Starting phenix.real_space_refine on Fri Dec 27 20:54:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dlq_27510/12_2024/8dlq_27510.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dlq_27510/12_2024/8dlq_27510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dlq_27510/12_2024/8dlq_27510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dlq_27510/12_2024/8dlq_27510.map" model { file = "/net/cci-nas-00/data/ceres_data/8dlq_27510/12_2024/8dlq_27510.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dlq_27510/12_2024/8dlq_27510.cif" } resolution = 2.77 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= 0.035 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 4190 2.51 5 N 1077 2.21 5 O 1248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6552 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1592 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: {'PTRANS': 27, '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: 5.63, per 1000 atoms: 0.86 Number of scatterers: 6552 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 1248 8.00 N 1077 7.00 C 4190 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 - 3.00 Amino acid : True - 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: 1.76 Conformation dependent library (CDL) restraints added in 1.1 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: 40 helices and 7 sheets defined 57.8% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 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 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.013A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.568A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.645A 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: 3.692A 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: 4.030A 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 147 through 155 Processing helix chain 'E' and resid 157 through 194 Proline residue: E 178 - end of helix removed outlier: 3.693A 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: 3.742A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.707A 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: 3.793A 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 Processing helix chain 'E' and resid 365 through 385 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: 4.296A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.890A 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: 3.509A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.315A 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: 3.654A 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: 4.420A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.630A 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: 3.851A 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: 3.864A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.739A 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: 3.578A 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: 6.123A 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: 6.521A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 326 hydrogen bonds defined for protein. 924 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: 1.78 Time building geometry restraints manager: 2.03 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: 2079 1.35 - 1.47: 1810 1.47 - 1.60: 2788 1.60 - 1.72: 0 1.72 - 1.85: 58 Bond restraints: 6735 Sorted by residual: bond pdb=" C1 NAG E 701 " pdb=" O5 NAG E 701 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C1 NAG E 703 " pdb=" O5 NAG E 703 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.95e+00 bond pdb=" C1 NAG E 702 " pdb=" O5 NAG E 702 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.52e+00 bond pdb=" C1 NAG E 704 " pdb=" O5 NAG E 704 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.58e+00 bond pdb=" C GLU E 145 " pdb=" N PRO E 146 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.31e+00 ... (remaining 6730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 8629 1.80 - 3.61: 455 3.61 - 5.41: 49 5.41 - 7.21: 15 7.21 - 9.01: 6 Bond angle restraints: 9154 Sorted by residual: angle pdb=" CA TYR B 495 " pdb=" CB TYR B 495 " pdb=" CG TYR B 495 " ideal model delta sigma weight residual 113.90 122.91 -9.01 1.80e+00 3.09e-01 2.51e+01 angle pdb=" CA TYR E 385 " pdb=" CB TYR E 385 " pdb=" CG TYR E 385 " ideal model delta sigma weight residual 113.90 122.12 -8.22 1.80e+00 3.09e-01 2.08e+01 angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.36 128.19 -5.83 1.42e+00 4.96e-01 1.69e+01 angle pdb=" CA ASN E 437 " pdb=" CB ASN E 437 " pdb=" CG ASN E 437 " ideal model delta sigma weight residual 112.60 116.03 -3.43 1.00e+00 1.00e+00 1.18e+01 angle pdb=" CA ASN B 360 " pdb=" CB ASN B 360 " pdb=" CG ASN B 360 " ideal model delta sigma weight residual 112.60 115.96 -3.36 1.00e+00 1.00e+00 1.13e+01 ... (remaining 9149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 3690 16.95 - 33.90: 309 33.90 - 50.85: 38 50.85 - 67.80: 17 67.80 - 84.75: 10 Dihedral angle restraints: 4064 sinusoidal: 1725 harmonic: 2339 Sorted by residual: 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 15.31 63.69 1 2.00e+01 2.50e-03 1.34e+01 dihedral pdb=" SG CYS E 133 " pdb=" CB CYS E 141 " pdb=" SG CYS E 141 " pdb=" CA CYS E 141 " ideal model delta sinusoidal sigma weight residual 79.00 16.53 62.47 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 -130.95 8.35 0 2.50e+00 1.60e-01 1.12e+01 ... (remaining 4061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 687 0.053 - 0.106: 213 0.106 - 0.159: 63 0.159 - 0.212: 14 0.212 - 0.265: 2 Chirality restraints: 979 Sorted by residual: 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 -2.36 -0.26 2.00e-01 2.50e+01 1.75e+00 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 2.25 0.26 2.00e-01 2.50e+01 1.69e+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 976 not shown) Planarity restraints: 1183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 169 " 0.014 2.00e-02 2.50e+03 2.91e-02 8.48e+00 pdb=" C ARG E 169 " -0.050 2.00e-02 2.50e+03 pdb=" O ARG E 169 " 0.019 2.00e-02 2.50e+03 pdb=" N SER E 170 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 495 " -0.030 2.00e-02 2.50e+03 1.96e-02 7.68e+00 pdb=" CG TYR B 495 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR B 495 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 495 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 495 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 495 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 495 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 495 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 589 " -0.046 5.00e-02 4.00e+02 6.90e-02 7.62e+00 pdb=" N PRO E 590 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO E 590 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 590 " -0.039 5.00e-02 4.00e+02 ... (remaining 1180 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1891 2.82 - 3.34: 6027 3.34 - 3.86: 11482 3.86 - 4.38: 13057 4.38 - 4.90: 22523 Nonbonded interactions: 54980 Sorted by model distance: nonbonded pdb=" OH TYR E 183 " pdb=" OD1 ASP E 509 " model vdw 2.296 3.040 nonbonded pdb=" O MET E 152 " pdb=" NH1 ARG E 161 " model vdw 2.353 3.120 nonbonded pdb=" O ASN E 117 " pdb=" ND2 ASN E 121 " model vdw 2.354 3.120 nonbonded pdb=" OH TYR E 237 " pdb=" O VAL E 485 " model vdw 2.370 3.040 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.384 3.040 ... (remaining 54975 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 4.050 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.130 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:15.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 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 : 0.006 0.083 6735 Z= 0.375 Angle : 0.909 9.012 9154 Z= 0.520 Chirality : 0.059 0.265 979 Planarity : 0.007 0.069 1176 Dihedral : 13.162 84.755 2546 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.43 % Allowed : 4.29 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.27), residues: 793 helix: 0.75 (0.24), residues: 391 sheet: 1.02 (0.65), residues: 42 loop : -0.35 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 566 HIS 0.004 0.001 HIS E 374 PHE 0.029 0.003 PHE E 369 TYR 0.046 0.002 TYR B 495 ARG 0.010 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 93 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.788 Fit side-chains REVERT: B 386 LYS cc_start: 0.8764 (pttm) cc_final: 0.8134 (pttm) REVERT: B 390 LEU cc_start: 0.8852 (mt) cc_final: 0.8415 (mt) REVERT: E 117 ASN cc_start: 0.8976 (t0) cc_final: 0.8351 (p0) REVERT: E 121 ASN cc_start: 0.8679 (m-40) cc_final: 0.8439 (m110) outliers start: 3 outliers final: 0 residues processed: 93 average time/residue: 1.5646 time to fit residues: 152.0371 Evaluate side-chains 56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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: 2.9990 chunk 59 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN E 42 GLN E 374 HIS E 552 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6735 Z= 0.234 Angle : 0.568 9.102 9154 Z= 0.294 Chirality : 0.042 0.147 979 Planarity : 0.005 0.042 1176 Dihedral : 5.017 49.335 1013 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.57 % Allowed : 10.29 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.28), residues: 793 helix: 1.47 (0.25), residues: 398 sheet: 1.00 (0.73), residues: 42 loop : -0.08 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 165 HIS 0.003 0.001 HIS E 374 PHE 0.018 0.001 PHE E 369 TYR 0.024 0.001 TYR B 495 ARG 0.005 0.000 ARG B 346 *********************** 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 70 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: B 528 LYS cc_start: 0.3619 (OUTLIER) cc_final: 0.3120 (pttp) REVERT: E 117 ASN cc_start: 0.9048 (t0) cc_final: 0.8379 (p0) REVERT: E 121 ASN cc_start: 0.8814 (m-40) cc_final: 0.8528 (m110) outliers start: 11 outliers final: 3 residues processed: 67 average time/residue: 1.4486 time to fit residues: 102.0565 Evaluate side-chains 57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain E residue 613 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6735 Z= 0.325 Angle : 0.595 10.155 9154 Z= 0.307 Chirality : 0.042 0.140 979 Planarity : 0.004 0.041 1176 Dihedral : 5.054 51.524 1013 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.26 % Favored : 98.61 % Rotamer: Outliers : 2.00 % Allowed : 11.86 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.29), residues: 793 helix: 1.73 (0.26), residues: 386 sheet: 0.84 (0.77), residues: 43 loop : 0.17 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 610 HIS 0.004 0.001 HIS E 374 PHE 0.020 0.002 PHE E 369 TYR 0.024 0.001 TYR B 495 ARG 0.004 0.000 ARG B 346 *********************** 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 69 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: B 528 LYS cc_start: 0.3794 (OUTLIER) cc_final: 0.3294 (pttp) REVERT: E 291 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8117 (pp) outliers start: 14 outliers final: 5 residues processed: 63 average time/residue: 1.5095 time to fit residues: 99.9185 Evaluate side-chains 57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain E residue 613 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 0.0970 chunk 7 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 43 optimal weight: 0.0040 chunk 1 optimal weight: 0.5980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6735 Z= 0.167 Angle : 0.510 7.810 9154 Z= 0.258 Chirality : 0.040 0.126 979 Planarity : 0.004 0.042 1176 Dihedral : 4.811 53.504 1013 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.86 % Allowed : 12.57 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.29), residues: 793 helix: 1.75 (0.26), residues: 400 sheet: 0.79 (0.77), residues: 43 loop : 0.22 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.016 0.001 PHE E 369 TYR 0.018 0.001 TYR E 613 ARG 0.004 0.000 ARG B 346 *********************** 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 67 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: B 518 LEU cc_start: 0.8772 (mt) cc_final: 0.8364 (tt) REVERT: B 528 LYS cc_start: 0.3554 (OUTLIER) cc_final: 0.3231 (pttp) REVERT: E 480 MET cc_start: 0.8968 (mtm) cc_final: 0.8758 (mtm) outliers start: 13 outliers final: 4 residues processed: 62 average time/residue: 1.6276 time to fit residues: 105.9833 Evaluate side-chains 56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 6735 Z= 0.422 Angle : 0.605 8.577 9154 Z= 0.310 Chirality : 0.044 0.133 979 Planarity : 0.004 0.039 1176 Dihedral : 5.083 53.672 1013 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.86 % Allowed : 12.86 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.29), residues: 793 helix: 1.64 (0.26), residues: 399 sheet: 0.85 (0.79), residues: 42 loop : 0.27 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.020 0.002 PHE E 369 TYR 0.023 0.002 TYR B 495 ARG 0.006 0.001 ARG B 346 *********************** 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 71 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 51 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: B 444 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8455 (ttpp) REVERT: B 528 LYS cc_start: 0.3757 (OUTLIER) cc_final: 0.3399 (pttp) outliers start: 20 outliers final: 5 residues processed: 64 average time/residue: 1.4076 time to fit residues: 94.8688 Evaluate side-chains 55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 43 optimal weight: 0.0040 chunk 55 optimal weight: 0.7980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6735 Z= 0.190 Angle : 0.526 7.015 9154 Z= 0.266 Chirality : 0.040 0.129 979 Planarity : 0.003 0.041 1176 Dihedral : 4.808 55.401 1013 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.29 % Allowed : 15.29 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.30), residues: 793 helix: 1.67 (0.26), residues: 407 sheet: 0.70 (0.78), residues: 43 loop : 0.29 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.016 0.001 PHE E 369 TYR 0.017 0.001 TYR B 495 ARG 0.006 0.000 ARG B 346 *********************** 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 62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8650 (pt0) cc_final: 0.8368 (pm20) REVERT: B 528 LYS cc_start: 0.3700 (OUTLIER) cc_final: 0.3471 (pttp) outliers start: 9 outliers final: 3 residues processed: 60 average time/residue: 1.4766 time to fit residues: 92.9434 Evaluate side-chains 53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 45 optimal weight: 0.0670 chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6735 Z= 0.193 Angle : 0.525 7.393 9154 Z= 0.264 Chirality : 0.040 0.126 979 Planarity : 0.003 0.041 1176 Dihedral : 4.683 55.702 1013 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.57 % Allowed : 15.00 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.30), residues: 793 helix: 1.76 (0.26), residues: 406 sheet: 0.90 (0.79), residues: 42 loop : 0.34 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.015 0.001 PHE E 369 TYR 0.017 0.001 TYR B 495 ARG 0.006 0.000 ARG B 346 *********************** 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 60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8662 (pt0) cc_final: 0.8390 (pm20) REVERT: B 518 LEU cc_start: 0.8912 (mt) cc_final: 0.8504 (tt) REVERT: B 528 LYS cc_start: 0.3781 (OUTLIER) cc_final: 0.3555 (pttp) outliers start: 11 outliers final: 3 residues processed: 56 average time/residue: 1.4662 time to fit residues: 86.3019 Evaluate side-chains 53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6735 Z= 0.267 Angle : 0.544 7.142 9154 Z= 0.276 Chirality : 0.041 0.129 979 Planarity : 0.004 0.040 1176 Dihedral : 4.781 56.020 1013 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.29 % Allowed : 15.29 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.30), residues: 793 helix: 1.72 (0.26), residues: 407 sheet: 0.90 (0.79), residues: 42 loop : 0.34 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.017 0.001 PHE E 369 TYR 0.020 0.001 TYR B 495 ARG 0.006 0.000 ARG B 346 *********************** 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 59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: B 518 LEU cc_start: 0.8873 (mt) cc_final: 0.8461 (tt) REVERT: B 528 LYS cc_start: 0.3840 (OUTLIER) cc_final: 0.3542 (pttp) outliers start: 9 outliers final: 3 residues processed: 56 average time/residue: 1.4089 time to fit residues: 83.0763 Evaluate side-chains 53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6735 Z= 0.222 Angle : 0.543 7.115 9154 Z= 0.272 Chirality : 0.040 0.127 979 Planarity : 0.003 0.040 1176 Dihedral : 4.726 56.337 1013 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.71 % Allowed : 16.00 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.30), residues: 793 helix: 1.74 (0.26), residues: 407 sheet: 0.89 (0.79), residues: 42 loop : 0.32 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.016 0.001 PHE E 369 TYR 0.017 0.001 TYR B 495 ARG 0.005 0.000 ARG B 346 *********************** 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 57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: B 518 LEU cc_start: 0.8902 (mt) cc_final: 0.8471 (tt) REVERT: B 528 LYS cc_start: 0.4006 (OUTLIER) cc_final: 0.3661 (pttp) outliers start: 5 outliers final: 3 residues processed: 55 average time/residue: 1.5119 time to fit residues: 87.2053 Evaluate side-chains 54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6735 Z= 0.242 Angle : 0.553 8.736 9154 Z= 0.279 Chirality : 0.041 0.128 979 Planarity : 0.003 0.040 1176 Dihedral : 4.739 56.454 1013 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.71 % Allowed : 16.43 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.30), residues: 793 helix: 1.77 (0.26), residues: 406 sheet: 0.91 (0.79), residues: 42 loop : 0.32 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.016 0.001 PHE E 369 TYR 0.022 0.001 TYR E 613 ARG 0.005 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 56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8502 (pm20) cc_final: 0.8115 (pm20) REVERT: B 528 LYS cc_start: 0.3912 (OUTLIER) cc_final: 0.3578 (pttp) outliers start: 5 outliers final: 3 residues processed: 55 average time/residue: 1.5568 time to fit residues: 89.9715 Evaluate side-chains 54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 26 optimal weight: 0.0030 chunk 64 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 493 GLN ** 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 = 0.3185 r_free = 0.3185 target = 0.066112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.049380 restraints weight = 17552.148| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 3.03 r_work: 0.2652 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6735 Z= 0.191 Angle : 0.532 8.861 9154 Z= 0.268 Chirality : 0.040 0.126 979 Planarity : 0.003 0.040 1176 Dihedral : 4.616 56.560 1013 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.71 % Allowed : 16.86 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.30), residues: 793 helix: 1.81 (0.26), residues: 406 sheet: 0.92 (0.79), residues: 42 loop : 0.33 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.016 0.001 PHE E 369 TYR 0.016 0.001 TYR B 495 ARG 0.005 0.000 ARG B 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2432.91 seconds wall clock time: 44 minutes 47.24 seconds (2687.24 seconds total)