Starting phenix.real_space_refine on Tue Feb 13 14:09:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjn_23879/02_2024/7mjn_23879.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjn_23879/02_2024/7mjn_23879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjn_23879/02_2024/7mjn_23879.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjn_23879/02_2024/7mjn_23879.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjn_23879/02_2024/7mjn_23879.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjn_23879/02_2024/7mjn_23879.pdb" } resolution = 3.29 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= 0.000 sd= 0.019 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 4175 2.51 5 N 1075 2.21 5 O 1239 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 431": "OD1" <-> "OD2" Residue "E TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 6526 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1594 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.08, per 1000 atoms: 0.63 Number of scatterers: 6526 At special positions: 0 Unit cell: (100, 72, 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 1239 8.00 N 1075 7.00 C 4175 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=2.03 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=2.03 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 322 " " NAG E 704 " - " ASN E 546 " Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.5 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: 38 helices and 5 sheets defined 56.3% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.587A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.924A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.622A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.519A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 52 removed outlier: 3.807A pdb=" N GLN E 24 " --> pdb=" O THR E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 removed outlier: 3.721A pdb=" N GLN E 81 " --> pdb=" O SER E 77 " (cutoff:3.500A) 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: 3.871A pdb=" N GLU E 87 " --> pdb=" O PRO E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 102 removed outlier: 4.017A pdb=" N ALA E 99 " --> pdb=" O LEU E 95 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU E 100 " --> pdb=" O GLN E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.639A 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 158 through 194 Proline residue: E 178 - end of helix Processing helix chain 'E' and resid 198 through 204 Processing helix chain 'E' and resid 205 through 207 No H-bonds generated for 'chain 'E' and resid 205 through 207' Processing helix chain 'E' and resid 221 through 249 removed outlier: 3.953A pdb=" N GLU E 227 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 3.721A pdb=" N MET E 249 " --> pdb=" O ARG E 245 " (cutoff:3.500A) 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 Processing helix chain 'E' and resid 294 through 300 Processing helix chain 'E' and resid 303 through 319 removed outlier: 3.636A pdb=" N VAL E 318 " --> pdb=" O PHE E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.538A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.707A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 413 removed outlier: 4.328A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU E 406 " --> pdb=" O GLU E 402 " (cutoff:3.500A) removed outlier: 3.718A 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: 4.122A pdb=" N PHE E 438 " --> pdb=" O THR E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 466 removed outlier: 4.564A 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 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 513 through 533 removed outlier: 4.282A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.631A pdb=" N LYS E 553 " --> pdb=" O GLU E 549 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 564 removed outlier: 4.247A pdb=" N GLU E 564 " --> pdb=" O GLY E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 575 removed outlier: 3.726A pdb=" N VAL E 573 " --> pdb=" O ALA E 569 " (cutoff:3.500A) 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: 3.757A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.932A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.070A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 309 hydrogen bonds defined for protein. 891 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: 1.63 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2080 1.35 - 1.47: 1755 1.47 - 1.59: 2816 1.59 - 1.71: 0 1.71 - 1.83: 58 Bond restraints: 6709 Sorted by residual: bond pdb=" C GLU E 145 " pdb=" N PRO E 146 " ideal model delta sigma weight residual 1.337 1.369 -0.033 1.06e-02 8.90e+03 9.53e+00 bond pdb=" C1 NAG E 701 " pdb=" O5 NAG E 701 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.09e+00 bond pdb=" C1 NAG E 702 " pdb=" O5 NAG E 702 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.73e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.69e+00 bond pdb=" C1 NAG E 703 " pdb=" O5 NAG E 703 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.29e+00 ... (remaining 6704 not shown) Histogram of bond angle deviations from ideal: 99.27 - 106.23: 208 106.23 - 113.19: 3447 113.19 - 120.16: 2488 120.16 - 127.12: 2870 127.12 - 134.08: 105 Bond angle restraints: 9118 Sorted by residual: angle pdb=" N GLY E 147 " pdb=" CA GLY E 147 " pdb=" C GLY E 147 " ideal model delta sigma weight residual 110.21 114.42 -4.21 9.10e-01 1.21e+00 2.14e+01 angle pdb=" C ASP E 292 " pdb=" N VAL E 293 " pdb=" CA VAL E 293 " ideal model delta sigma weight residual 121.97 130.09 -8.12 1.80e+00 3.09e-01 2.04e+01 angle pdb=" O GLY E 147 " pdb=" C GLY E 147 " pdb=" N LEU E 148 " ideal model delta sigma weight residual 121.85 124.37 -2.52 5.60e-01 3.19e+00 2.02e+01 angle pdb=" CG ARG B 346 " pdb=" CD ARG B 346 " pdb=" NE ARG B 346 " ideal model delta sigma weight residual 112.00 120.75 -8.75 2.20e+00 2.07e-01 1.58e+01 angle pdb=" N LYS E 234 " pdb=" CA LYS E 234 " pdb=" C LYS E 234 " ideal model delta sigma weight residual 113.16 117.91 -4.75 1.42e+00 4.96e-01 1.12e+01 ... (remaining 9113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 3652 17.64 - 35.27: 302 35.27 - 52.91: 57 52.91 - 70.54: 8 70.54 - 88.18: 5 Dihedral angle restraints: 4024 sinusoidal: 1685 harmonic: 2339 Sorted by residual: 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 180.00 159.52 20.48 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA TRP E 606 " pdb=" C TRP E 606 " pdb=" N SER E 607 " pdb=" CA SER E 607 " ideal model delta harmonic sigma weight residual 180.00 159.99 20.01 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ILE E 233 " pdb=" C ILE E 233 " pdb=" N LYS E 234 " pdb=" CA LYS E 234 " ideal model delta harmonic sigma weight residual -180.00 -161.38 -18.62 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 4021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 710 0.049 - 0.097: 176 0.097 - 0.146: 67 0.146 - 0.195: 10 0.195 - 0.243: 5 Chirality restraints: 968 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 -2.39 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB VAL E 447 " pdb=" CA VAL E 447 " pdb=" CG1 VAL E 447 " pdb=" CG2 VAL E 447 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CG LEU E 520 " pdb=" CB LEU E 520 " pdb=" CD1 LEU E 520 " pdb=" CD2 LEU E 520 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 965 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 462 " 0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO B 463 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 463 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 463 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 467 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.49e+00 pdb=" CG ASP B 467 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASP B 467 " -0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP B 467 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN E 134 " -0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO E 135 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO E 135 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 135 " -0.026 5.00e-02 4.00e+02 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1922 2.82 - 3.34: 6061 3.34 - 3.86: 10993 3.86 - 4.38: 12649 4.38 - 4.90: 21926 Nonbonded interactions: 53551 Sorted by model distance: nonbonded pdb=" OH TYR E 183 " pdb=" OD1 ASP E 509 " model vdw 2.295 2.440 nonbonded pdb=" OD1 ASP E 494 " pdb=" OG1 THR E 496 " model vdw 2.305 2.440 nonbonded pdb=" OH TYR E 215 " pdb=" OE1 GLU E 571 " model vdw 2.352 2.440 nonbonded pdb=" OG SER B 383 " pdb=" OG1 THR B 385 " model vdw 2.354 2.440 nonbonded pdb=" O PHE E 314 " pdb=" OG SER E 317 " model vdw 2.378 2.440 ... (remaining 53546 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.400 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: 13.470 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.200 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 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 0.053 6709 Z= 0.285 Angle : 0.844 9.434 9118 Z= 0.462 Chirality : 0.053 0.243 968 Planarity : 0.007 0.054 1175 Dihedral : 13.379 88.178 2506 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: -1.29 (0.27), residues: 793 helix: -0.80 (0.23), residues: 374 sheet: 0.98 (0.78), residues: 51 loop : -1.07 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 165 HIS 0.006 0.002 HIS E 378 PHE 0.016 0.002 PHE E 369 TYR 0.015 0.002 TYR E 237 ARG 0.013 0.001 ARG E 115 *********************** 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 57 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.850 Fit side-chains REVERT: B 506 GLN cc_start: 0.8870 (mt0) cc_final: 0.8656 (mt0) REVERT: E 123 MET cc_start: 0.9504 (mmt) cc_final: 0.9287 (mmt) REVERT: E 190 MET cc_start: 0.9238 (tmm) cc_final: 0.9036 (tmm) REVERT: E 249 MET cc_start: 0.9160 (mmm) cc_final: 0.8745 (mmt) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1897 time to fit residues: 15.1241 Evaluate side-chains 41 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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: 0.8550 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6709 Z= 0.346 Angle : 0.603 7.285 9118 Z= 0.312 Chirality : 0.042 0.162 968 Planarity : 0.004 0.038 1175 Dihedral : 5.544 57.560 971 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.71 % Allowed : 5.00 % Favored : 94.29 % 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: 0.12 (0.29), residues: 793 helix: 0.73 (0.25), residues: 389 sheet: 0.01 (0.74), residues: 60 loop : -0.57 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 165 HIS 0.005 0.001 HIS E 34 PHE 0.013 0.001 PHE E 369 TYR 0.018 0.002 TYR B 453 ARG 0.004 0.001 ARG E 115 *********************** 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 51 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: E 123 MET cc_start: 0.9411 (mmt) cc_final: 0.9181 (mmt) REVERT: E 190 MET cc_start: 0.9154 (tmm) cc_final: 0.8953 (tmm) REVERT: E 249 MET cc_start: 0.9060 (mmm) cc_final: 0.8617 (mmt) outliers start: 5 outliers final: 2 residues processed: 49 average time/residue: 0.1802 time to fit residues: 12.6799 Evaluate side-chains 41 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain E residue 143 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 0.0060 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 19 optimal weight: 0.0370 chunk 71 optimal weight: 0.0570 chunk 77 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.2592 ------------------------------------------------------------------------------- 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: 0.8496 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 6709 Z= 0.132 Angle : 0.505 9.665 9118 Z= 0.250 Chirality : 0.039 0.150 968 Planarity : 0.003 0.031 1175 Dihedral : 4.940 57.026 971 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.57 % Allowed : 7.57 % Favored : 91.86 % 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: 0.67 (0.30), residues: 793 helix: 1.29 (0.26), residues: 386 sheet: 0.25 (0.79), residues: 50 loop : -0.41 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 165 HIS 0.003 0.001 HIS E 378 PHE 0.011 0.001 PHE E 369 TYR 0.011 0.001 TYR B 369 ARG 0.002 0.000 ARG E 115 *********************** 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 49 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.733 Fit side-chains REVERT: B 506 GLN cc_start: 0.8916 (mt0) cc_final: 0.8658 (mt0) REVERT: E 190 MET cc_start: 0.9174 (tmm) cc_final: 0.8967 (tmm) REVERT: E 249 MET cc_start: 0.9065 (mmm) cc_final: 0.8626 (mmt) REVERT: E 323 MET cc_start: 0.9256 (mmp) cc_final: 0.8837 (mmp) REVERT: E 462 MET cc_start: 0.9088 (mmm) cc_final: 0.8884 (mtm) outliers start: 4 outliers final: 0 residues processed: 46 average time/residue: 0.1761 time to fit residues: 11.6939 Evaluate side-chains 38 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 4.9990 chunk 7 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 chunk 72 optimal weight: 0.0770 chunk 76 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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: 0.8502 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6709 Z= 0.136 Angle : 0.478 8.668 9118 Z= 0.239 Chirality : 0.039 0.147 968 Planarity : 0.003 0.032 1175 Dihedral : 4.505 55.937 971 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.71 % Allowed : 8.86 % Favored : 90.43 % 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: 1.00 (0.30), residues: 793 helix: 1.62 (0.27), residues: 386 sheet: 0.08 (0.78), residues: 48 loop : -0.25 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 165 HIS 0.002 0.001 HIS E 378 PHE 0.010 0.001 PHE E 369 TYR 0.014 0.001 TYR B 369 ARG 0.002 0.000 ARG E 115 *********************** 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 47 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.751 Fit side-chains REVERT: B 506 GLN cc_start: 0.8911 (mt0) cc_final: 0.8608 (mt0) REVERT: E 190 MET cc_start: 0.9188 (tmm) cc_final: 0.8964 (tmm) REVERT: E 249 MET cc_start: 0.9029 (mmm) cc_final: 0.8605 (mmt) REVERT: E 323 MET cc_start: 0.9221 (mmp) cc_final: 0.8809 (mmp) REVERT: E 474 MET cc_start: 0.8432 (mmp) cc_final: 0.7798 (mmm) outliers start: 5 outliers final: 0 residues processed: 45 average time/residue: 0.1716 time to fit residues: 11.2918 Evaluate side-chains 39 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 6709 Z= 0.328 Angle : 0.572 8.866 9118 Z= 0.289 Chirality : 0.042 0.133 968 Planarity : 0.003 0.038 1175 Dihedral : 4.654 56.112 971 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.57 % Allowed : 9.86 % Favored : 89.57 % 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: 1.04 (0.30), residues: 793 helix: 1.63 (0.27), residues: 394 sheet: -0.10 (0.77), residues: 48 loop : -0.22 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 165 HIS 0.005 0.001 HIS E 34 PHE 0.014 0.001 PHE E 523 TYR 0.016 0.001 TYR B 453 ARG 0.002 0.000 ARG B 357 *********************** 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 43 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: E 249 MET cc_start: 0.9040 (mmm) cc_final: 0.8597 (mmt) REVERT: E 462 MET cc_start: 0.8945 (mtm) cc_final: 0.8713 (mtm) outliers start: 4 outliers final: 0 residues processed: 42 average time/residue: 0.1616 time to fit residues: 10.1986 Evaluate side-chains 37 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.8538 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6709 Z= 0.230 Angle : 0.545 9.592 9118 Z= 0.270 Chirality : 0.041 0.135 968 Planarity : 0.003 0.038 1175 Dihedral : 4.529 55.828 971 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.40 % Favored : 97.48 % Rotamer: Outliers : 0.57 % Allowed : 10.71 % Favored : 88.71 % 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: 1.14 (0.30), residues: 793 helix: 1.81 (0.27), residues: 387 sheet: -0.32 (0.73), residues: 50 loop : -0.21 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 69 HIS 0.004 0.001 HIS E 34 PHE 0.012 0.001 PHE E 523 TYR 0.015 0.001 TYR B 369 ARG 0.002 0.000 ARG E 115 *********************** 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 47 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.841 Fit side-chains REVERT: B 506 GLN cc_start: 0.8951 (mt0) cc_final: 0.8654 (mt0) REVERT: E 249 MET cc_start: 0.9049 (mmm) cc_final: 0.8603 (mmt) outliers start: 4 outliers final: 1 residues processed: 47 average time/residue: 0.1683 time to fit residues: 11.8132 Evaluate side-chains 38 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 525 CYS 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: 0.7980 chunk 42 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 0.0980 chunk 22 optimal weight: 0.7980 chunk 14 optimal weight: 0.0570 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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: 0.8517 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6709 Z= 0.167 Angle : 0.516 10.298 9118 Z= 0.254 Chirality : 0.040 0.147 968 Planarity : 0.003 0.038 1175 Dihedral : 4.334 55.457 971 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.27 % Favored : 97.60 % Rotamer: Outliers : 0.71 % Allowed : 11.29 % Favored : 88.00 % 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: 1.25 (0.31), residues: 793 helix: 1.87 (0.27), residues: 387 sheet: -0.14 (0.75), residues: 48 loop : -0.14 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 165 HIS 0.003 0.001 HIS E 378 PHE 0.010 0.001 PHE E 523 TYR 0.014 0.001 TYR B 369 ARG 0.002 0.000 ARG B 403 *********************** 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 45 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 0.788 Fit side-chains REVERT: B 406 GLU cc_start: 0.8424 (pm20) cc_final: 0.8060 (pm20) REVERT: B 506 GLN cc_start: 0.8919 (mt0) cc_final: 0.8637 (mt0) REVERT: E 249 MET cc_start: 0.9039 (mmm) cc_final: 0.8597 (mmt) outliers start: 5 outliers final: 1 residues processed: 44 average time/residue: 0.1650 time to fit residues: 10.8121 Evaluate side-chains 39 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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: 0.8529 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6709 Z= 0.210 Angle : 0.533 8.713 9118 Z= 0.263 Chirality : 0.040 0.143 968 Planarity : 0.003 0.038 1175 Dihedral : 4.330 55.698 971 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.27 % Favored : 97.60 % Rotamer: Outliers : 0.71 % Allowed : 11.57 % Favored : 87.71 % 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: 1.32 (0.31), residues: 793 helix: 1.90 (0.27), residues: 387 sheet: -0.11 (0.76), residues: 48 loop : -0.07 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 165 HIS 0.003 0.001 HIS E 34 PHE 0.011 0.001 PHE E 523 TYR 0.014 0.001 TYR B 369 ARG 0.002 0.000 ARG B 403 *********************** 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 43 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.744 Fit side-chains REVERT: B 506 GLN cc_start: 0.8936 (mt0) cc_final: 0.8644 (mt0) REVERT: E 249 MET cc_start: 0.9023 (mmm) cc_final: 0.8580 (mmt) REVERT: E 270 MET cc_start: 0.9228 (tpp) cc_final: 0.8074 (tpp) outliers start: 5 outliers final: 3 residues processed: 42 average time/residue: 0.1610 time to fit residues: 10.2227 Evaluate side-chains 39 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain E residue 143 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 0.0060 chunk 75 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- 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: 0.8538 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6709 Z= 0.246 Angle : 0.549 8.981 9118 Z= 0.270 Chirality : 0.041 0.138 968 Planarity : 0.003 0.038 1175 Dihedral : 4.375 55.669 971 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.40 % Favored : 97.48 % Rotamer: Outliers : 0.86 % Allowed : 11.43 % Favored : 87.71 % 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: 1.36 (0.31), residues: 793 helix: 1.93 (0.27), residues: 387 sheet: -0.14 (0.75), residues: 48 loop : -0.03 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 PHE 0.013 0.001 PHE E 523 TYR 0.013 0.001 TYR B 369 ARG 0.002 0.000 ARG B 403 *********************** 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 44 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.783 Fit side-chains REVERT: B 406 GLU cc_start: 0.8321 (pm20) cc_final: 0.8078 (pm20) REVERT: B 506 GLN cc_start: 0.8924 (mt0) cc_final: 0.8627 (mt0) REVERT: E 249 MET cc_start: 0.9020 (mmm) cc_final: 0.8582 (mmt) REVERT: E 270 MET cc_start: 0.9255 (tpp) cc_final: 0.8134 (tpp) outliers start: 6 outliers final: 5 residues processed: 42 average time/residue: 0.1677 time to fit residues: 10.7532 Evaluate side-chains 41 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 320 LEU 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: 0.8980 chunk 72 optimal weight: 0.0980 chunk 62 optimal weight: 2.9990 chunk 6 optimal weight: 0.0170 chunk 48 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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: 0.8514 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6709 Z= 0.163 Angle : 0.537 11.348 9118 Z= 0.259 Chirality : 0.040 0.150 968 Planarity : 0.003 0.038 1175 Dihedral : 4.286 55.529 971 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.02 % Favored : 97.86 % Rotamer: Outliers : 0.57 % Allowed : 12.14 % Favored : 87.29 % 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: 1.39 (0.31), residues: 793 helix: 1.92 (0.27), residues: 389 sheet: -0.20 (0.76), residues: 48 loop : 0.04 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 69 HIS 0.002 0.001 HIS E 378 PHE 0.012 0.001 PHE E 314 TYR 0.012 0.001 TYR B 369 ARG 0.001 0.000 ARG B 403 ********************** 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 44 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.774 Fit side-chains REVERT: B 406 GLU cc_start: 0.8354 (pm20) cc_final: 0.7871 (pm20) REVERT: B 506 GLN cc_start: 0.8956 (mt0) cc_final: 0.8653 (mt0) REVERT: E 249 MET cc_start: 0.9020 (mmm) cc_final: 0.8584 (mmt) REVERT: E 270 MET cc_start: 0.9196 (tpp) cc_final: 0.8128 (tpp) REVERT: E 462 MET cc_start: 0.9205 (mmm) cc_final: 0.8866 (mtm) outliers start: 4 outliers final: 3 residues processed: 43 average time/residue: 0.1670 time to fit residues: 10.7672 Evaluate side-chains 40 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 320 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.055135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.041328 restraints weight = 28148.630| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 3.88 r_work: 0.2591 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6709 Z= 0.281 Angle : 0.582 12.115 9118 Z= 0.283 Chirality : 0.041 0.137 968 Planarity : 0.003 0.039 1175 Dihedral : 4.424 55.793 971 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.65 % Favored : 97.23 % Rotamer: Outliers : 0.71 % Allowed : 12.00 % Favored : 87.29 % 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: 1.28 (0.31), residues: 793 helix: 1.79 (0.27), residues: 397 sheet: -0.25 (0.76), residues: 48 loop : -0.00 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 PHE 0.014 0.001 PHE E 314 TYR 0.012 0.001 TYR B 369 ARG 0.002 0.000 ARG B 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1711.83 seconds wall clock time: 32 minutes 48.02 seconds (1968.02 seconds total)