Starting phenix.real_space_refine on Tue Feb 13 14:27:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxy_25510/02_2024/7sxy_25510.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxy_25510/02_2024/7sxy_25510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxy_25510/02_2024/7sxy_25510.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxy_25510/02_2024/7sxy_25510.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxy_25510/02_2024/7sxy_25510.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxy_25510/02_2024/7sxy_25510.pdb" } resolution = 2.79 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= -0.002 sd= 0.036 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 1080 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-5238/modules/chem_data/mon_lib" Total number of atoms: 6557 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1590 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain: "E" Number of atoms: 4869 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Conformer: "B" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} bond proxies already assigned to first conformer: 4990 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: 6.07, per 1000 atoms: 0.93 Number of scatterers: 6557 At special positions: 0 Unit cell: (80, 83, 121, 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 1080 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: 2.62 Conformation dependent library (CDL) restraints added in 2.0 seconds 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1502 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 7 sheets defined 57.8% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 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 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.674A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.832A 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: 3.742A 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: 4.034A 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: 3.942A 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: 3.707A 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: 3.682A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.762A 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: 3.765A 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: 3.545A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.658A 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: 4.219A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.937A 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 Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.344A 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: 3.706A 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: 4.397A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.623A 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: 3.905A 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: 3.860A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.772A 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: 3.657A 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: 6.069A 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: 6.304A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 325 hydrogen bonds defined for protein. 917 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: 1.80 Time building geometry restraints manager: 2.83 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: 2087 1.35 - 1.47: 1785 1.47 - 1.60: 2811 1.60 - 1.72: 0 1.72 - 1.85: 58 Bond restraints: 6741 Sorted by residual: 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 6.50e+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 5.63e+00 bond pdb=" C1 NAG E 703 " pdb=" O5 NAG E 703 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.38e+00 bond pdb=" C1 NAG E 705 " pdb=" O5 NAG E 705 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.07e+00 bond pdb=" C1 NAG E 706 " pdb=" O5 NAG E 706 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.75e+00 ... (remaining 6736 not shown) Histogram of bond angle deviations from ideal: 98.08 - 105.30: 159 105.30 - 112.51: 3296 112.51 - 119.73: 2420 119.73 - 126.95: 3171 126.95 - 134.16: 117 Bond angle restraints: 9163 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 122.82 128.94 -6.12 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 114.40 123.47 -9.07 2.30e+00 1.89e-01 1.55e+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 112.70 122.82 -10.12 3.00e+00 1.11e-01 1.14e+01 angle pdb=" N LYS E 234 " pdb=" CA LYS E 234 " pdb=" C LYS E 234 " ideal model delta sigma weight residual 113.16 117.77 -4.61 1.42e+00 4.96e-01 1.05e+01 ... (remaining 9158 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 3701 17.13 - 34.25: 306 34.25 - 51.37: 42 51.37 - 68.50: 10 68.50 - 85.62: 12 Dihedral angle restraints: 4071 sinusoidal: 1729 harmonic: 2342 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 -43.13 -42.87 1 1.00e+01 1.00e-02 2.56e+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 16.37 62.63 1 2.00e+01 2.50e-03 1.30e+01 dihedral pdb=" CA ALA E 396 " pdb=" C ALA E 396 " pdb=" N ASN E 397 " pdb=" CA ASN E 397 " ideal model delta harmonic sigma weight residual 180.00 163.63 16.37 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 4068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 698 0.051 - 0.102: 202 0.102 - 0.153: 63 0.153 - 0.203: 13 0.203 - 0.254: 3 Chirality restraints: 979 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 2.26 0.25 2.00e-01 2.50e+01 1.62e+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 -2.39 -0.24 2.00e-01 2.50e+01 1.42e+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 1.06e+00 ... (remaining 976 not shown) Planarity restraints: 1186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 169 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C ARG E 169 " -0.059 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 2.73e-02 7.43e+00 pdb=" C TRP E 168 " -0.047 2.00e-02 2.50e+03 pdb=" O TRP E 168 " 0.017 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=" C GLU E 589 " -0.043 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO E 590 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO E 590 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 590 " -0.037 5.00e-02 4.00e+02 ... (remaining 1183 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1911 2.82 - 3.34: 6008 3.34 - 3.86: 11540 3.86 - 4.38: 13065 4.38 - 4.90: 22546 Nonbonded interactions: 55070 Sorted by model distance: nonbonded pdb=" OH TYR E 183 " pdb=" OD1 ASP E 509 " model vdw 2.303 2.440 nonbonded pdb=" OG1 THR B 500 " pdb=" OH TYR E 41 " model vdw 2.317 2.440 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.333 2.440 nonbonded pdb=" OE1 GLU B 406 " pdb=" OH TYR B 495 " model vdw 2.343 2.440 nonbonded pdb=" OH TYR E 237 " pdb=" O VAL E 485 " model vdw 2.353 2.440 ... (remaining 55065 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=0.50 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: 4.790 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: 15.880 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.000 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 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:12.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 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 0.057 6741 Z= 0.343 Angle : 0.840 10.116 9163 Z= 0.455 Chirality : 0.056 0.254 979 Planarity : 0.007 0.065 1179 Dihedral : 13.174 85.622 2551 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % 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: -0.48 (0.26), residues: 794 helix: -0.05 (0.23), residues: 396 sheet: 0.71 (0.65), residues: 52 loop : -0.67 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 473 HIS 0.004 0.001 HIS E 374 PHE 0.029 0.003 PHE E 369 TYR 0.033 0.002 TYR E 385 ARG 0.011 0.001 ARG E 460 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.804 Fit side-chains revert: symmetry clash REVERT: E 156 LEU cc_start: 0.9544 (mm) cc_final: 0.8932 (tm) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 1.4420 time to fit residues: 108.9322 Evaluate side-chains 51 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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: 0.3980 chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 501 ASN ** E 34 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** E 325 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6741 Z= 0.286 Angle : 0.588 7.648 9163 Z= 0.300 Chirality : 0.042 0.142 979 Planarity : 0.005 0.046 1179 Dihedral : 5.284 57.317 1014 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.14 % Allowed : 8.56 % Favored : 90.30 % 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: 0.89 (0.28), residues: 794 helix: 1.18 (0.25), residues: 390 sheet: 0.73 (0.67), residues: 53 loop : 0.00 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.018 0.002 PHE E 400 TYR 0.015 0.001 TYR E 385 ARG 0.002 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.724 Fit side-chains REVERT: B 406 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8239 (mt-10) REVERT: E 91 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8752 (tm) REVERT: E 480 MET cc_start: 0.9100 (mtp) cc_final: 0.8874 (mtm) outliers start: 8 outliers final: 3 residues processed: 53 average time/residue: 1.4014 time to fit residues: 78.3132 Evaluate side-chains 52 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 366 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6741 Z= 0.229 Angle : 0.533 7.305 9163 Z= 0.272 Chirality : 0.041 0.139 979 Planarity : 0.004 0.039 1179 Dihedral : 4.981 56.624 1014 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.86 % Allowed : 9.84 % Favored : 89.30 % 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: 1.22 (0.29), residues: 794 helix: 1.46 (0.26), residues: 390 sheet: 0.53 (0.66), residues: 53 loop : 0.24 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.018 0.001 PHE E 369 TYR 0.015 0.001 TYR E 385 ARG 0.002 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.877 Fit side-chains REVERT: B 406 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8538 (mt-10) REVERT: E 91 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8776 (tm) REVERT: E 332 MET cc_start: 0.8409 (ttp) cc_final: 0.8208 (ttm) REVERT: E 366 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8184 (ttp) outliers start: 6 outliers final: 1 residues processed: 51 average time/residue: 1.6615 time to fit residues: 89.5206 Evaluate side-chains 49 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 366 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 0.2980 chunk 76 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** ** E 34 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6741 Z= 0.193 Angle : 0.518 7.573 9163 Z= 0.261 Chirality : 0.040 0.132 979 Planarity : 0.004 0.039 1179 Dihedral : 4.776 56.937 1014 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.28 % Allowed : 9.70 % Favored : 89.02 % 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: 1.28 (0.29), residues: 794 helix: 1.54 (0.26), residues: 393 sheet: 0.61 (0.68), residues: 53 loop : 0.21 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 165 HIS 0.005 0.001 HIS E 374 PHE 0.016 0.001 PHE E 369 TYR 0.018 0.001 TYR E 50 ARG 0.001 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 47 time to evaluate : 0.762 Fit side-chains REVERT: B 406 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8514 (mt-10) REVERT: E 55 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.8079 (p) REVERT: E 91 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8754 (tm) REVERT: E 332 MET cc_start: 0.8429 (ttp) cc_final: 0.8126 (ttm) REVERT: E 366 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8169 (ttp) outliers start: 9 outliers final: 1 residues processed: 50 average time/residue: 1.3599 time to fit residues: 71.8865 Evaluate side-chains 51 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 474 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 68 optimal weight: 0.2980 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 0.0980 chunk 44 optimal weight: 0.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- 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** ** E 34 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6741 Z= 0.173 Angle : 0.497 7.770 9163 Z= 0.251 Chirality : 0.040 0.130 979 Planarity : 0.004 0.038 1179 Dihedral : 4.639 57.200 1014 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.43 % Allowed : 9.99 % Favored : 88.59 % 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: 1.40 (0.29), residues: 794 helix: 1.69 (0.26), residues: 392 sheet: 0.65 (0.70), residues: 53 loop : 0.20 (0.32), residues: 349 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 0.015 0.001 PHE E 369 TYR 0.013 0.001 TYR E 385 ARG 0.001 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.765 Fit side-chains REVERT: E 55 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.8075 (p) REVERT: E 91 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8759 (tm) REVERT: E 366 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8207 (ttp) outliers start: 10 outliers final: 1 residues processed: 54 average time/residue: 1.3292 time to fit residues: 76.0316 Evaluate side-chains 49 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 474 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 0.0010 chunk 73 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- 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** ** E 34 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** E 508 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6741 Z= 0.193 Angle : 0.511 8.824 9163 Z= 0.257 Chirality : 0.040 0.128 979 Planarity : 0.004 0.038 1179 Dihedral : 4.610 57.123 1014 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.14 % Allowed : 10.56 % Favored : 88.30 % 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: 1.49 (0.29), residues: 794 helix: 1.64 (0.26), residues: 396 sheet: 0.62 (0.71), residues: 53 loop : 0.42 (0.33), residues: 345 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 0.013 0.001 TYR E 385 ARG 0.001 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.725 Fit side-chains REVERT: E 55 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.8072 (p) REVERT: E 91 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8765 (tm) REVERT: E 156 LEU cc_start: 0.9504 (mm) cc_final: 0.9083 (tm) REVERT: E 366 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8193 (ttp) outliers start: 8 outliers final: 2 residues processed: 52 average time/residue: 1.3357 time to fit residues: 73.4484 Evaluate side-chains 50 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 474 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 3.9990 chunk 64 optimal weight: 0.4980 chunk 42 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 46 optimal weight: 0.1980 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 501 ASN ** E 34 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6741 Z= 0.180 Angle : 0.502 8.318 9163 Z= 0.252 Chirality : 0.040 0.128 979 Planarity : 0.003 0.038 1179 Dihedral : 4.549 57.439 1014 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.14 % Allowed : 10.70 % Favored : 88.16 % 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: 1.43 (0.29), residues: 794 helix: 1.54 (0.25), residues: 404 sheet: 0.55 (0.71), residues: 53 loop : 0.43 (0.34), residues: 337 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 0.015 0.001 PHE E 369 TYR 0.012 0.001 TYR E 385 ARG 0.001 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.942 Fit side-chains REVERT: E 55 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.8097 (p) REVERT: E 91 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8767 (tm) REVERT: E 156 LEU cc_start: 0.9505 (mm) cc_final: 0.9095 (tm) REVERT: E 366 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8197 (ttp) REVERT: E 480 MET cc_start: 0.9066 (mtp) cc_final: 0.8860 (mtp) outliers start: 8 outliers final: 3 residues processed: 52 average time/residue: 1.5782 time to fit residues: 86.6226 Evaluate side-chains 52 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 474 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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 501 ASN ** E 34 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6741 Z= 0.285 Angle : 0.552 8.069 9163 Z= 0.278 Chirality : 0.041 0.128 979 Planarity : 0.004 0.039 1179 Dihedral : 4.698 56.930 1014 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.14 % Allowed : 10.84 % Favored : 88.02 % 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: 1.59 (0.30), residues: 794 helix: 1.62 (0.26), residues: 395 sheet: 0.55 (0.72), residues: 53 loop : 0.64 (0.35), residues: 346 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 0.016 0.001 TYR E 385 ARG 0.002 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.841 Fit side-chains REVERT: B 406 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8476 (mt-10) REVERT: E 55 THR cc_start: 0.8503 (OUTLIER) cc_final: 0.8155 (p) REVERT: E 91 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8812 (tm) REVERT: E 156 LEU cc_start: 0.9510 (mm) cc_final: 0.9108 (tm) REVERT: E 366 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8253 (ttp) outliers start: 8 outliers final: 3 residues processed: 50 average time/residue: 1.3933 time to fit residues: 73.8019 Evaluate side-chains 52 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 366 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 52 optimal weight: 0.0370 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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** ** E 34 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6741 Z= 0.187 Angle : 0.514 7.943 9163 Z= 0.256 Chirality : 0.040 0.125 979 Planarity : 0.004 0.041 1179 Dihedral : 4.572 57.455 1014 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.86 % Allowed : 11.27 % Favored : 87.87 % 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: 1.58 (0.30), residues: 794 helix: 1.65 (0.26), residues: 396 sheet: 0.49 (0.71), residues: 53 loop : 0.59 (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 0.015 0.001 PHE E 369 TYR 0.012 0.001 TYR E 385 ARG 0.001 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 1.092 Fit side-chains REVERT: B 406 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8497 (mt-10) REVERT: E 55 THR cc_start: 0.8479 (OUTLIER) cc_final: 0.8149 (p) REVERT: E 91 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8778 (tm) REVERT: E 156 LEU cc_start: 0.9494 (mm) cc_final: 0.9091 (tm) REVERT: E 366 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8247 (ttp) REVERT: E 480 MET cc_start: 0.9081 (mtp) cc_final: 0.8848 (mtp) outliers start: 6 outliers final: 2 residues processed: 49 average time/residue: 1.5089 time to fit residues: 78.6548 Evaluate side-chains 51 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 366 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 62 optimal weight: 0.0020 chunk 6 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 57 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 overall best weight: 0.6388 ------------------------------------------------------------------------------- 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 501 ASN ** E 34 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8556 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6741 Z= 0.188 Angle : 0.523 9.519 9163 Z= 0.260 Chirality : 0.040 0.127 979 Planarity : 0.004 0.041 1179 Dihedral : 4.546 57.372 1014 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.00 % Allowed : 11.27 % Favored : 87.73 % 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: 1.64 (0.30), residues: 794 helix: 1.70 (0.26), residues: 395 sheet: 0.49 (0.72), residues: 53 loop : 0.63 (0.35), residues: 346 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 0.015 0.001 PHE E 369 TYR 0.013 0.001 TYR E 385 ARG 0.001 0.000 ARG B 466 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.838 Fit side-chains REVERT: B 406 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8469 (mt-10) REVERT: E 55 THR cc_start: 0.8466 (OUTLIER) cc_final: 0.8179 (p) REVERT: E 91 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8778 (tm) REVERT: E 156 LEU cc_start: 0.9488 (mm) cc_final: 0.9095 (tm) REVERT: E 366 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8217 (ttp) outliers start: 7 outliers final: 3 residues processed: 49 average time/residue: 1.4868 time to fit residues: 76.7918 Evaluate side-chains 52 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 366 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: 0.0970 chunk 26 optimal weight: 0.0870 chunk 64 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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** ** E 34 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 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 = 0.3293 r_free = 0.3293 target = 0.070751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.053548 restraints weight = 17393.844| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.09 r_work: 0.2747 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6741 Z= 0.165 Angle : 0.506 9.382 9163 Z= 0.251 Chirality : 0.039 0.126 979 Planarity : 0.004 0.041 1179 Dihedral : 4.481 57.542 1014 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.86 % Allowed : 11.27 % Favored : 87.87 % 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: 1.67 (0.30), residues: 794 helix: 1.73 (0.26), residues: 395 sheet: 0.97 (0.79), residues: 43 loop : 0.55 (0.34), residues: 356 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 0.015 0.001 PHE E 369 TYR 0.012 0.001 TYR E 385 ARG 0.001 0.000 ARG B 466 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2504.39 seconds wall clock time: 45 minutes 59.43 seconds (2759.43 seconds total)