Starting phenix.real_space_refine on Sun Aug 4 05:53:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzb_38792/08_2024/8xzb_38792_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzb_38792/08_2024/8xzb_38792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzb_38792/08_2024/8xzb_38792.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzb_38792/08_2024/8xzb_38792.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzb_38792/08_2024/8xzb_38792_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzb_38792/08_2024/8xzb_38792_neut.cif" } resolution = 3.12 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4271 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 38 5.16 5 C 4110 2.51 5 N 1058 2.21 5 O 1205 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 206": "OD1" <-> "OD2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A ASP 303": "OD1" <-> "OD2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A ASP 382": "OD1" <-> "OD2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6412 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4885 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 29, 'TRANS': 566} Chain: "C" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1526 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 13, 'TRANS': 177} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.36, per 1000 atoms: 0.68 Number of scatterers: 6412 At special positions: 0 Unit cell: (75.21, 83.49, 120.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 38 16.00 O 1205 8.00 N 1058 7.00 C 4110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.65 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: 2.38 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 374 " 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 5 sheets defined 56.8% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.534A pdb=" N TYR A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A 38 " --> pdb=" O TYR A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 82 removed outlier: 3.746A pdb=" N THR A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.742A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 218 through 252 removed outlier: 3.817A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.521A pdb=" N ASP A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 268 removed outlier: 3.935A pdb=" N GLY A 268 " --> pdb=" O HIS A 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 265 through 268' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.695A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 Processing helix chain 'A' and resid 397 through 414 removed outlier: 4.119A pdb=" N HIS A 401 " --> pdb=" O ASN A 397 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 466 removed outlier: 3.512A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 485 Processing helix chain 'A' and resid 498 through 503 removed outlier: 3.623A pdb=" N SER A 502 " --> pdb=" O CYS A 498 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU A 503 " --> pdb=" O ASP A 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 498 through 503' Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 534 removed outlier: 4.062A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 561 removed outlier: 3.581A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.552A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 602 removed outlier: 4.636A pdb=" N ASN A 601 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER A 602 " --> pdb=" O GLN A 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 330 Processing helix chain 'C' and resid 352 through 358 removed outlier: 3.642A pdb=" N TYR C 356 " --> pdb=" O TYR C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 395 removed outlier: 3.765A pdb=" N ARG C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 392 through 395' Processing helix chain 'C' and resid 404 through 409 Processing helix chain 'C' and resid 425 through 430 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.310A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.445A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.690A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER C 386 " --> pdb=" O GLU C 341 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ASN C 381 " --> pdb=" O GLU C 502 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU C 502 " --> pdb=" O ASN C 381 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 439 through 441 311 hydrogen bonds defined for protein. 924 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.61 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1962 1.33 - 1.45: 1141 1.45 - 1.57: 3437 1.57 - 1.69: 1 1.69 - 1.81: 60 Bond restraints: 6601 Sorted by residual: bond pdb=" C LYS A 564 " pdb=" N PRO A 565 " ideal model delta sigma weight residual 1.330 1.389 -0.059 1.25e-02 6.40e+03 2.26e+01 bond pdb=" CA ILE A 233 " pdb=" C ILE A 233 " ideal model delta sigma weight residual 1.518 1.568 -0.049 1.13e-02 7.83e+03 1.91e+01 bond pdb=" CA PRO C 469 " pdb=" C PRO C 469 " ideal model delta sigma weight residual 1.517 1.556 -0.039 9.30e-03 1.16e+04 1.73e+01 bond pdb=" C PRO C 469 " pdb=" N PRO C 470 " ideal model delta sigma weight residual 1.333 1.362 -0.029 7.80e-03 1.64e+04 1.37e+01 bond pdb=" CA GLN A 325 " pdb=" C GLN A 325 " ideal model delta sigma weight residual 1.524 1.571 -0.047 1.28e-02 6.10e+03 1.34e+01 ... (remaining 6596 not shown) Histogram of bond angle deviations from ideal: 97.66 - 105.42: 211 105.42 - 113.18: 3136 113.18 - 120.94: 3933 120.94 - 128.70: 1614 128.70 - 136.46: 85 Bond angle restraints: 8979 Sorted by residual: angle pdb=" N TYR A 202 " pdb=" CA TYR A 202 " pdb=" C TYR A 202 " ideal model delta sigma weight residual 111.07 97.66 13.41 1.07e+00 8.73e-01 1.57e+02 angle pdb=" N LYS A 112 " pdb=" CA LYS A 112 " pdb=" C LYS A 112 " ideal model delta sigma weight residual 111.36 98.79 12.57 1.09e+00 8.42e-01 1.33e+02 angle pdb=" N GLU C 327 " pdb=" CA GLU C 327 " pdb=" C GLU C 327 " ideal model delta sigma weight residual 111.28 123.82 -12.54 1.09e+00 8.42e-01 1.32e+02 angle pdb=" N PRO C 469 " pdb=" CA PRO C 469 " pdb=" C PRO C 469 " ideal model delta sigma weight residual 110.70 124.43 -13.73 1.22e+00 6.72e-01 1.27e+02 angle pdb=" N GLU A 212 " pdb=" CA GLU A 212 " pdb=" C GLU A 212 " ideal model delta sigma weight residual 111.07 122.83 -11.76 1.07e+00 8.73e-01 1.21e+02 ... (remaining 8974 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 3375 17.64 - 35.27: 334 35.27 - 52.90: 121 52.90 - 70.54: 41 70.54 - 88.17: 12 Dihedral angle restraints: 3883 sinusoidal: 1561 harmonic: 2322 Sorted by residual: dihedral pdb=" N PRO C 469 " pdb=" C PRO C 469 " pdb=" CA PRO C 469 " pdb=" CB PRO C 469 " ideal model delta harmonic sigma weight residual 115.10 127.99 -12.89 0 2.50e+00 1.60e-01 2.66e+01 dihedral pdb=" N PHE A 512 " pdb=" C PHE A 512 " pdb=" CA PHE A 512 " pdb=" CB PHE A 512 " ideal model delta harmonic sigma weight residual 122.80 110.27 12.53 0 2.50e+00 1.60e-01 2.51e+01 dihedral pdb=" C PHE A 512 " pdb=" N PHE A 512 " pdb=" CA PHE A 512 " pdb=" CB PHE A 512 " ideal model delta harmonic sigma weight residual -122.60 -110.20 -12.40 0 2.50e+00 1.60e-01 2.46e+01 ... (remaining 3880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 700 0.126 - 0.252: 180 0.252 - 0.378: 40 0.378 - 0.504: 11 0.504 - 0.630: 2 Chirality restraints: 933 Sorted by residual: chirality pdb=" CA PRO C 469 " pdb=" N PRO C 469 " pdb=" C PRO C 469 " pdb=" CB PRO C 469 " both_signs ideal model delta sigma weight residual False 2.72 2.09 0.63 2.00e-01 2.50e+01 9.91e+00 chirality pdb=" CA PHE C 460 " pdb=" N PHE C 460 " pdb=" C PHE C 460 " pdb=" CB PHE C 460 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.60e+00 chirality pdb=" CA ASN C 473 " pdb=" N ASN C 473 " pdb=" C ASN C 473 " pdb=" CB ASN C 473 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.34e+00 ... (remaining 930 not shown) Planarity restraints: 1160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 468 " -0.076 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO C 469 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO C 469 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 469 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR C 332 " -0.019 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" C THR C 332 " 0.066 2.00e-02 2.50e+03 pdb=" O THR C 332 " -0.025 2.00e-02 2.50e+03 pdb=" N LYS C 333 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 145 " 0.063 5.00e-02 4.00e+02 9.40e-02 1.41e+01 pdb=" N PRO A 146 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " 0.055 5.00e-02 4.00e+02 ... (remaining 1157 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 35 2.53 - 3.12: 5026 3.12 - 3.72: 10271 3.72 - 4.31: 14654 4.31 - 4.90: 23115 Nonbonded interactions: 53101 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 701 " model vdw 1.941 2.230 nonbonded pdb=" O ASN C 330 " pdb=" OD1 ASN C 330 " model vdw 2.076 3.040 nonbonded pdb=" OD1 ASN C 427 " pdb=" N ILE C 428 " model vdw 2.106 3.120 nonbonded pdb=" OD1 ASP C 351 " pdb=" N TYR C 352 " model vdw 2.188 3.120 nonbonded pdb=" CB TYR C 440 " pdb=" OH TYR C 481 " model vdw 2.198 3.440 ... (remaining 53096 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.480 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.160 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 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 : 0.007 0.059 6601 Z= 0.442 Angle : 1.640 13.730 8979 Z= 1.182 Chirality : 0.126 0.630 933 Planarity : 0.009 0.114 1160 Dihedral : 17.473 88.173 2390 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.51 % Allowed : 1.66 % Favored : 97.83 % Rotamer: Outliers : 4.45 % Allowed : 14.49 % Favored : 81.06 % Cbeta Deviations : 1.07 % 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: 2.75 (0.29), residues: 783 helix: 3.39 (0.25), residues: 379 sheet: 2.08 (0.69), residues: 49 loop : 0.02 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.018 0.002 PHE A 512 TYR 0.018 0.002 TYR A 385 ARG 0.003 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 121 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 329 PHE cc_start: 0.6610 (t80) cc_final: 0.6032 (t80) REVERT: C 419 CYS cc_start: 0.6266 (m) cc_final: 0.5481 (m) outliers start: 31 outliers final: 2 residues processed: 144 average time/residue: 0.2418 time to fit residues: 43.4065 Evaluate side-chains 62 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain C residue 465 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 32 optimal weight: 0.0980 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 96 GLN A 194 ASN A 373 HIS A 401 HIS A 546 ASN A 598 GLN C 330 ASN C 381 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6601 Z= 0.318 Angle : 0.727 10.032 8979 Z= 0.398 Chirality : 0.046 0.218 933 Planarity : 0.006 0.044 1160 Dihedral : 5.901 57.014 869 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.53 % Favored : 98.21 % Rotamer: Outliers : 3.01 % Allowed : 16.50 % Favored : 80.49 % 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: 2.02 (0.29), residues: 783 helix: 2.61 (0.26), residues: 383 sheet: 0.83 (0.68), residues: 51 loop : 0.01 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 271 HIS 0.005 0.001 HIS A 265 PHE 0.028 0.002 PHE C 483 TYR 0.024 0.002 TYR A 613 ARG 0.004 0.001 ARG C 395 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 67 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 82 average time/residue: 0.1890 time to fit residues: 20.9928 Evaluate side-chains 69 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain C residue 360 PHE Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 465 LYS Chi-restraints excluded: chain C residue 467 CYS Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 496 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 76 optimal weight: 0.0370 chunk 63 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 56 optimal weight: 0.2980 chunk 53 optimal weight: 0.6980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 194 ASN C 473 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6601 Z= 0.189 Angle : 0.612 10.708 8979 Z= 0.328 Chirality : 0.042 0.270 933 Planarity : 0.004 0.037 1160 Dihedral : 5.291 54.204 865 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.17 % Favored : 97.70 % Rotamer: Outliers : 2.15 % Allowed : 16.07 % Favored : 81.78 % 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: 2.07 (0.30), residues: 783 helix: 2.57 (0.26), residues: 388 sheet: 0.65 (0.71), residues: 46 loop : 0.14 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.010 0.001 HIS A 401 PHE 0.016 0.001 PHE C 483 TYR 0.028 0.001 TYR A 613 ARG 0.003 0.000 ARG C 395 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 64 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 76 average time/residue: 0.2071 time to fit residues: 20.7832 Evaluate side-chains 67 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 496 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 37 optimal weight: 0.0870 chunk 67 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 overall best weight: 2.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6601 Z= 0.300 Angle : 0.636 11.594 8979 Z= 0.338 Chirality : 0.042 0.182 933 Planarity : 0.004 0.042 1160 Dihedral : 5.045 25.742 861 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.55 % Favored : 97.32 % Rotamer: Outliers : 2.30 % Allowed : 15.78 % Favored : 81.92 % 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: 1.99 (0.30), residues: 783 helix: 2.44 (0.25), residues: 388 sheet: 0.59 (0.79), residues: 40 loop : 0.19 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 165 HIS 0.006 0.001 HIS A 401 PHE 0.017 0.002 PHE A 523 TYR 0.024 0.001 TYR A 613 ARG 0.004 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 62 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 366 MET cc_start: 0.5965 (mtp) cc_final: 0.5558 (ttm) outliers start: 16 outliers final: 9 residues processed: 74 average time/residue: 0.2160 time to fit residues: 21.1343 Evaluate side-chains 67 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 417 MET Chi-restraints excluded: chain C residue 465 LYS Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 496 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 31 optimal weight: 0.0670 chunk 64 optimal weight: 20.0000 chunk 52 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 0.0570 chunk 14 optimal weight: 1.9990 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 424 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6601 Z= 0.169 Angle : 0.581 12.405 8979 Z= 0.302 Chirality : 0.040 0.186 933 Planarity : 0.004 0.046 1160 Dihedral : 4.718 22.655 861 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.55 % Favored : 97.32 % Rotamer: Outliers : 1.58 % Allowed : 16.93 % Favored : 81.49 % 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: 1.97 (0.30), residues: 783 helix: 2.44 (0.26), residues: 390 sheet: 0.64 (0.79), residues: 40 loop : 0.14 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 163 HIS 0.002 0.001 HIS A 265 PHE 0.018 0.001 PHE C 361 TYR 0.024 0.001 TYR A 613 ARG 0.003 0.000 ARG C 395 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 69 average time/residue: 0.2182 time to fit residues: 20.0020 Evaluate side-chains 64 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 417 MET Chi-restraints excluded: chain C residue 496 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 0.2980 chunk 75 optimal weight: 7.9990 chunk 62 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 chunk 24 optimal weight: 0.0070 chunk 39 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 overall best weight: 0.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6601 Z= 0.161 Angle : 0.556 14.023 8979 Z= 0.286 Chirality : 0.039 0.172 933 Planarity : 0.004 0.047 1160 Dihedral : 4.521 21.735 861 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.43 % Favored : 97.45 % Rotamer: Outliers : 2.01 % Allowed : 17.36 % Favored : 80.63 % 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: 2.03 (0.30), residues: 783 helix: 2.59 (0.25), residues: 388 sheet: 0.46 (0.77), residues: 38 loop : 0.08 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 163 HIS 0.006 0.001 HIS A 378 PHE 0.011 0.001 PHE C 325 TYR 0.023 0.001 TYR A 613 ARG 0.003 0.000 ARG C 449 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 69 average time/residue: 0.2000 time to fit residues: 18.3737 Evaluate side-chains 68 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 366 CYS Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 465 LYS Chi-restraints excluded: chain C residue 467 CYS Chi-restraints excluded: chain C residue 496 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 63 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6601 Z= 0.203 Angle : 0.570 11.394 8979 Z= 0.293 Chirality : 0.039 0.194 933 Planarity : 0.004 0.046 1160 Dihedral : 4.497 21.797 861 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.17 % Favored : 97.70 % Rotamer: Outliers : 1.72 % Allowed : 17.79 % Favored : 80.49 % 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: 2.06 (0.30), residues: 783 helix: 2.64 (0.26), residues: 388 sheet: 0.36 (0.78), residues: 38 loop : 0.06 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 165 HIS 0.003 0.001 HIS A 378 PHE 0.013 0.001 PHE C 361 TYR 0.022 0.001 TYR A 613 ARG 0.004 0.000 ARG C 449 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 time to evaluate : 0.788 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 62 average time/residue: 0.2233 time to fit residues: 18.3298 Evaluate side-chains 64 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 366 CYS Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 465 LYS Chi-restraints excluded: chain C residue 467 CYS Chi-restraints excluded: chain C residue 496 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 0.0870 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 0.0270 chunk 59 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 72 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.5620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6601 Z= 0.157 Angle : 0.552 11.988 8979 Z= 0.281 Chirality : 0.038 0.193 933 Planarity : 0.004 0.046 1160 Dihedral : 4.345 20.855 861 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.15 % Allowed : 18.51 % Favored : 80.34 % 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: 2.00 (0.30), residues: 783 helix: 2.59 (0.26), residues: 394 sheet: 0.42 (0.81), residues: 38 loop : -0.01 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 163 HIS 0.002 0.000 HIS A 265 PHE 0.015 0.001 PHE C 325 TYR 0.022 0.001 TYR A 613 ARG 0.005 0.000 ARG C 449 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.7029 (mmm) cc_final: 0.6733 (mtt) outliers start: 8 outliers final: 5 residues processed: 65 average time/residue: 0.2209 time to fit residues: 19.0973 Evaluate side-chains 60 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 496 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6601 Z= 0.203 Angle : 0.579 10.234 8979 Z= 0.297 Chirality : 0.039 0.176 933 Planarity : 0.004 0.047 1160 Dihedral : 4.399 19.722 861 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.68 % Favored : 97.19 % Rotamer: Outliers : 1.00 % Allowed : 19.23 % Favored : 79.77 % 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: 2.03 (0.30), residues: 783 helix: 2.65 (0.26), residues: 394 sheet: 0.46 (0.81), residues: 38 loop : -0.06 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 165 HIS 0.003 0.001 HIS A 378 PHE 0.039 0.001 PHE C 501 TYR 0.021 0.001 TYR A 613 ARG 0.005 0.000 ARG C 449 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.7000 (mmm) cc_final: 0.6761 (mtt) outliers start: 7 outliers final: 5 residues processed: 57 average time/residue: 0.2319 time to fit residues: 17.4957 Evaluate side-chains 57 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 465 LYS Chi-restraints excluded: chain C residue 496 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.0030 chunk 71 optimal weight: 3.9990 chunk 61 optimal weight: 0.0050 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 37 optimal weight: 0.3980 chunk 49 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 overall best weight: 0.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6601 Z= 0.169 Angle : 0.568 11.103 8979 Z= 0.290 Chirality : 0.038 0.179 933 Planarity : 0.004 0.047 1160 Dihedral : 4.318 19.612 861 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.72 % Allowed : 20.09 % Favored : 79.20 % 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: 1.95 (0.30), residues: 783 helix: 2.62 (0.26), residues: 394 sheet: 0.47 (0.84), residues: 40 loop : -0.15 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 477 HIS 0.001 0.000 HIS A 378 PHE 0.025 0.001 PHE C 325 TYR 0.021 0.001 TYR A 613 ARG 0.004 0.000 ARG C 449 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 58 average time/residue: 0.2216 time to fit residues: 17.3933 Evaluate side-chains 58 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 496 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 3.9990 chunk 61 optimal weight: 0.0870 chunk 25 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 70 optimal weight: 0.0040 chunk 41 optimal weight: 6.9990 overall best weight: 0.4970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.055873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.040703 restraints weight = 28000.322| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 5.12 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.5465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6601 Z= 0.167 Angle : 0.590 14.530 8979 Z= 0.296 Chirality : 0.039 0.171 933 Planarity : 0.004 0.048 1160 Dihedral : 4.264 19.457 861 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.57 % Allowed : 20.23 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.30), residues: 783 helix: 2.65 (0.26), residues: 394 sheet: 0.30 (0.84), residues: 40 loop : -0.18 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 163 HIS 0.002 0.000 HIS A 378 PHE 0.025 0.001 PHE C 325 TYR 0.021 0.001 TYR A 385 ARG 0.004 0.000 ARG C 449 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1640.48 seconds wall clock time: 29 minutes 51.42 seconds (1791.42 seconds total)