Starting phenix.real_space_refine on Tue Feb 13 14:17:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dln_27507/02_2024/8dln_27507.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dln_27507/02_2024/8dln_27507.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dln_27507/02_2024/8dln_27507.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dln_27507/02_2024/8dln_27507.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dln_27507/02_2024/8dln_27507.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dln_27507/02_2024/8dln_27507.pdb" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4190 2.51 5 N 1078 2.21 5 O 1248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 497": "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: 6553 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1593 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 4.80, per 1000 atoms: 0.73 Number of scatterers: 6553 At special positions: 0 Unit cell: (77, 85, 123, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1248 8.00 N 1078 7.00 C 4190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 2.45 Conformation dependent library (CDL) restraints added in 1.4 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 7 sheets defined 57.0% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.403A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.725A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.697A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 removed outlier: 3.563A pdb=" N GLN E 81 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.727A 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: 4.072A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 147 through 155 Processing helix chain 'E' and resid 157 through 194 Proline residue: E 178 - end of helix removed outlier: 3.732A 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: 3.762A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.743A 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: 3.795A 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: 3.585A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.693A 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: 4.294A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.526A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.318A 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: 3.665A 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: 4.425A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.618A 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: 3.877A 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: 3.985A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.814A 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: 3.790A 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: 6.052A 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: 6.363A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 912 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: 1.81 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2079 1.35 - 1.47: 1795 1.47 - 1.60: 2804 1.60 - 1.72: 0 1.72 - 1.85: 58 Bond restraints: 6736 Sorted by residual: bond pdb=" C1 NAG E 702 " pdb=" O5 NAG E 702 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.23e+00 bond pdb=" C1 NAG E 704 " pdb=" O5 NAG E 704 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.26e+00 bond pdb=" C1 NAG E 703 " pdb=" O5 NAG E 703 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.72e+00 bond pdb=" C1 NAG E 705 " pdb=" O5 NAG E 705 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.65e+00 bond pdb=" C1 NAG E 706 " pdb=" O5 NAG E 706 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.53e+00 ... (remaining 6731 not shown) Histogram of bond angle deviations from ideal: 98.31 - 105.46: 170 105.46 - 112.62: 3349 112.62 - 119.78: 2334 119.78 - 126.93: 3184 126.93 - 134.09: 118 Bond angle restraints: 9155 Sorted by residual: angle pdb=" CA TYR B 495 " pdb=" CB TYR B 495 " pdb=" CG TYR B 495 " ideal model delta sigma weight residual 113.90 123.90 -10.00 1.80e+00 3.09e-01 3.09e+01 angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.36 128.33 -5.97 1.42e+00 4.96e-01 1.77e+01 angle pdb=" CA CYS E 141 " pdb=" CB CYS E 141 " pdb=" SG CYS E 141 " ideal model delta sigma weight residual 114.40 123.02 -8.62 2.30e+00 1.89e-01 1.41e+01 angle pdb=" CA ASN E 437 " pdb=" CB ASN E 437 " pdb=" CG ASN E 437 " ideal model delta sigma weight residual 112.60 116.03 -3.43 1.00e+00 1.00e+00 1.18e+01 angle pdb=" C TYR B 495 " pdb=" CA TYR B 495 " pdb=" CB TYR B 495 " ideal model delta sigma weight residual 110.78 105.54 5.24 1.60e+00 3.91e-01 1.07e+01 ... (remaining 9150 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 3688 17.19 - 34.37: 310 34.37 - 51.55: 44 51.55 - 68.74: 12 68.74 - 85.92: 11 Dihedral angle restraints: 4065 sinusoidal: 1726 harmonic: 2339 Sorted by residual: dihedral pdb=" CB CYS E 133 " pdb=" SG CYS E 133 " pdb=" SG CYS E 141 " pdb=" CB CYS E 141 " ideal model delta sinusoidal sigma weight residual -86.00 -46.48 -39.52 1 1.00e+01 1.00e-02 2.19e+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 14.60 64.40 1 2.00e+01 2.50e-03 1.36e+01 dihedral pdb=" C ASN B 360 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " pdb=" CB ASN B 360 " ideal model delta harmonic sigma weight residual -122.60 -130.75 8.15 0 2.50e+00 1.60e-01 1.06e+01 ... (remaining 4062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 701 0.052 - 0.105: 197 0.105 - 0.157: 64 0.157 - 0.209: 14 0.209 - 0.261: 2 Chirality restraints: 978 Sorted by residual: chirality pdb=" CA ASN B 360 " pdb=" N ASN B 360 " pdb=" C ASN B 360 " pdb=" CB ASN B 360 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.71e+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 -2.38 -0.25 2.00e-01 2.50e+01 1.55e+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 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 975 not shown) Planarity restraints: 1184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 495 " -0.030 2.00e-02 2.50e+03 1.88e-02 7.09e+00 pdb=" CG TYR B 495 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR B 495 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 495 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 495 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 495 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 495 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR B 495 " -0.003 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 6.41e-02 6.58e+00 pdb=" N PRO E 590 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO E 590 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 590 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 499 " -0.043 5.00e-02 4.00e+02 6.39e-02 6.53e+00 pdb=" N PRO E 500 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO E 500 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 500 " -0.036 5.00e-02 4.00e+02 ... (remaining 1181 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1941 2.82 - 3.34: 5987 3.34 - 3.86: 11373 3.86 - 4.38: 12873 4.38 - 4.90: 22360 Nonbonded interactions: 54534 Sorted by model distance: nonbonded pdb=" OH TYR E 183 " pdb=" OD1 ASP E 509 " model vdw 2.303 2.440 nonbonded pdb=" OD1 ASN B 487 " pdb=" OH TYR E 83 " model vdw 2.330 2.440 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.351 2.440 nonbonded pdb=" O MET E 152 " pdb=" NH1 ARG E 161 " model vdw 2.357 2.520 nonbonded pdb=" O ASN E 117 " pdb=" ND2 ASN E 121 " model vdw 2.366 2.520 ... (remaining 54529 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: 2.860 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: 0.000 Extract box with map and model: 13.360 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 22.500 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 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 0.064 6736 Z= 0.344 Angle : 0.860 10.004 9155 Z= 0.481 Chirality : 0.056 0.261 978 Planarity : 0.007 0.064 1177 Dihedral : 13.351 85.924 2547 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.29 % Allowed : 3.57 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.26), residues: 793 helix: 0.33 (0.22), residues: 387 sheet: 1.07 (0.72), residues: 43 loop : -0.73 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 69 HIS 0.007 0.001 HIS E 34 PHE 0.027 0.003 PHE E 369 TYR 0.043 0.002 TYR B 495 ARG 0.011 0.001 ARG E 460 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 0.812 Fit side-chains revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8276 (m-30) cc_final: 0.7950 (m-30) REVERT: E 143 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8945 (mp) REVERT: E 562 LYS cc_start: 0.9196 (tttt) cc_final: 0.8983 (tttp) REVERT: E 589 GLU cc_start: 0.7916 (tp30) cc_final: 0.7473 (tp30) outliers start: 2 outliers final: 0 residues processed: 117 average time/residue: 0.2564 time to fit residues: 37.5252 Evaluate side-chains 59 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 143 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.0570 chunk 59 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 overall best weight: 1.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN E 374 HIS E 552 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6736 Z= 0.244 Angle : 0.566 9.726 9155 Z= 0.289 Chirality : 0.042 0.142 978 Planarity : 0.005 0.040 1177 Dihedral : 5.442 57.472 1015 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.86 % Allowed : 8.43 % Favored : 90.71 % 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: 1.15 (0.28), residues: 793 helix: 1.59 (0.25), residues: 383 sheet: 0.84 (0.72), residues: 43 loop : -0.07 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 165 HIS 0.005 0.001 HIS E 34 PHE 0.018 0.001 PHE E 369 TYR 0.018 0.001 TYR B 495 ARG 0.007 0.000 ARG B 457 *********************** 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 69 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8242 (m-30) cc_final: 0.7723 (m-30) REVERT: E 152 MET cc_start: 0.8352 (mmp) cc_final: 0.8011 (mmt) REVERT: E 249 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8690 (mtm) REVERT: E 474 MET cc_start: 0.8584 (mmt) cc_final: 0.8123 (mmt) outliers start: 6 outliers final: 3 residues processed: 66 average time/residue: 0.2868 time to fit residues: 23.7590 Evaluate side-chains 62 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 458 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 0.9990 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: 2.9990 chunk 77 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6736 Z= 0.218 Angle : 0.526 8.779 9155 Z= 0.267 Chirality : 0.041 0.134 978 Planarity : 0.004 0.042 1177 Dihedral : 4.992 56.626 1013 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.00 % Allowed : 8.71 % Favored : 89.29 % 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: 1.52 (0.29), residues: 793 helix: 1.85 (0.26), residues: 383 sheet: 0.74 (0.74), residues: 43 loop : 0.23 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 PHE 0.016 0.001 PHE E 369 TYR 0.014 0.001 TYR E 385 ARG 0.004 0.000 ARG B 457 *********************** 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 75 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 249 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8717 (mtm) outliers start: 14 outliers final: 5 residues processed: 69 average time/residue: 0.2448 time to fit residues: 21.7302 Evaluate side-chains 62 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 458 LYS Chi-restraints excluded: chain E residue 471 ASP Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 72 optimal weight: 0.4980 chunk 76 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6736 Z= 0.198 Angle : 0.510 7.458 9155 Z= 0.259 Chirality : 0.040 0.129 978 Planarity : 0.004 0.044 1177 Dihedral : 4.847 56.836 1013 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.00 % Allowed : 9.71 % Favored : 88.29 % 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: 1.65 (0.29), residues: 793 helix: 1.92 (0.26), residues: 389 sheet: 0.79 (0.77), residues: 43 loop : 0.32 (0.32), residues: 361 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 B 495 ARG 0.002 0.000 ARG E 559 *********************** 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 72 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 58 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 62 MET cc_start: 0.8970 (ttm) cc_final: 0.8515 (ttm) REVERT: E 152 MET cc_start: 0.8285 (mmp) cc_final: 0.7859 (mmt) REVERT: E 249 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8712 (mtm) outliers start: 14 outliers final: 6 residues processed: 67 average time/residue: 0.2718 time to fit residues: 23.0393 Evaluate side-chains 63 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 295 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 471 ASP Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 65 optimal weight: 0.0970 chunk 52 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 19 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6736 Z= 0.166 Angle : 0.491 5.643 9155 Z= 0.249 Chirality : 0.040 0.128 978 Planarity : 0.003 0.043 1177 Dihedral : 4.670 56.790 1013 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.86 % Allowed : 10.57 % Favored : 87.57 % 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: 1.83 (0.29), residues: 793 helix: 2.03 (0.25), residues: 394 sheet: 0.99 (0.80), residues: 43 loop : 0.41 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.013 0.001 PHE E 369 TYR 0.012 0.001 TYR E 613 ARG 0.002 0.000 ARG E 559 *********************** 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 73 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 1.013 Fit side-chains REVERT: B 405 ASP cc_start: 0.8175 (m-30) cc_final: 0.7688 (m-30) REVERT: E 22 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8225 (tm-30) REVERT: E 62 MET cc_start: 0.9016 (ttm) cc_final: 0.8605 (ttm) REVERT: E 152 MET cc_start: 0.8367 (mmp) cc_final: 0.7878 (mmt) REVERT: E 249 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8685 (mtm) REVERT: E 291 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8761 (mt) outliers start: 13 outliers final: 7 residues processed: 68 average time/residue: 0.3065 time to fit residues: 26.5060 Evaluate side-chains 66 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 295 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 471 ASP Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 chunk 43 optimal weight: 0.0040 chunk 55 optimal weight: 0.7980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6736 Z= 0.160 Angle : 0.486 5.503 9155 Z= 0.247 Chirality : 0.040 0.187 978 Planarity : 0.003 0.043 1177 Dihedral : 4.586 56.900 1013 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.71 % Allowed : 10.86 % Favored : 87.43 % 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: 1.84 (0.29), residues: 793 helix: 1.98 (0.25), residues: 402 sheet: 1.01 (0.80), residues: 43 loop : 0.45 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.013 0.001 PHE E 369 TYR 0.011 0.001 TYR E 385 ARG 0.004 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: B 388 ASN cc_start: 0.8563 (p0) cc_final: 0.8316 (m110) REVERT: B 405 ASP cc_start: 0.8147 (m-30) cc_final: 0.7679 (m-30) REVERT: E 22 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8194 (tm-30) REVERT: E 249 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8699 (mtm) REVERT: E 291 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8760 (mt) outliers start: 12 outliers final: 8 residues processed: 64 average time/residue: 0.2547 time to fit residues: 21.0051 Evaluate side-chains 67 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 295 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 471 ASP Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.0770 chunk 64 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 76 optimal weight: 0.3980 chunk 47 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6736 Z= 0.181 Angle : 0.509 10.839 9155 Z= 0.253 Chirality : 0.040 0.147 978 Planarity : 0.003 0.042 1177 Dihedral : 4.587 57.031 1013 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.57 % Allowed : 11.43 % Favored : 87.00 % 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: 1.92 (0.29), residues: 793 helix: 2.02 (0.25), residues: 403 sheet: 1.02 (0.80), residues: 43 loop : 0.53 (0.33), residues: 347 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 0.012 0.001 PHE E 369 TYR 0.019 0.001 TYR B 365 ARG 0.005 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 22 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8167 (tm-30) REVERT: E 152 MET cc_start: 0.8062 (mmp) cc_final: 0.7649 (mmt) REVERT: E 249 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8708 (mtm) outliers start: 11 outliers final: 8 residues processed: 62 average time/residue: 0.2537 time to fit residues: 20.2947 Evaluate side-chains 65 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 295 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 471 ASP Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8494 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6736 Z= 0.200 Angle : 0.514 9.816 9155 Z= 0.256 Chirality : 0.040 0.138 978 Planarity : 0.003 0.042 1177 Dihedral : 4.626 57.014 1013 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.57 % Allowed : 11.14 % 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: 1.94 (0.29), residues: 793 helix: 2.02 (0.26), residues: 403 sheet: 0.88 (0.79), residues: 43 loop : 0.58 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.013 0.001 PHE E 369 TYR 0.018 0.001 TYR B 365 ARG 0.005 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: E 22 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8206 (tm-30) REVERT: E 152 MET cc_start: 0.8204 (mmp) cc_final: 0.7635 (mmt) REVERT: E 249 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8731 (mtm) outliers start: 11 outliers final: 7 residues processed: 61 average time/residue: 0.2658 time to fit residues: 20.7287 Evaluate side-chains 63 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 295 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 471 ASP Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 67 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 498 GLN ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN E 522 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6736 Z= 0.331 Angle : 0.583 11.145 9155 Z= 0.293 Chirality : 0.042 0.149 978 Planarity : 0.004 0.040 1177 Dihedral : 5.008 57.301 1013 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.29 % Allowed : 12.00 % Favored : 86.71 % 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: 1.86 (0.30), residues: 793 helix: 1.93 (0.26), residues: 401 sheet: 0.65 (0.77), residues: 43 loop : 0.61 (0.33), residues: 349 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 0.015 0.001 PHE E 369 TYR 0.021 0.001 TYR B 365 ARG 0.007 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 152 MET cc_start: 0.8310 (mmp) cc_final: 0.7809 (mmt) REVERT: E 249 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8737 (mtm) outliers start: 9 outliers final: 7 residues processed: 60 average time/residue: 0.3438 time to fit residues: 27.9434 Evaluate side-chains 63 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 295 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 471 ASP Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6736 Z= 0.216 Angle : 0.533 10.884 9155 Z= 0.266 Chirality : 0.040 0.128 978 Planarity : 0.003 0.040 1177 Dihedral : 4.852 57.041 1013 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.29 % Allowed : 12.29 % Favored : 86.43 % 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: 1.85 (0.30), residues: 793 helix: 1.93 (0.26), residues: 403 sheet: 0.60 (0.77), residues: 43 loop : 0.61 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.013 0.001 PHE E 369 TYR 0.019 0.001 TYR B 365 ARG 0.005 0.000 ARG B 457 ********************** 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 64 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: B 471 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8585 (mm-30) REVERT: E 152 MET cc_start: 0.8258 (mmp) cc_final: 0.7743 (mmt) REVERT: E 249 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8685 (mtm) outliers start: 9 outliers final: 7 residues processed: 59 average time/residue: 0.2636 time to fit residues: 20.0269 Evaluate side-chains 63 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 295 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 471 ASP Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 0.1980 chunk 71 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.067873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.051436 restraints weight = 19056.570| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 3.30 r_work: 0.2726 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6736 Z= 0.238 Angle : 0.538 10.762 9155 Z= 0.268 Chirality : 0.041 0.128 978 Planarity : 0.003 0.040 1177 Dihedral : 4.837 57.010 1013 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.29 % Allowed : 12.43 % Favored : 86.29 % 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: 1.84 (0.30), residues: 793 helix: 1.91 (0.26), residues: 404 sheet: 0.49 (0.76), residues: 43 loop : 0.63 (0.34), 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 0.013 0.001 PHE E 369 TYR 0.019 0.001 TYR B 365 ARG 0.005 0.000 ARG B 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1760.96 seconds wall clock time: 32 minutes 47.44 seconds (1967.44 seconds total)