Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 3 12:42:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzl_20962/10_2023/6uzl_20962.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzl_20962/10_2023/6uzl_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_20962/10_2023/6uzl_20962.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzl_20962/10_2023/6uzl_20962.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzl_20962/10_2023/6uzl_20962.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzl_20962/10_2023/6uzl_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 4.42, per 1000 atoms: 0.63 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: 3.22 Conformation dependent library (CDL) restraints added in 1.2 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: 0.58 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: 2.17 Time building geometry restraints manager: 3.37 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: 0.840 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: 3.890 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 24.090 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.150 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.820 ------------------------------------------------------------------------------- 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 *********************** 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 : 0.864 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 outliers start: 1 outliers final: 0 residues processed: 230 average time/residue: 0.1872 time to fit residues: 56.8083 Evaluate side-chains 176 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 0.847 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0750 ------------------------------------------------------------------------------- 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: 1.9990 chunk 44 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 0.0870 chunk 50 optimal weight: 9.9990 chunk 61 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- 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 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7090 Z= 0.213 Angle : 0.665 6.805 9661 Z= 0.360 Chirality : 0.043 0.145 1212 Planarity : 0.005 0.085 1249 Dihedral : 4.818 19.976 1106 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 0.18 % Allowed : 4.72 % Favored : 95.10 % 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: -1.90 (0.24), residues: 1058 helix: -0.49 (0.18), residues: 726 sheet: -1.57 (0.88), residues: 34 loop : -2.96 (0.33), residues: 298 *********************** 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 244 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 243 time to evaluate : 0.793 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 outliers start: 1 outliers final: 0 residues processed: 243 average time/residue: 0.1526 time to fit residues: 51.4617 Evaluate side-chains 194 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 0.784 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1040 ------------------------------------------------------------------------------- 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: 6.9990 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 96 optimal weight: 0.0980 chunk 104 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 32 optimal weight: 0.0770 chunk 77 optimal weight: 2.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- 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 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7090 Z= 0.187 Angle : 0.637 7.252 9661 Z= 0.336 Chirality : 0.043 0.165 1212 Planarity : 0.005 0.081 1249 Dihedral : 4.413 21.340 1106 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 0.18 % Allowed : 3.99 % Favored : 95.83 % 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: -0.43 (0.26), residues: 1058 helix: 0.71 (0.19), residues: 730 sheet: -1.46 (0.86), residues: 34 loop : -2.68 (0.34), residues: 294 *********************** 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 229 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 228 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 228 average time/residue: 0.1439 time to fit residues: 46.3288 Evaluate side-chains 192 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 0.791 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0467 ------------------------------------------------------------------------------- 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: 4.9990 chunk 50 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 102 optimal weight: 30.0000 chunk 91 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 191 ASN ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 7090 Z= 0.385 Angle : 0.796 10.116 9661 Z= 0.442 Chirality : 0.046 0.167 1212 Planarity : 0.006 0.066 1249 Dihedral : 4.929 20.869 1106 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 24.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 0.36 % Allowed : 5.81 % Favored : 93.83 % 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: -0.98 (0.25), residues: 1058 helix: 0.24 (0.19), residues: 732 sheet: -1.08 (0.98), residues: 24 loop : -2.76 (0.34), residues: 302 *********************** 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 213 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 211 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 211 average time/residue: 0.1487 time to fit residues: 43.9153 Evaluate side-chains 173 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 0.846 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1258 ------------------------------------------------------------------------------- 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: 1.9990 chunk 1 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 87 optimal weight: 0.0670 chunk 70 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 91 optimal weight: 20.0000 chunk 25 optimal weight: 0.7980 chunk 34 optimal weight: 30.0000 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN A 198 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7090 Z= 0.192 Angle : 0.659 13.594 9661 Z= 0.344 Chirality : 0.043 0.222 1212 Planarity : 0.005 0.077 1249 Dihedral : 4.453 22.978 1106 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % 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: -0.05 (0.26), residues: 1058 helix: 0.94 (0.19), residues: 729 sheet: -1.04 (1.04), residues: 24 loop : -2.34 (0.34), residues: 305 *********************** 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 223 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1449 time to fit residues: 45.7795 Evaluate side-chains 186 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 0.730 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9779 ------------------------------------------------------------------------------- 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: 10.0000 chunk 60 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 85 optimal weight: 0.0570 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 98 optimal weight: 30.0000 overall best weight: 1.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7890 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7090 Z= 0.207 Angle : 0.660 8.458 9661 Z= 0.355 Chirality : 0.044 0.171 1212 Planarity : 0.005 0.075 1249 Dihedral : 4.365 17.847 1106 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % 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: 0.01 (0.26), residues: 1058 helix: 0.95 (0.19), residues: 729 sheet: -0.95 (1.06), residues: 24 loop : -2.23 (0.35), residues: 305 *********************** 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 218 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1428 time to fit residues: 44.6626 Evaluate side-chains 190 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 0.820 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1067 ------------------------------------------------------------------------------- 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: 0.6980 chunk 58 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 63 optimal weight: 0.0970 chunk 62 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7832 moved from start: 0.5675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7090 Z= 0.180 Angle : 0.649 6.809 9661 Z= 0.340 Chirality : 0.044 0.198 1212 Planarity : 0.005 0.078 1249 Dihedral : 4.212 17.992 1106 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % 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: 0.40 (0.27), residues: 1058 helix: 1.21 (0.19), residues: 732 sheet: -0.75 (1.07), residues: 24 loop : -2.02 (0.36), residues: 302 *********************** 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 221 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1501 time to fit residues: 46.7985 Evaluate side-chains 194 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 0.840 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1489 ------------------------------------------------------------------------------- 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: 3.9990 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 64 optimal weight: 0.4980 chunk 69 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 92 optimal weight: 30.0000 chunk 97 optimal weight: 8.9990 chunk 89 optimal weight: 0.0270 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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: 0.7825 moved from start: 0.5962 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 : 0.655 8.742 9661 Z= 0.345 Chirality : 0.044 0.181 1212 Planarity : 0.005 0.077 1249 Dihedral : 4.074 17.918 1106 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: 0.59 (0.27), residues: 1058 helix: 1.33 (0.20), residues: 731 sheet: -0.74 (1.05), residues: 24 loop : -1.86 (0.37), residues: 303 *********************** 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 238 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.1493 time to fit residues: 49.6886 Evaluate side-chains 190 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 0.834 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0838 ------------------------------------------------------------------------------- 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: 5.9990 chunk 97 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 30.0000 chunk 74 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 86 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 94 optimal weight: 30.0000 chunk 62 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 195 ASN ** 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: 0.7904 moved from start: 0.5988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7090 Z= 0.234 Angle : 0.692 6.780 9661 Z= 0.373 Chirality : 0.046 0.223 1212 Planarity : 0.005 0.075 1249 Dihedral : 4.228 20.793 1106 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % 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: 0.32 (0.27), residues: 1058 helix: 1.15 (0.20), residues: 730 sheet: -1.49 (0.78), residues: 45 loop : -1.93 (0.39), residues: 283 *********************** 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 219 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.1418 time to fit residues: 44.4436 Evaluate side-chains 178 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.788 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1261 ------------------------------------------------------------------------------- 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: 0.9980 chunk 47 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 105 optimal weight: 20.0000 chunk 97 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 307 GLN ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.6239 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= 0.199 Angle : 0.704 12.521 9661 Z= 0.366 Chirality : 0.046 0.211 1212 Planarity : 0.005 0.075 1249 Dihedral : 4.153 19.898 1106 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % 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: 0.47 (0.27), residues: 1058 helix: 1.20 (0.20), residues: 736 sheet: -0.52 (1.00), residues: 29 loop : -1.86 (0.38), residues: 293 ********************** 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 238 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.1464 time to fit residues: 49.6889 Evaluate side-chains 178 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.745 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0165 ------------------------------------------------------------------------------- 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: 6.9990 chunk 77 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 35 optimal weight: 50.0000 chunk 86 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.079937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.061202 restraints weight = 29684.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.063232 restraints weight = 19554.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.064736 restraints weight = 14150.287| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.6328 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= 0.225 Angle : 0.713 8.225 9661 Z= 0.378 Chirality : 0.046 0.241 1212 Planarity : 0.005 0.075 1249 Dihedral : 4.196 20.434 1106 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % 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: 0.50 (0.27), residues: 1058 helix: 1.18 (0.20), residues: 741 sheet: -0.89 (0.82), residues: 44 loop : -1.76 (0.40), residues: 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1569.95 seconds wall clock time: 29 minutes 7.19 seconds (1747.19 seconds total)