Starting phenix.real_space_refine on Tue Feb 13 16:55:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzl_20962/02_2024/6uzl_20962.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzl_20962/02_2024/6uzl_20962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzl_20962/02_2024/6uzl_20962.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzl_20962/02_2024/6uzl_20962.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzl_20962/02_2024/6uzl_20962.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzl_20962/02_2024/6uzl_20962.pdb" } resolution = 4.4 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= 0.002 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 44 5.16 5 C 4412 2.51 5 N 1250 2.21 5 O 1302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 133": "OE1" <-> "OE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "B GLU 208": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7008 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 3502 Classifications: {'peptide': 531} Incomplete info: {'truncation_to_alanine': 176} Link IDs: {'PTRANS': 13, 'TRANS': 517} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 621 Unresolved non-hydrogen angles: 794 Unresolved non-hydrogen dihedrals: 486 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 6, 'ASN:plan1': 12, 'ASP:plan': 14, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 356 Chain: "B" Number of atoms: 3506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 3506 Classifications: {'peptide': 531} Incomplete info: {'truncation_to_alanine': 175} Link IDs: {'PTRANS': 13, 'TRANS': 517} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 617 Unresolved non-hydrogen angles: 789 Unresolved non-hydrogen dihedrals: 483 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 6, 'ASN:plan1': 12, 'ASP:plan': 14, 'PHE:plan': 5, 'GLU:plan': 15, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 352 Time building chain proxies: 4.07, per 1000 atoms: 0.58 Number of scatterers: 7008 At special positions: 0 Unit cell: (73, 86, 124, 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 44 16.00 O 1302 8.00 N 1250 7.00 C 4412 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 1.5 seconds 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1988 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 2 sheets defined 72.8% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 removed outlier: 3.734A pdb=" N LEU A 16 " --> pdb=" O THR A 12 " (cutoff:3.500A) Proline residue: A 18 - end of helix Processing helix chain 'A' and resid 23 through 54 removed outlier: 3.700A pdb=" N LEU A 27 " --> pdb=" O PHE A 23 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 48 " --> pdb=" O MET A 44 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 65 through 111 removed outlier: 4.281A pdb=" N LEU A 69 " --> pdb=" O VAL A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.701A pdb=" N LYS A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 162 removed outlier: 4.645A pdb=" N ILE A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 193 Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 195 through 221 removed outlier: 3.650A pdb=" N THR A 199 " --> pdb=" O ASN A 195 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LYS A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLU A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 268 removed outlier: 3.891A pdb=" N SER A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASP A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 280 through 324 Proline residue: A 297 - end of helix removed outlier: 4.477A pdb=" N THR A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASN A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 390 removed outlier: 3.604A pdb=" N SER A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 419 Processing helix chain 'A' and resid 432 through 438 Processing helix chain 'A' and resid 446 through 458 Processing helix chain 'A' and resid 459 through 466 removed outlier: 3.618A pdb=" N LYS A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 472 Processing helix chain 'A' and resid 474 through 479 removed outlier: 4.015A pdb=" N VAL A 479 " --> pdb=" O GLU A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 498 Processing helix chain 'A' and resid 512 through 528 Processing helix chain 'B' and resid 12 through 21 Proline residue: B 18 - end of helix Processing helix chain 'B' and resid 23 through 54 removed outlier: 3.864A pdb=" N LEU B 27 " --> pdb=" O PHE B 23 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 61 through 110 Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 112 through 119 removed outlier: 3.858A pdb=" N GLN B 119 " --> pdb=" O PHE B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 162 Processing helix chain 'B' and resid 164 through 213 Proline residue: B 176 - end of helix removed outlier: 3.897A pdb=" N GLY B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 221 Processing helix chain 'B' and resid 222 through 272 removed outlier: 3.760A pdb=" N GLU B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 280 through 324 Proline residue: B 297 - end of helix removed outlier: 3.875A pdb=" N ASN B 303 " --> pdb=" O LYS B 299 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLN B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ARG B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY B 311 " --> pdb=" O GLN B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 390 Processing helix chain 'B' and resid 401 through 405 removed outlier: 3.701A pdb=" N GLY B 404 " --> pdb=" O LEU B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 419 removed outlier: 3.653A pdb=" N ARG B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASN B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 438 Processing helix chain 'B' and resid 446 through 457 Processing helix chain 'B' and resid 459 through 465 removed outlier: 3.686A pdb=" N ILE B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN B 464 " --> pdb=" O MET B 460 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 465 " --> pdb=" O ASP B 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 459 through 465' Processing helix chain 'B' and resid 474 through 479 removed outlier: 3.924A pdb=" N VAL B 479 " --> pdb=" O GLU B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 498 Processing helix chain 'B' and resid 512 through 528 Processing sheet with id=AA1, first strand: chain 'A' and resid 362 through 366 removed outlier: 4.932A pdb=" N ILE A 362 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN A 346 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 501 through 503 568 hydrogen bonds defined for protein. 1677 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: 2.13 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2375 1.34 - 1.46: 1326 1.46 - 1.58: 3305 1.58 - 1.70: 0 1.70 - 1.82: 84 Bond restraints: 7090 Sorted by residual: bond pdb=" CA LEU A 374 " pdb=" C LEU A 374 " ideal model delta sigma weight residual 1.523 1.442 0.081 1.34e-02 5.57e+03 3.64e+01 bond pdb=" CA ARG B 360 " pdb=" C ARG B 360 " ideal model delta sigma weight residual 1.523 1.565 -0.042 1.30e-02 5.92e+03 1.05e+01 bond pdb=" N LEU B 359 " pdb=" CA LEU B 359 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.13e+00 bond pdb=" CA ALA B 358 " pdb=" C ALA B 358 " ideal model delta sigma weight residual 1.521 1.556 -0.035 1.20e-02 6.94e+03 8.45e+00 bond pdb=" CA PRO B 357 " pdb=" C PRO B 357 " ideal model delta sigma weight residual 1.520 1.558 -0.039 1.42e-02 4.96e+03 7.44e+00 ... (remaining 7085 not shown) Histogram of bond angle deviations from ideal: 99.72 - 106.58: 142 106.58 - 113.43: 4072 113.43 - 120.29: 2400 120.29 - 127.15: 3005 127.15 - 134.00: 42 Bond angle restraints: 9661 Sorted by residual: angle pdb=" N ARG B 360 " pdb=" CA ARG B 360 " pdb=" C ARG B 360 " ideal model delta sigma weight residual 111.28 125.61 -14.33 1.09e+00 8.42e-01 1.73e+02 angle pdb=" N THR B 348 " pdb=" CA THR B 348 " pdb=" C THR B 348 " ideal model delta sigma weight residual 110.35 121.78 -11.43 1.36e+00 5.41e-01 7.06e+01 angle pdb=" C ILE B 366 " pdb=" N PRO B 367 " pdb=" CA PRO B 367 " ideal model delta sigma weight residual 119.76 127.63 -7.87 1.03e+00 9.43e-01 5.84e+01 angle pdb=" N LEU B 364 " pdb=" CA LEU B 364 " pdb=" C LEU B 364 " ideal model delta sigma weight residual 109.60 119.00 -9.40 1.53e+00 4.27e-01 3.78e+01 angle pdb=" N PRO B 352 " pdb=" CA PRO B 352 " pdb=" C PRO B 352 " ideal model delta sigma weight residual 112.47 100.15 12.32 2.06e+00 2.36e-01 3.58e+01 ... (remaining 9656 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.92: 3805 14.92 - 29.84: 338 29.84 - 44.77: 87 44.77 - 59.69: 13 59.69 - 74.61: 6 Dihedral angle restraints: 4249 sinusoidal: 1189 harmonic: 3060 Sorted by residual: dihedral pdb=" CA TYR B 410 " pdb=" C TYR B 410 " pdb=" N THR B 411 " pdb=" CA THR B 411 " ideal model delta harmonic sigma weight residual -180.00 -152.92 -27.08 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA TYR A 351 " pdb=" C TYR A 351 " pdb=" N PRO A 352 " pdb=" CA PRO A 352 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA ARG A 408 " pdb=" C ARG A 408 " pdb=" N GLU A 409 " pdb=" CA GLU A 409 " ideal model delta harmonic sigma weight residual 180.00 156.34 23.66 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 4246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1096 0.086 - 0.171: 104 0.171 - 0.256: 8 0.256 - 0.342: 3 0.342 - 0.427: 1 Chirality restraints: 1212 Sorted by residual: chirality pdb=" CA ARG B 360 " pdb=" N ARG B 360 " pdb=" C ARG B 360 " pdb=" CB ARG B 360 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.57e+00 chirality pdb=" CA THR B 348 " pdb=" N THR B 348 " pdb=" C THR B 348 " pdb=" CB THR B 348 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA ILE B 395 " pdb=" N ILE B 395 " pdb=" C ILE B 395 " pdb=" CB ILE B 395 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 1209 not shown) Planarity restraints: 1249 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 356 " 0.018 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C VAL B 356 " -0.059 2.00e-02 2.50e+03 pdb=" O VAL B 356 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO B 357 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 272 " -0.055 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO B 273 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 273 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 273 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 329 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.76e+00 pdb=" C ASP B 329 " -0.038 2.00e-02 2.50e+03 pdb=" O ASP B 329 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU B 330 " 0.013 2.00e-02 2.50e+03 ... (remaining 1246 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 900 2.74 - 3.28: 8956 3.28 - 3.82: 11836 3.82 - 4.36: 13870 4.36 - 4.90: 20724 Nonbonded interactions: 56286 Sorted by model distance: nonbonded pdb=" O ASN A 37 " pdb=" OG SER A 40 " model vdw 2.198 2.440 nonbonded pdb=" O GLY A 282 " pdb=" OG1 THR A 285 " model vdw 2.201 2.440 nonbonded pdb=" O ILE B 128 " pdb=" OG SER B 132 " model vdw 2.202 2.440 nonbonded pdb=" O ALA B 368 " pdb=" N LYS B 370 " model vdw 2.204 2.520 nonbonded pdb=" O ALA B 314 " pdb=" OG1 THR B 317 " model vdw 2.204 2.440 ... (remaining 56281 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 11 through 148 or (resid 149 and (name N or name CA or nam \ e C or name O or name CB )) or resid 150 through 541)) } 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 group one per residue 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.930 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 23.240 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 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 0.081 7090 Z= 0.335 Angle : 1.004 14.330 9661 Z= 0.657 Chirality : 0.053 0.427 1212 Planarity : 0.005 0.083 1249 Dihedral : 13.211 74.610 2261 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 27.71 Ramachandran Plot: Outliers : 0.76 % Allowed : 15.12 % Favored : 84.12 % Rotamer: Outliers : 0.18 % Allowed : 8.17 % Favored : 91.65 % 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: -4.74 (0.19), residues: 1058 helix: -2.76 (0.14), residues: 692 sheet: -2.46 (0.91), residues: 29 loop : -3.69 (0.27), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 91 HIS 0.003 0.001 HIS A 214 PHE 0.021 0.002 PHE B 157 TYR 0.011 0.002 TYR A 83 ARG 0.005 0.001 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 229 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.9183 (mmm) cc_final: 0.8789 (mmm) REVERT: A 83 TYR cc_start: 0.8478 (m-10) cc_final: 0.8031 (m-80) REVERT: A 98 MET cc_start: 0.8924 (mmm) cc_final: 0.8522 (tpp) REVERT: A 105 PHE cc_start: 0.9279 (m-10) cc_final: 0.8806 (m-80) REVERT: A 111 MET cc_start: 0.9219 (mmp) cc_final: 0.8914 (mmm) REVERT: A 156 LEU cc_start: 0.9562 (mt) cc_final: 0.9025 (pp) REVERT: A 158 ILE cc_start: 0.9469 (mm) cc_final: 0.9264 (mm) REVERT: A 161 PHE cc_start: 0.8924 (m-10) cc_final: 0.8591 (m-10) REVERT: A 209 GLN cc_start: 0.9219 (pt0) cc_final: 0.8725 (tm-30) REVERT: A 228 LYS cc_start: 0.9699 (mttt) cc_final: 0.9320 (mmtm) REVERT: A 231 ASP cc_start: 0.9302 (m-30) cc_final: 0.9091 (m-30) REVERT: A 267 LEU cc_start: 0.9493 (mt) cc_final: 0.9287 (mt) REVERT: A 291 MET cc_start: 0.9079 (mmm) cc_final: 0.8651 (tpt) REVERT: A 296 ARG cc_start: 0.5657 (mtt180) cc_final: 0.4845 (ttm170) REVERT: A 303 ASN cc_start: 0.9512 (m-40) cc_final: 0.9244 (p0) REVERT: A 312 MET cc_start: 0.8752 (mmm) cc_final: 0.8347 (mtt) REVERT: B 74 LEU cc_start: 0.9685 (mt) cc_final: 0.9440 (mt) REVERT: B 75 MET cc_start: 0.9407 (mmm) cc_final: 0.8855 (mmm) REVERT: B 83 TYR cc_start: 0.8427 (m-10) cc_final: 0.8076 (m-80) REVERT: B 98 MET cc_start: 0.9249 (ttm) cc_final: 0.8957 (ttm) REVERT: B 105 PHE cc_start: 0.9308 (m-80) cc_final: 0.9005 (m-80) REVERT: B 131 ASP cc_start: 0.8735 (m-30) cc_final: 0.8425 (m-30) REVERT: B 159 MET cc_start: 0.8620 (mmp) cc_final: 0.7703 (tpp) REVERT: B 161 PHE cc_start: 0.8780 (m-10) cc_final: 0.8436 (m-10) REVERT: B 163 TYR cc_start: 0.8903 (m-10) cc_final: 0.7258 (m-80) REVERT: B 215 LYS cc_start: 0.9564 (mttt) cc_final: 0.9364 (mmtt) REVERT: B 228 LYS cc_start: 0.9834 (mttt) cc_final: 0.9403 (mmmm) REVERT: B 261 LEU cc_start: 0.9463 (mt) cc_final: 0.8966 (tp) REVERT: B 296 ARG cc_start: 0.5254 (mtt180) cc_final: 0.4607 (ttm-80) outliers start: 1 outliers final: 0 residues processed: 230 average time/residue: 0.1814 time to fit residues: 54.7770 Evaluate side-chains 188 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 27 optimal weight: 0.5980 chunk 54 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 0.0870 chunk 50 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN A 191 ASN ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7090 Z= 0.194 Angle : 0.651 7.152 9661 Z= 0.350 Chirality : 0.043 0.147 1212 Planarity : 0.005 0.086 1249 Dihedral : 4.763 21.345 1106 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 0.18 % Allowed : 4.36 % Favored : 95.46 % 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: -1.72 (0.24), residues: 1058 helix: -0.36 (0.18), residues: 725 sheet: -1.54 (0.87), residues: 34 loop : -2.87 (0.33), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 66 HIS 0.004 0.001 HIS A 214 PHE 0.033 0.002 PHE A 308 TYR 0.009 0.001 TYR A 87 ARG 0.003 0.000 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 247 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.9106 (mmm) cc_final: 0.8867 (mmm) REVERT: A 105 PHE cc_start: 0.9374 (m-10) cc_final: 0.9044 (m-80) REVERT: A 133 GLU cc_start: 0.9377 (mt-10) cc_final: 0.9147 (pt0) REVERT: A 158 ILE cc_start: 0.9386 (mm) cc_final: 0.9033 (mm) REVERT: A 161 PHE cc_start: 0.8754 (m-10) cc_final: 0.8380 (m-10) REVERT: A 208 GLU cc_start: 0.9322 (tm-30) cc_final: 0.9102 (tm-30) REVERT: A 209 GLN cc_start: 0.8932 (pt0) cc_final: 0.8685 (tm-30) REVERT: A 211 LEU cc_start: 0.9568 (mt) cc_final: 0.9154 (mt) REVERT: A 214 HIS cc_start: 0.7775 (m90) cc_final: 0.7153 (m90) REVERT: A 224 GLU cc_start: 0.9418 (mp0) cc_final: 0.9005 (mp0) REVERT: A 228 LYS cc_start: 0.9650 (mttt) cc_final: 0.9288 (mmtm) REVERT: A 231 ASP cc_start: 0.9184 (m-30) cc_final: 0.8687 (m-30) REVERT: A 235 ASN cc_start: 0.9322 (m-40) cc_final: 0.8573 (m-40) REVERT: A 291 MET cc_start: 0.8934 (mmm) cc_final: 0.8446 (tpt) REVERT: A 296 ARG cc_start: 0.5963 (mtt180) cc_final: 0.5323 (ttm170) REVERT: A 303 ASN cc_start: 0.9595 (m110) cc_final: 0.9050 (p0) REVERT: A 304 VAL cc_start: 0.8893 (t) cc_final: 0.8154 (t) REVERT: A 312 MET cc_start: 0.8797 (mmm) cc_final: 0.8307 (mpp) REVERT: B 54 ASP cc_start: 0.9360 (m-30) cc_final: 0.8805 (t0) REVERT: B 67 MET cc_start: 0.9247 (mpp) cc_final: 0.8906 (mpp) REVERT: B 75 MET cc_start: 0.9408 (mmm) cc_final: 0.8689 (mmm) REVERT: B 87 TYR cc_start: 0.8547 (t80) cc_final: 0.8315 (t80) REVERT: B 98 MET cc_start: 0.9193 (ttm) cc_final: 0.8776 (ttm) REVERT: B 105 PHE cc_start: 0.9159 (m-80) cc_final: 0.8924 (m-80) REVERT: B 131 ASP cc_start: 0.8588 (m-30) cc_final: 0.8242 (m-30) REVERT: B 161 PHE cc_start: 0.8710 (m-10) cc_final: 0.8309 (m-10) REVERT: B 163 TYR cc_start: 0.8762 (m-10) cc_final: 0.8522 (m-10) REVERT: B 196 MET cc_start: 0.7886 (tpt) cc_final: 0.6965 (tpp) REVERT: B 200 MET cc_start: 0.8881 (mtm) cc_final: 0.8514 (mmm) REVERT: B 210 MET cc_start: 0.8485 (mmp) cc_final: 0.8283 (mmp) REVERT: B 215 LYS cc_start: 0.9536 (mttt) cc_final: 0.9223 (mmtt) REVERT: B 228 LYS cc_start: 0.9816 (mttt) cc_final: 0.9331 (mmmm) REVERT: B 240 GLN cc_start: 0.8877 (mm-40) cc_final: 0.8510 (tp40) REVERT: B 261 LEU cc_start: 0.9234 (mt) cc_final: 0.8813 (tp) REVERT: B 291 MET cc_start: 0.9081 (ttt) cc_final: 0.8151 (tpt) REVERT: B 296 ARG cc_start: 0.5164 (mtt180) cc_final: 0.4387 (ttp-170) REVERT: B 328 LYS cc_start: 0.8969 (mmtm) cc_final: 0.8595 (mmtt) REVERT: B 329 ASP cc_start: 0.8780 (m-30) cc_final: 0.7979 (t0) outliers start: 1 outliers final: 0 residues processed: 247 average time/residue: 0.1662 time to fit residues: 56.3814 Evaluate side-chains 201 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 26 optimal weight: 0.3980 chunk 96 optimal weight: 0.6980 chunk 104 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7090 Z= 0.178 Angle : 0.624 8.234 9661 Z= 0.328 Chirality : 0.043 0.157 1212 Planarity : 0.004 0.081 1249 Dihedral : 4.315 20.477 1106 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.54 % Allowed : 4.72 % Favored : 94.74 % 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: -0.20 (0.26), residues: 1058 helix: 0.87 (0.19), residues: 730 sheet: -1.40 (0.87), residues: 34 loop : -2.55 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 165 HIS 0.003 0.001 HIS A 107 PHE 0.022 0.002 PHE B 288 TYR 0.015 0.001 TYR A 163 ARG 0.002 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 252 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASN cc_start: 0.9098 (t0) cc_final: 0.8813 (t0) REVERT: A 75 MET cc_start: 0.9066 (mmm) cc_final: 0.8724 (mmm) REVERT: A 105 PHE cc_start: 0.9435 (m-10) cc_final: 0.8986 (m-80) REVERT: A 107 HIS cc_start: 0.8491 (m170) cc_final: 0.8133 (m170) REVERT: A 131 ASP cc_start: 0.8579 (m-30) cc_final: 0.8363 (m-30) REVERT: A 158 ILE cc_start: 0.9268 (mm) cc_final: 0.8968 (mm) REVERT: A 161 PHE cc_start: 0.8799 (m-10) cc_final: 0.8415 (m-10) REVERT: A 211 LEU cc_start: 0.9642 (mt) cc_final: 0.9383 (mt) REVERT: A 231 ASP cc_start: 0.9068 (m-30) cc_final: 0.8538 (m-30) REVERT: A 235 ASN cc_start: 0.9311 (m-40) cc_final: 0.8544 (m-40) REVERT: A 261 LEU cc_start: 0.9063 (mp) cc_final: 0.8810 (tp) REVERT: A 291 MET cc_start: 0.8875 (mmm) cc_final: 0.8526 (tpt) REVERT: A 296 ARG cc_start: 0.5916 (mtt180) cc_final: 0.5572 (ttt180) REVERT: A 303 ASN cc_start: 0.9485 (m110) cc_final: 0.9081 (p0) REVERT: A 312 MET cc_start: 0.8826 (mmm) cc_final: 0.8236 (mtt) REVERT: B 54 ASP cc_start: 0.9303 (m-30) cc_final: 0.8870 (t0) REVERT: B 67 MET cc_start: 0.9243 (mpp) cc_final: 0.8995 (mpp) REVERT: B 75 MET cc_start: 0.9391 (mmm) cc_final: 0.8679 (mmm) REVERT: B 87 TYR cc_start: 0.8581 (t80) cc_final: 0.8297 (t80) REVERT: B 98 MET cc_start: 0.9084 (ttm) cc_final: 0.8682 (ttm) REVERT: B 121 THR cc_start: 0.9345 (t) cc_final: 0.9120 (t) REVERT: B 131 ASP cc_start: 0.8570 (m-30) cc_final: 0.8359 (m-30) REVERT: B 156 LEU cc_start: 0.9491 (mt) cc_final: 0.9159 (pp) REVERT: B 161 PHE cc_start: 0.8703 (m-10) cc_final: 0.8278 (m-10) REVERT: B 196 MET cc_start: 0.7423 (tpt) cc_final: 0.7039 (tpp) REVERT: B 200 MET cc_start: 0.8791 (mtm) cc_final: 0.8518 (mmm) REVERT: B 214 HIS cc_start: 0.8062 (m90) cc_final: 0.7852 (m90) REVERT: B 215 LYS cc_start: 0.9527 (mttt) cc_final: 0.9294 (mmmt) REVERT: B 228 LYS cc_start: 0.9811 (mttt) cc_final: 0.9344 (mmmm) REVERT: B 231 ASP cc_start: 0.9431 (m-30) cc_final: 0.9023 (m-30) REVERT: B 235 ASN cc_start: 0.9457 (m-40) cc_final: 0.9160 (m-40) REVERT: B 242 MET cc_start: 0.9124 (mpp) cc_final: 0.8690 (mmt) REVERT: B 261 LEU cc_start: 0.9205 (mt) cc_final: 0.8722 (tp) REVERT: B 291 MET cc_start: 0.9029 (ttt) cc_final: 0.8098 (tpt) REVERT: B 294 LEU cc_start: 0.9552 (mt) cc_final: 0.9309 (mt) REVERT: B 296 ARG cc_start: 0.5540 (mtt180) cc_final: 0.4809 (ttp-170) REVERT: B 312 MET cc_start: 0.8952 (mmm) cc_final: 0.8626 (mmm) REVERT: B 325 GLU cc_start: 0.9289 (mt-10) cc_final: 0.9057 (tt0) REVERT: B 328 LYS cc_start: 0.9042 (mmtm) cc_final: 0.8518 (mmtt) REVERT: B 329 ASP cc_start: 0.8758 (m-30) cc_final: 0.7944 (t0) outliers start: 3 outliers final: 0 residues processed: 253 average time/residue: 0.1494 time to fit residues: 52.4180 Evaluate side-chains 206 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 46 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 20.0000 chunk 102 optimal weight: 30.0000 chunk 91 optimal weight: 20.0000 chunk 27 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 overall best weight: 3.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7090 Z= 0.326 Angle : 0.736 8.523 9661 Z= 0.401 Chirality : 0.045 0.142 1212 Planarity : 0.005 0.070 1249 Dihedral : 4.604 20.493 1106 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.36 % Allowed : 3.27 % Favored : 96.37 % 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: -0.36 (0.26), residues: 1058 helix: 0.69 (0.19), residues: 728 sheet: -1.56 (0.77), residues: 39 loop : -2.37 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 91 HIS 0.010 0.003 HIS A 107 PHE 0.027 0.002 PHE B 288 TYR 0.007 0.001 TYR B 162 ARG 0.004 0.001 ARG A 238 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 220 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.9103 (mmm) cc_final: 0.8797 (mmm) REVERT: A 105 PHE cc_start: 0.9397 (m-80) cc_final: 0.8947 (m-80) REVERT: A 131 ASP cc_start: 0.8732 (m-30) cc_final: 0.8423 (m-30) REVERT: A 133 GLU cc_start: 0.9419 (mt-10) cc_final: 0.9118 (mt-10) REVERT: A 158 ILE cc_start: 0.9392 (mm) cc_final: 0.9086 (mm) REVERT: A 159 MET cc_start: 0.9166 (tpp) cc_final: 0.8877 (tpp) REVERT: A 161 PHE cc_start: 0.8809 (m-10) cc_final: 0.8383 (m-10) REVERT: A 231 ASP cc_start: 0.9130 (m-30) cc_final: 0.8846 (m-30) REVERT: A 296 ARG cc_start: 0.5837 (mtt180) cc_final: 0.5574 (mtt180) REVERT: A 303 ASN cc_start: 0.9460 (m110) cc_final: 0.9214 (p0) REVERT: A 312 MET cc_start: 0.8817 (mmm) cc_final: 0.8327 (mtt) REVERT: B 75 MET cc_start: 0.9452 (mmm) cc_final: 0.9222 (mmm) REVERT: B 98 MET cc_start: 0.9117 (ttm) cc_final: 0.8844 (ttm) REVERT: B 105 PHE cc_start: 0.9211 (m-80) cc_final: 0.8873 (m-80) REVERT: B 131 ASP cc_start: 0.8589 (m-30) cc_final: 0.8257 (m-30) REVERT: B 149 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8276 (mp0) REVERT: B 161 PHE cc_start: 0.8761 (m-10) cc_final: 0.8347 (m-10) REVERT: B 200 MET cc_start: 0.8940 (mtm) cc_final: 0.8705 (mmm) REVERT: B 208 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8777 (tm-30) REVERT: B 210 MET cc_start: 0.8317 (mmp) cc_final: 0.8043 (mmp) REVERT: B 215 LYS cc_start: 0.9500 (mttt) cc_final: 0.9265 (mmmt) REVERT: B 231 ASP cc_start: 0.9495 (m-30) cc_final: 0.9182 (m-30) REVERT: B 242 MET cc_start: 0.9199 (mpp) cc_final: 0.8939 (mmt) REVERT: B 288 PHE cc_start: 0.9399 (m-80) cc_final: 0.9183 (m-80) REVERT: B 296 ARG cc_start: 0.5377 (mtt180) cc_final: 0.4799 (ttm170) REVERT: B 328 LYS cc_start: 0.9098 (mmtm) cc_final: 0.8684 (mmtt) REVERT: B 329 ASP cc_start: 0.8837 (m-30) cc_final: 0.8098 (t0) outliers start: 2 outliers final: 0 residues processed: 220 average time/residue: 0.1554 time to fit residues: 47.1249 Evaluate side-chains 183 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 182 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 87 optimal weight: 0.0030 chunk 70 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 52 optimal weight: 30.0000 chunk 91 optimal weight: 20.0000 chunk 25 optimal weight: 0.9990 chunk 34 optimal weight: 0.0770 overall best weight: 0.5150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7090 Z= 0.179 Angle : 0.622 8.306 9661 Z= 0.328 Chirality : 0.043 0.137 1212 Planarity : 0.004 0.080 1249 Dihedral : 4.253 21.556 1106 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.18 % Allowed : 2.54 % Favored : 97.28 % 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: 0.42 (0.27), residues: 1058 helix: 1.32 (0.19), residues: 733 sheet: -1.32 (0.79), residues: 39 loop : -2.28 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 165 HIS 0.004 0.001 HIS A 107 PHE 0.030 0.002 PHE B 288 TYR 0.006 0.001 TYR A 163 ARG 0.002 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 250 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.9498 (mt) cc_final: 0.9279 (mt) REVERT: A 75 MET cc_start: 0.9038 (mmm) cc_final: 0.8705 (mmm) REVERT: A 105 PHE cc_start: 0.9381 (m-80) cc_final: 0.8962 (m-80) REVERT: A 131 ASP cc_start: 0.8576 (m-30) cc_final: 0.8300 (m-30) REVERT: A 159 MET cc_start: 0.8945 (tpp) cc_final: 0.8614 (tpp) REVERT: A 161 PHE cc_start: 0.8648 (m-10) cc_final: 0.8192 (m-10) REVERT: A 214 HIS cc_start: 0.7800 (m90) cc_final: 0.6845 (m-70) REVERT: A 231 ASP cc_start: 0.9030 (m-30) cc_final: 0.8490 (m-30) REVERT: A 261 LEU cc_start: 0.9083 (mp) cc_final: 0.8823 (mt) REVERT: A 291 MET cc_start: 0.8875 (mmm) cc_final: 0.8431 (tpt) REVERT: A 296 ARG cc_start: 0.5727 (mtt180) cc_final: 0.5394 (ttt180) REVERT: A 303 ASN cc_start: 0.9295 (m110) cc_final: 0.9093 (p0) REVERT: A 312 MET cc_start: 0.8762 (mmm) cc_final: 0.8259 (mtt) REVERT: B 54 ASP cc_start: 0.9412 (m-30) cc_final: 0.8909 (t0) REVERT: B 75 MET cc_start: 0.9390 (mmm) cc_final: 0.9081 (mmm) REVERT: B 98 MET cc_start: 0.9063 (ttm) cc_final: 0.8506 (ttm) REVERT: B 102 ARG cc_start: 0.8871 (ttm170) cc_final: 0.8263 (mtt-85) REVERT: B 105 PHE cc_start: 0.9017 (m-80) cc_final: 0.8460 (m-80) REVERT: B 121 THR cc_start: 0.9385 (p) cc_final: 0.9078 (t) REVERT: B 131 ASP cc_start: 0.8485 (m-30) cc_final: 0.8220 (m-30) REVERT: B 133 GLU cc_start: 0.9062 (pt0) cc_final: 0.8846 (pt0) REVERT: B 156 LEU cc_start: 0.9475 (mt) cc_final: 0.9076 (pp) REVERT: B 161 PHE cc_start: 0.8684 (m-10) cc_final: 0.8248 (m-10) REVERT: B 224 GLU cc_start: 0.9478 (mp0) cc_final: 0.9258 (mp0) REVERT: B 242 MET cc_start: 0.9126 (mpp) cc_final: 0.8723 (mmt) REVERT: B 291 MET cc_start: 0.9073 (ttt) cc_final: 0.8091 (tpt) REVERT: B 294 LEU cc_start: 0.9540 (mt) cc_final: 0.9260 (mt) REVERT: B 296 ARG cc_start: 0.5579 (mtt180) cc_final: 0.4724 (ttm170) REVERT: B 328 LYS cc_start: 0.9126 (mmtm) cc_final: 0.8716 (mmtt) REVERT: B 329 ASP cc_start: 0.8774 (m-30) cc_final: 0.8050 (t0) outliers start: 1 outliers final: 0 residues processed: 250 average time/residue: 0.1447 time to fit residues: 50.7374 Evaluate side-chains 198 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 53 optimal weight: 7.9990 chunk 98 optimal weight: 30.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.5038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7090 Z= 0.219 Angle : 0.666 9.446 9661 Z= 0.355 Chirality : 0.044 0.161 1212 Planarity : 0.004 0.074 1249 Dihedral : 4.235 22.502 1106 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % 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: 0.51 (0.27), residues: 1058 helix: 1.36 (0.20), residues: 734 sheet: -1.20 (0.82), residues: 39 loop : -2.19 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 91 HIS 0.004 0.001 HIS A 107 PHE 0.034 0.002 PHE B 288 TYR 0.010 0.001 TYR B 87 ARG 0.006 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.9478 (mt) cc_final: 0.9241 (mt) REVERT: A 75 MET cc_start: 0.9101 (mmm) cc_final: 0.8644 (mmm) REVERT: A 98 MET cc_start: 0.8818 (tpp) cc_final: 0.8315 (tpp) REVERT: A 100 MET cc_start: 0.9466 (mmm) cc_final: 0.9220 (mmp) REVERT: A 105 PHE cc_start: 0.9410 (m-80) cc_final: 0.8872 (m-80) REVERT: A 131 ASP cc_start: 0.8671 (m-30) cc_final: 0.8379 (m-30) REVERT: A 159 MET cc_start: 0.8980 (tpp) cc_final: 0.8680 (tpp) REVERT: A 161 PHE cc_start: 0.8580 (m-10) cc_final: 0.8179 (m-10) REVERT: A 208 GLU cc_start: 0.9244 (tm-30) cc_final: 0.8853 (tm-30) REVERT: A 212 LYS cc_start: 0.9416 (mttt) cc_final: 0.8950 (pttp) REVERT: A 231 ASP cc_start: 0.9050 (m-30) cc_final: 0.8692 (m-30) REVERT: A 235 ASN cc_start: 0.9228 (m-40) cc_final: 0.8470 (m-40) REVERT: A 242 MET cc_start: 0.9215 (mmp) cc_final: 0.8997 (mmm) REVERT: A 261 LEU cc_start: 0.9121 (mp) cc_final: 0.8852 (mt) REVERT: A 291 MET cc_start: 0.8943 (mmm) cc_final: 0.8460 (tpt) REVERT: A 296 ARG cc_start: 0.5764 (mtt180) cc_final: 0.5197 (ttm170) REVERT: A 301 LEU cc_start: 0.9190 (mt) cc_final: 0.8981 (mp) REVERT: A 312 MET cc_start: 0.8793 (mmm) cc_final: 0.8296 (mtt) REVERT: B 54 ASP cc_start: 0.9443 (m-30) cc_final: 0.9002 (t0) REVERT: B 75 MET cc_start: 0.9410 (mmm) cc_final: 0.9088 (mmm) REVERT: B 98 MET cc_start: 0.9105 (ttm) cc_final: 0.8818 (ttm) REVERT: B 105 PHE cc_start: 0.9095 (m-80) cc_final: 0.8638 (m-80) REVERT: B 121 THR cc_start: 0.9407 (p) cc_final: 0.9117 (t) REVERT: B 127 ARG cc_start: 0.9076 (tpp80) cc_final: 0.8762 (tpp-160) REVERT: B 160 MET cc_start: 0.9084 (ptp) cc_final: 0.8791 (ptp) REVERT: B 161 PHE cc_start: 0.8731 (m-10) cc_final: 0.8267 (m-10) REVERT: B 242 MET cc_start: 0.9125 (mpp) cc_final: 0.8876 (mmm) REVERT: B 296 ARG cc_start: 0.5544 (mtt180) cc_final: 0.4846 (ttm170) REVERT: B 328 LYS cc_start: 0.9033 (mmtm) cc_final: 0.8677 (mmtt) REVERT: B 329 ASP cc_start: 0.8800 (m-30) cc_final: 0.8099 (t0) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1535 time to fit residues: 49.3968 Evaluate side-chains 194 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 86 optimal weight: 0.0070 chunk 57 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7090 Z= 0.189 Angle : 0.652 13.303 9661 Z= 0.343 Chirality : 0.044 0.221 1212 Planarity : 0.005 0.080 1249 Dihedral : 4.079 17.654 1106 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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: 0.72 (0.27), residues: 1058 helix: 1.48 (0.20), residues: 735 sheet: -1.09 (0.82), residues: 39 loop : -1.98 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 91 HIS 0.004 0.001 HIS A 107 PHE 0.028 0.002 PHE A 308 TYR 0.010 0.001 TYR B 87 ARG 0.004 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.9458 (mt) cc_final: 0.9209 (mt) REVERT: A 75 MET cc_start: 0.9059 (mmm) cc_final: 0.8584 (mmm) REVERT: A 98 MET cc_start: 0.8717 (tpp) cc_final: 0.8143 (tpp) REVERT: A 100 MET cc_start: 0.9405 (mmm) cc_final: 0.9148 (mmp) REVERT: A 105 PHE cc_start: 0.9336 (m-80) cc_final: 0.8817 (m-80) REVERT: A 127 ARG cc_start: 0.8920 (tpp-160) cc_final: 0.8680 (tpp-160) REVERT: A 131 ASP cc_start: 0.8624 (m-30) cc_final: 0.8395 (m-30) REVERT: A 133 GLU cc_start: 0.9499 (mt-10) cc_final: 0.9126 (pt0) REVERT: A 159 MET cc_start: 0.8802 (tpp) cc_final: 0.8585 (tpp) REVERT: A 160 MET cc_start: 0.8769 (ptp) cc_final: 0.8551 (ptp) REVERT: A 161 PHE cc_start: 0.8539 (m-10) cc_final: 0.8125 (m-10) REVERT: A 208 GLU cc_start: 0.9201 (tm-30) cc_final: 0.8818 (tm-30) REVERT: A 212 LYS cc_start: 0.9395 (mttt) cc_final: 0.8915 (pttp) REVERT: A 231 ASP cc_start: 0.8952 (m-30) cc_final: 0.8656 (m-30) REVERT: A 235 ASN cc_start: 0.9152 (m-40) cc_final: 0.8597 (m110) REVERT: A 291 MET cc_start: 0.8906 (mmm) cc_final: 0.8472 (tpt) REVERT: A 296 ARG cc_start: 0.5838 (mtt180) cc_final: 0.5486 (ttt180) REVERT: A 312 MET cc_start: 0.8726 (mmm) cc_final: 0.8265 (mtt) REVERT: B 54 ASP cc_start: 0.9404 (m-30) cc_final: 0.8880 (t0) REVERT: B 75 MET cc_start: 0.9384 (mmm) cc_final: 0.9146 (mmm) REVERT: B 98 MET cc_start: 0.9023 (ttm) cc_final: 0.8739 (ttm) REVERT: B 105 PHE cc_start: 0.9053 (m-80) cc_final: 0.8587 (m-80) REVERT: B 121 THR cc_start: 0.9382 (p) cc_final: 0.9095 (t) REVERT: B 127 ARG cc_start: 0.8982 (tpp80) cc_final: 0.8711 (tpp-160) REVERT: B 156 LEU cc_start: 0.9470 (mt) cc_final: 0.9095 (pp) REVERT: B 161 PHE cc_start: 0.8664 (m-10) cc_final: 0.8198 (m-10) REVERT: B 231 ASP cc_start: 0.9357 (m-30) cc_final: 0.9099 (m-30) REVERT: B 242 MET cc_start: 0.9137 (mpp) cc_final: 0.8698 (mmt) REVERT: B 291 MET cc_start: 0.9068 (ttt) cc_final: 0.8037 (tpt) REVERT: B 294 LEU cc_start: 0.9557 (mt) cc_final: 0.9295 (mt) REVERT: B 296 ARG cc_start: 0.5466 (mtt180) cc_final: 0.4721 (ttm170) REVERT: B 328 LYS cc_start: 0.9042 (mmtm) cc_final: 0.8663 (mmtt) REVERT: B 329 ASP cc_start: 0.8752 (m-30) cc_final: 0.8030 (t0) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.1519 time to fit residues: 53.4186 Evaluate side-chains 197 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 64 optimal weight: 0.0770 chunk 69 optimal weight: 0.9990 chunk 50 optimal weight: 30.0000 chunk 9 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 89 optimal weight: 30.0000 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.5721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7090 Z= 0.190 Angle : 0.666 10.603 9661 Z= 0.346 Chirality : 0.045 0.169 1212 Planarity : 0.004 0.077 1249 Dihedral : 4.024 18.748 1106 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % 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: 0.78 (0.27), residues: 1058 helix: 1.46 (0.20), residues: 735 sheet: -1.06 (0.82), residues: 39 loop : -1.76 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 91 HIS 0.004 0.001 HIS A 107 PHE 0.020 0.001 PHE B 56 TYR 0.012 0.001 TYR A 87 ARG 0.003 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.9445 (mt) cc_final: 0.9199 (mt) REVERT: A 98 MET cc_start: 0.8745 (tpp) cc_final: 0.8166 (tpp) REVERT: A 100 MET cc_start: 0.9384 (mmm) cc_final: 0.9147 (mmp) REVERT: A 105 PHE cc_start: 0.9291 (m-80) cc_final: 0.8827 (m-80) REVERT: A 131 ASP cc_start: 0.8641 (m-30) cc_final: 0.8376 (m-30) REVERT: A 133 GLU cc_start: 0.9508 (mt-10) cc_final: 0.9058 (pt0) REVERT: A 161 PHE cc_start: 0.8502 (m-10) cc_final: 0.8073 (m-10) REVERT: A 208 GLU cc_start: 0.9190 (tm-30) cc_final: 0.8800 (tm-30) REVERT: A 211 LEU cc_start: 0.9652 (mt) cc_final: 0.9188 (mt) REVERT: A 212 LYS cc_start: 0.9414 (mttt) cc_final: 0.8980 (pttp) REVERT: A 214 HIS cc_start: 0.7879 (m90) cc_final: 0.7278 (m90) REVERT: A 231 ASP cc_start: 0.8972 (m-30) cc_final: 0.8630 (m-30) REVERT: A 235 ASN cc_start: 0.9197 (m-40) cc_final: 0.8683 (m110) REVERT: A 242 MET cc_start: 0.9237 (mmp) cc_final: 0.8947 (mmm) REVERT: A 291 MET cc_start: 0.8880 (mmm) cc_final: 0.8464 (tpt) REVERT: A 296 ARG cc_start: 0.5719 (mtt180) cc_final: 0.5305 (ttt180) REVERT: A 312 MET cc_start: 0.8678 (mmm) cc_final: 0.8276 (mtt) REVERT: B 54 ASP cc_start: 0.9394 (m-30) cc_final: 0.8831 (t0) REVERT: B 75 MET cc_start: 0.9384 (mmm) cc_final: 0.9167 (mmm) REVERT: B 98 MET cc_start: 0.9042 (ttm) cc_final: 0.7567 (ttm) REVERT: B 102 ARG cc_start: 0.8895 (ttm170) cc_final: 0.8242 (ttm110) REVERT: B 105 PHE cc_start: 0.9004 (m-80) cc_final: 0.8646 (m-80) REVERT: B 121 THR cc_start: 0.9377 (p) cc_final: 0.9091 (t) REVERT: B 127 ARG cc_start: 0.8974 (tpp80) cc_final: 0.8731 (tpp-160) REVERT: B 156 LEU cc_start: 0.9503 (mt) cc_final: 0.9136 (pp) REVERT: B 161 PHE cc_start: 0.8535 (m-10) cc_final: 0.8087 (m-10) REVERT: B 231 ASP cc_start: 0.9332 (m-30) cc_final: 0.9059 (m-30) REVERT: B 242 MET cc_start: 0.9091 (mpp) cc_final: 0.8765 (mmt) REVERT: B 288 PHE cc_start: 0.8792 (m-80) cc_final: 0.8562 (m-80) REVERT: B 291 MET cc_start: 0.9015 (ttt) cc_final: 0.8061 (tpt) REVERT: B 294 LEU cc_start: 0.9584 (mt) cc_final: 0.9378 (mt) REVERT: B 296 ARG cc_start: 0.5696 (mtt180) cc_final: 0.5254 (ttp-170) REVERT: B 329 ASP cc_start: 0.8788 (m-30) cc_final: 0.8033 (t0) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.1562 time to fit residues: 52.5180 Evaluate side-chains 190 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 41 optimal weight: 0.0020 chunk 74 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 86 optimal weight: 0.0030 chunk 90 optimal weight: 8.9990 chunk 94 optimal weight: 0.4980 chunk 62 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.6078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7090 Z= 0.185 Angle : 0.658 8.893 9661 Z= 0.340 Chirality : 0.044 0.160 1212 Planarity : 0.004 0.080 1249 Dihedral : 3.937 15.925 1106 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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: 0.82 (0.27), residues: 1058 helix: 1.50 (0.20), residues: 727 sheet: -0.95 (0.91), residues: 35 loop : -1.71 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 91 HIS 0.004 0.001 HIS A 107 PHE 0.017 0.001 PHE B 56 TYR 0.008 0.001 TYR A 163 ARG 0.001 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.9429 (mt) cc_final: 0.9213 (mt) REVERT: A 75 MET cc_start: 0.9182 (mmm) cc_final: 0.8951 (mmm) REVERT: A 98 MET cc_start: 0.8766 (tpp) cc_final: 0.8025 (tpp) REVERT: A 100 MET cc_start: 0.9354 (mmm) cc_final: 0.9099 (mmp) REVERT: A 105 PHE cc_start: 0.9275 (m-80) cc_final: 0.8633 (m-80) REVERT: A 131 ASP cc_start: 0.8607 (m-30) cc_final: 0.8293 (m-30) REVERT: A 133 GLU cc_start: 0.9501 (mt-10) cc_final: 0.9059 (pt0) REVERT: A 161 PHE cc_start: 0.8318 (m-10) cc_final: 0.7998 (m-10) REVERT: A 180 ILE cc_start: 0.9048 (tt) cc_final: 0.8790 (pt) REVERT: A 208 GLU cc_start: 0.9115 (tm-30) cc_final: 0.8697 (tm-30) REVERT: A 211 LEU cc_start: 0.9628 (mt) cc_final: 0.9158 (mt) REVERT: A 212 LYS cc_start: 0.9388 (mttt) cc_final: 0.9038 (pttp) REVERT: A 214 HIS cc_start: 0.7894 (m90) cc_final: 0.7272 (m90) REVERT: A 231 ASP cc_start: 0.8978 (m-30) cc_final: 0.8648 (m-30) REVERT: A 235 ASN cc_start: 0.9191 (m-40) cc_final: 0.8661 (m110) REVERT: A 242 MET cc_start: 0.9158 (mmp) cc_final: 0.8947 (mmm) REVERT: A 261 LEU cc_start: 0.8818 (mp) cc_final: 0.8430 (tp) REVERT: A 296 ARG cc_start: 0.5724 (mtt180) cc_final: 0.5090 (ttm170) REVERT: A 312 MET cc_start: 0.8652 (mmm) cc_final: 0.8248 (mtt) REVERT: B 16 LEU cc_start: 0.9485 (mt) cc_final: 0.8926 (pp) REVERT: B 54 ASP cc_start: 0.9364 (m-30) cc_final: 0.8789 (t0) REVERT: B 75 MET cc_start: 0.9347 (mmm) cc_final: 0.9139 (mmm) REVERT: B 98 MET cc_start: 0.9086 (ttm) cc_final: 0.7749 (ttm) REVERT: B 102 ARG cc_start: 0.8815 (ttm170) cc_final: 0.8245 (ttm170) REVERT: B 105 PHE cc_start: 0.8914 (m-80) cc_final: 0.8585 (m-80) REVERT: B 121 THR cc_start: 0.9346 (p) cc_final: 0.9068 (t) REVERT: B 131 ASP cc_start: 0.8577 (m-30) cc_final: 0.8312 (m-30) REVERT: B 153 ILE cc_start: 0.9377 (tt) cc_final: 0.8653 (tp) REVERT: B 156 LEU cc_start: 0.9481 (mt) cc_final: 0.9138 (pp) REVERT: B 231 ASP cc_start: 0.9303 (m-30) cc_final: 0.8644 (m-30) REVERT: B 235 ASN cc_start: 0.9570 (m-40) cc_final: 0.9158 (m110) REVERT: B 242 MET cc_start: 0.9059 (mpp) cc_final: 0.8830 (mpp) REVERT: B 288 PHE cc_start: 0.8761 (m-80) cc_final: 0.8418 (m-80) REVERT: B 291 MET cc_start: 0.9016 (ttt) cc_final: 0.8011 (tpt) REVERT: B 294 LEU cc_start: 0.9560 (mt) cc_final: 0.9168 (mt) REVERT: B 329 ASP cc_start: 0.8799 (m-30) cc_final: 0.8016 (t0) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.1528 time to fit residues: 52.6508 Evaluate side-chains 199 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 105 optimal weight: 40.0000 chunk 97 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.6235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7090 Z= 0.211 Angle : 0.690 8.496 9661 Z= 0.358 Chirality : 0.046 0.236 1212 Planarity : 0.005 0.077 1249 Dihedral : 3.977 17.431 1106 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: 0.84 (0.27), residues: 1058 helix: 1.50 (0.20), residues: 733 sheet: -1.32 (0.84), residues: 40 loop : -1.64 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 91 HIS 0.004 0.001 HIS A 107 PHE 0.019 0.001 PHE B 56 TYR 0.014 0.002 TYR B 87 ARG 0.003 0.000 ARG B 148 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.9414 (mt) cc_final: 0.9182 (mt) REVERT: A 75 MET cc_start: 0.9183 (mmm) cc_final: 0.8967 (mmm) REVERT: A 98 MET cc_start: 0.8827 (tpp) cc_final: 0.8338 (tpp) REVERT: A 100 MET cc_start: 0.9386 (mmm) cc_final: 0.9129 (mmp) REVERT: A 105 PHE cc_start: 0.9270 (m-80) cc_final: 0.8849 (m-80) REVERT: A 131 ASP cc_start: 0.8684 (m-30) cc_final: 0.8391 (m-30) REVERT: A 133 GLU cc_start: 0.9314 (mt-10) cc_final: 0.8922 (mt-10) REVERT: A 161 PHE cc_start: 0.8381 (m-10) cc_final: 0.8065 (m-10) REVERT: A 180 ILE cc_start: 0.9051 (tt) cc_final: 0.8806 (pt) REVERT: A 204 THR cc_start: 0.8935 (m) cc_final: 0.8677 (p) REVERT: A 208 GLU cc_start: 0.9123 (tm-30) cc_final: 0.8721 (tm-30) REVERT: A 211 LEU cc_start: 0.9648 (mt) cc_final: 0.9185 (mt) REVERT: A 212 LYS cc_start: 0.9394 (mttt) cc_final: 0.9042 (pttp) REVERT: A 214 HIS cc_start: 0.7902 (m90) cc_final: 0.7358 (m90) REVERT: A 231 ASP cc_start: 0.8988 (m-30) cc_final: 0.8680 (m-30) REVERT: A 235 ASN cc_start: 0.9223 (m-40) cc_final: 0.8717 (m110) REVERT: A 261 LEU cc_start: 0.8924 (mp) cc_final: 0.8513 (tp) REVERT: A 312 MET cc_start: 0.8661 (mmm) cc_final: 0.8274 (mtt) REVERT: B 54 ASP cc_start: 0.9404 (m-30) cc_final: 0.8819 (t0) REVERT: B 75 MET cc_start: 0.9361 (mmm) cc_final: 0.9039 (mmm) REVERT: B 98 MET cc_start: 0.9115 (ttm) cc_final: 0.7662 (ttm) REVERT: B 102 ARG cc_start: 0.8870 (ttm170) cc_final: 0.8257 (ttm170) REVERT: B 105 PHE cc_start: 0.8958 (m-80) cc_final: 0.8607 (m-80) REVERT: B 121 THR cc_start: 0.9369 (p) cc_final: 0.9073 (t) REVERT: B 131 ASP cc_start: 0.8488 (m-30) cc_final: 0.8194 (m-30) REVERT: B 231 ASP cc_start: 0.9182 (m-30) cc_final: 0.8839 (m-30) REVERT: B 242 MET cc_start: 0.9088 (mpp) cc_final: 0.8841 (mmt) REVERT: B 288 PHE cc_start: 0.8831 (m-80) cc_final: 0.8491 (m-80) REVERT: B 291 MET cc_start: 0.9061 (ttt) cc_final: 0.8044 (tpt) REVERT: B 312 MET cc_start: 0.8757 (tpp) cc_final: 0.7851 (tpp) REVERT: B 329 ASP cc_start: 0.8816 (m-30) cc_final: 0.7984 (t0) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.1475 time to fit residues: 48.2516 Evaluate side-chains 189 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 35 optimal weight: 40.0000 chunk 86 optimal weight: 0.0030 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.080090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.061735 restraints weight = 29412.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.063690 restraints weight = 19476.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.065146 restraints weight = 14157.431| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.6230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7090 Z= 0.247 Angle : 0.703 8.048 9661 Z= 0.368 Chirality : 0.046 0.216 1212 Planarity : 0.005 0.075 1249 Dihedral : 4.168 18.234 1106 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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: 0.75 (0.28), residues: 1058 helix: 1.32 (0.20), residues: 738 sheet: -1.39 (0.78), residues: 45 loop : -1.39 (0.41), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 91 HIS 0.004 0.001 HIS A 107 PHE 0.032 0.002 PHE A 308 TYR 0.017 0.002 TYR B 162 ARG 0.003 0.000 ARG B 148 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1693.17 seconds wall clock time: 31 minutes 20.79 seconds (1880.79 seconds total)