihedral : 4.451 58.224 1013 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.29 % Allowed : 13.71 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.30), residues: 793 helix: 1.80 (0.25), residues: 411 sheet: 0.67 (0.74), residues: 41 loop : 0.70 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.003 0.001 HIS E 374 PHE 0.014 0.001 PHE E 369 TYR 0.009 0.001 TYR E 516 ARG 0.003 0.000 ARG B 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1719.81 seconds wall clock time: 33 minutes 4.05 seconds (1984.05 seconds total)