Starting phenix.real_space_refine on Sun Dec 29 22:05:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wsh_32758/12_2024/7wsh_32758.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsh_32758/12_2024/7wsh_32758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wsh_32758/12_2024/7wsh_32758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsh_32758/12_2024/7wsh_32758.map" model { file = "/net/cci-nas-00/data/ceres_data/7wsh_32758/12_2024/7wsh_32758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsh_32758/12_2024/7wsh_32758.cif" } resolution = 2.89 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= 0.061 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 6216 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 37 5.16 5 C 4119 2.51 5 N 1082 2.21 5 O 1218 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6457 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4899 Classifications: {'peptide': 598} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 568} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.06, per 1000 atoms: 0.78 Number of scatterers: 6457 At special positions: 0 Unit cell: (72.921, 84.963, 127.11, 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 37 16.00 O 1218 8.00 N 1082 7.00 C 4119 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG B 601 " - " ASN B 343 " Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 915.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 56.9% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.720A pdb=" N GLU A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.655A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.550A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 194 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: 4.074A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.835A pdb=" N ASP A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) 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 318 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.562A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.589A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.610A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 414 removed outlier: 3.688A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 446 removed outlier: 3.577A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 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 484 removed outlier: 3.636A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.083A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.835A pdb=" N MET A 557 " --> pdb=" O THR A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.827A 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 599 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.556A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.971A 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: 3.522A pdb=" N THR A 347 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.559A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 318 hydrogen bonds defined for protein. 912 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.76 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2086 1.34 - 1.46: 1704 1.46 - 1.58: 2793 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6641 Sorted by residual: bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.63e+00 bond pdb=" C5 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" C3 NAG B 601 " pdb=" O3 NAG B 601 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.02e+00 bond pdb=" CA ILE A 54 " pdb=" CB ILE A 54 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.05e-02 9.07e+03 7.03e-01 bond pdb=" C2 NAG B 601 " pdb=" N2 NAG B 601 " ideal model delta sigma weight residual 1.439 1.453 -0.014 2.00e-02 2.50e+03 5.22e-01 ... (remaining 6636 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 8743 1.02 - 2.03: 212 2.03 - 3.05: 46 3.05 - 4.07: 16 4.07 - 5.09: 8 Bond angle restraints: 9025 Sorted by residual: angle pdb=" CA GLY A 352 " pdb=" C GLY A 352 " pdb=" N LYS A 353 " ideal model delta sigma weight residual 114.23 117.49 -3.26 8.80e-01 1.29e+00 1.37e+01 angle pdb=" CA GLY A 352 " pdb=" C GLY A 352 " pdb=" O GLY A 352 " ideal model delta sigma weight residual 122.33 119.83 2.50 8.10e-01 1.52e+00 9.53e+00 angle pdb=" CA GLN A 101 " pdb=" C GLN A 101 " pdb=" N HIS A 102 " ideal model delta sigma weight residual 118.27 121.46 -3.19 1.59e+00 3.96e-01 4.02e+00 angle pdb=" N GLY A 352 " pdb=" CA GLY A 352 " pdb=" C GLY A 352 " ideal model delta sigma weight residual 111.85 109.84 2.01 1.06e+00 8.90e-01 3.61e+00 angle pdb=" N GLY B 496 " pdb=" CA GLY B 496 " pdb=" C GLY B 496 " ideal model delta sigma weight residual 113.18 109.00 4.18 2.37e+00 1.78e-01 3.11e+00 ... (remaining 9020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.23: 3704 15.23 - 30.46: 177 30.46 - 45.68: 48 45.68 - 60.91: 9 60.91 - 76.14: 2 Dihedral angle restraints: 3940 sinusoidal: 1611 harmonic: 2329 Sorted by residual: dihedral pdb=" CA VAL A 342 " pdb=" C VAL A 342 " pdb=" N VAL A 343 " pdb=" CA VAL A 343 " ideal model delta harmonic sigma weight residual 180.00 164.48 15.52 0 5.00e+00 4.00e-02 9.64e+00 dihedral pdb=" N GLN B 493 " pdb=" CA GLN B 493 " pdb=" CB GLN B 493 " pdb=" CG GLN B 493 " ideal model delta sinusoidal sigma weight residual -180.00 -125.71 -54.29 3 1.50e+01 4.44e-03 9.27e+00 dihedral pdb=" CA TYR A 497 " pdb=" C TYR A 497 " pdb=" N CYS A 498 " pdb=" CA CYS A 498 " ideal model delta harmonic sigma weight residual 180.00 164.82 15.18 0 5.00e+00 4.00e-02 9.21e+00 ... (remaining 3937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 487 0.025 - 0.050: 279 0.050 - 0.075: 108 0.075 - 0.100: 45 0.100 - 0.124: 19 Chirality restraints: 938 Sorted by residual: chirality pdb=" CA ILE A 88 " pdb=" N ILE A 88 " pdb=" C ILE A 88 " pdb=" CB ILE A 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.65e-01 chirality pdb=" CA VAL A 343 " pdb=" N VAL A 343 " pdb=" C VAL A 343 " pdb=" CB VAL A 343 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.38e-01 ... (remaining 935 not shown) Planarity restraints: 1173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " 0.019 5.00e-02 4.00e+02 2.95e-02 1.39e+00 pdb=" N PRO B 521 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 582 " -0.019 5.00e-02 4.00e+02 2.88e-02 1.32e+00 pdb=" N PRO A 583 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 388 " 0.018 5.00e-02 4.00e+02 2.71e-02 1.17e+00 pdb=" N PRO A 389 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 389 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 389 " 0.015 5.00e-02 4.00e+02 ... (remaining 1170 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 123 2.69 - 3.24: 6431 3.24 - 3.80: 10582 3.80 - 4.35: 15128 4.35 - 4.90: 24081 Nonbonded interactions: 56345 Sorted by model distance: nonbonded pdb=" OE1 GLU B 406 " pdb=" OH TYR B 495 " model vdw 2.140 3.040 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 901 " model vdw 2.152 2.230 nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 901 " model vdw 2.163 2.230 nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.174 3.040 nonbonded pdb=" OG1 THR A 276 " pdb=" OG1 THR A 445 " model vdw 2.282 3.040 ... (remaining 56340 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: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.210 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 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 : 0.003 0.026 6641 Z= 0.165 Angle : 0.445 5.085 9025 Z= 0.237 Chirality : 0.039 0.124 938 Planarity : 0.003 0.030 1172 Dihedral : 10.058 76.137 2425 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.72 % Allowed : 3.87 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.03 (0.29), residues: 789 helix: 0.03 (0.26), residues: 391 sheet: 0.80 (0.87), residues: 41 loop : 0.02 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.009 0.001 PHE A 428 TYR 0.016 0.001 TYR A 385 ARG 0.002 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 153 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: A 79 GLN cc_start: 0.7481 (tp40) cc_final: 0.7241 (tp40) REVERT: A 114 GLN cc_start: 0.7554 (pt0) cc_final: 0.7232 (tp-100) REVERT: A 332 MET cc_start: 0.7917 (ttp) cc_final: 0.7660 (ttp) outliers start: 5 outliers final: 2 residues processed: 156 average time/residue: 1.2953 time to fit residues: 211.6519 Evaluate side-chains 102 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 82 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 0.2980 chunk 70 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 228 GLN A 325 GLN A 586 ASN B 354 ASN B 409 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6641 Z= 0.191 Angle : 0.529 5.958 9025 Z= 0.281 Chirality : 0.042 0.152 938 Planarity : 0.004 0.036 1172 Dihedral : 5.074 50.936 892 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.15 % Allowed : 13.20 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.34 (0.29), residues: 789 helix: 0.40 (0.26), residues: 398 sheet: 0.55 (0.79), residues: 43 loop : 0.17 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.010 0.001 PHE A 428 TYR 0.021 0.001 TYR A 385 ARG 0.007 0.001 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: A 79 GLN cc_start: 0.7544 (tp40) cc_final: 0.7166 (tp40) REVERT: A 171 GLU cc_start: 0.7306 (mp0) cc_final: 0.7095 (mm-30) outliers start: 15 outliers final: 7 residues processed: 112 average time/residue: 1.2065 time to fit residues: 142.2116 Evaluate side-chains 100 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 445 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 0.0980 chunk 58 optimal weight: 0.0470 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 76 optimal weight: 0.3980 chunk 63 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 overall best weight: 0.3478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 325 GLN A 401 HIS B 354 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6641 Z= 0.138 Angle : 0.468 5.674 9025 Z= 0.244 Chirality : 0.040 0.129 938 Planarity : 0.004 0.036 1172 Dihedral : 4.674 37.295 892 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.58 % Allowed : 13.20 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.64 (0.29), residues: 789 helix: 0.73 (0.26), residues: 395 sheet: 0.50 (0.79), residues: 43 loop : 0.23 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.025 0.001 PHE A 314 TYR 0.019 0.001 TYR A 385 ARG 0.006 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: A 79 GLN cc_start: 0.7531 (tp40) cc_final: 0.7256 (tp40) outliers start: 18 outliers final: 6 residues processed: 117 average time/residue: 1.2491 time to fit residues: 153.6065 Evaluate side-chains 95 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 443 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 71 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 20 optimal weight: 0.0270 chunk 62 optimal weight: 0.0020 chunk 42 optimal weight: 1.9990 overall best weight: 0.4846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 325 GLN B 354 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6641 Z= 0.153 Angle : 0.478 5.857 9025 Z= 0.247 Chirality : 0.040 0.137 938 Planarity : 0.004 0.035 1172 Dihedral : 4.391 26.739 891 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.30 % Allowed : 15.06 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.29), residues: 789 helix: 0.79 (0.26), residues: 404 sheet: 0.41 (0.77), residues: 43 loop : 0.29 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.020 0.001 PHE A 314 TYR 0.019 0.001 TYR A 385 ARG 0.006 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: A 79 GLN cc_start: 0.7498 (tp40) cc_final: 0.7116 (tp40) REVERT: A 171 GLU cc_start: 0.7348 (mp0) cc_final: 0.7101 (mm-30) REVERT: A 419 LYS cc_start: 0.8098 (ttmm) cc_final: 0.7707 (ttmm) REVERT: A 470 LYS cc_start: 0.8053 (mtmm) cc_final: 0.7733 (mtmp) REVERT: A 578 ASN cc_start: 0.7767 (OUTLIER) cc_final: 0.7488 (p0) outliers start: 16 outliers final: 9 residues processed: 111 average time/residue: 1.2787 time to fit residues: 149.2167 Evaluate side-chains 106 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 483 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 64 optimal weight: 0.0470 chunk 52 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 325 GLN B 493 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6641 Z= 0.182 Angle : 0.488 5.914 9025 Z= 0.252 Chirality : 0.041 0.142 938 Planarity : 0.004 0.035 1172 Dihedral : 4.364 26.613 891 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.58 % Allowed : 16.07 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.76 (0.29), residues: 789 helix: 0.81 (0.26), residues: 404 sheet: 0.43 (0.77), residues: 43 loop : 0.32 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.018 0.001 PHE A 314 TYR 0.020 0.001 TYR A 385 ARG 0.008 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.818 Fit side-chains revert: symmetry clash REVERT: A 79 GLN cc_start: 0.7495 (tp40) cc_final: 0.7024 (tp-100) REVERT: A 98 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.7166 (tt0) REVERT: A 470 LYS cc_start: 0.8045 (mtmm) cc_final: 0.7738 (mtmp) REVERT: A 578 ASN cc_start: 0.7863 (OUTLIER) cc_final: 0.7584 (p0) REVERT: B 494 SER cc_start: 0.8452 (m) cc_final: 0.8185 (t) outliers start: 18 outliers final: 13 residues processed: 109 average time/residue: 1.1839 time to fit residues: 136.2031 Evaluate side-chains 109 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 483 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 98 GLN A 299 ASN A 325 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6641 Z= 0.192 Angle : 0.489 6.135 9025 Z= 0.254 Chirality : 0.041 0.143 938 Planarity : 0.004 0.037 1172 Dihedral : 4.366 26.493 891 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.16 % Allowed : 16.07 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.29), residues: 789 helix: 0.84 (0.26), residues: 404 sheet: 0.46 (0.78), residues: 43 loop : 0.32 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.016 0.001 PHE A 314 TYR 0.021 0.001 TYR A 385 ARG 0.006 0.001 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: A 79 GLN cc_start: 0.7505 (tp40) cc_final: 0.7037 (tp-100) REVERT: A 98 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.7134 (tt0) REVERT: A 171 GLU cc_start: 0.7379 (mp0) cc_final: 0.6705 (mp0) REVERT: A 175 GLN cc_start: 0.8550 (mt0) cc_final: 0.8272 (mt0) REVERT: A 470 LYS cc_start: 0.8029 (mtmm) cc_final: 0.7721 (mtmp) REVERT: A 578 ASN cc_start: 0.7869 (OUTLIER) cc_final: 0.7589 (p0) REVERT: B 494 SER cc_start: 0.8491 (m) cc_final: 0.8202 (t) outliers start: 22 outliers final: 13 residues processed: 113 average time/residue: 1.1655 time to fit residues: 138.8776 Evaluate side-chains 109 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 483 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 98 GLN A 322 ASN A 325 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6641 Z= 0.174 Angle : 0.491 6.549 9025 Z= 0.254 Chirality : 0.041 0.139 938 Planarity : 0.004 0.036 1172 Dihedral : 4.320 26.221 891 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.30 % Allowed : 16.50 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.81 (0.29), residues: 789 helix: 0.87 (0.26), residues: 404 sheet: 0.48 (0.78), residues: 43 loop : 0.32 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.016 0.001 PHE A 314 TYR 0.019 0.001 TYR A 385 ARG 0.006 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 79 GLN cc_start: 0.7513 (tp40) cc_final: 0.7053 (tp-100) REVERT: A 98 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.7093 (tt0) REVERT: A 171 GLU cc_start: 0.7386 (mp0) cc_final: 0.7077 (mp0) REVERT: A 175 GLN cc_start: 0.8549 (mt0) cc_final: 0.8330 (mt0) REVERT: A 470 LYS cc_start: 0.8017 (mtmm) cc_final: 0.7716 (mtmp) REVERT: A 578 ASN cc_start: 0.7875 (OUTLIER) cc_final: 0.7598 (p0) REVERT: B 414 GLN cc_start: 0.8102 (tp-100) cc_final: 0.7846 (tp40) REVERT: B 494 SER cc_start: 0.8461 (m) cc_final: 0.8168 (t) outliers start: 23 outliers final: 12 residues processed: 112 average time/residue: 1.1243 time to fit residues: 132.9847 Evaluate side-chains 106 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 483 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: 0.6980 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 68 optimal weight: 0.4980 chunk 72 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 98 GLN A 322 ASN A 325 GLN A 401 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6641 Z= 0.189 Angle : 0.497 6.398 9025 Z= 0.258 Chirality : 0.041 0.144 938 Planarity : 0.004 0.036 1172 Dihedral : 4.334 26.397 891 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.16 % Allowed : 17.22 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.85 (0.29), residues: 789 helix: 0.94 (0.26), residues: 398 sheet: 0.52 (0.79), residues: 43 loop : 0.29 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.015 0.001 PHE A 314 TYR 0.020 0.001 TYR A 385 ARG 0.007 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 79 GLN cc_start: 0.7516 (tp40) cc_final: 0.7053 (tp-100) REVERT: A 98 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.7095 (tt0) REVERT: A 171 GLU cc_start: 0.7404 (mp0) cc_final: 0.7111 (mp0) REVERT: A 175 GLN cc_start: 0.8543 (mt0) cc_final: 0.8336 (mt0) REVERT: A 470 LYS cc_start: 0.8011 (mtmm) cc_final: 0.7707 (mtmp) REVERT: A 578 ASN cc_start: 0.7901 (OUTLIER) cc_final: 0.7610 (p0) REVERT: A 600 ARG cc_start: 0.7099 (mmm-85) cc_final: 0.6867 (ptm160) REVERT: B 414 GLN cc_start: 0.8127 (tp-100) cc_final: 0.7917 (tp40) REVERT: B 494 SER cc_start: 0.8482 (m) cc_final: 0.8168 (t) outliers start: 22 outliers final: 13 residues processed: 108 average time/residue: 1.1610 time to fit residues: 132.1284 Evaluate side-chains 106 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 483 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.0980 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 63 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 69 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6641 Z= 0.150 Angle : 0.484 6.662 9025 Z= 0.251 Chirality : 0.040 0.137 938 Planarity : 0.004 0.035 1172 Dihedral : 4.240 25.772 891 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.30 % Allowed : 17.50 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.96 (0.29), residues: 789 helix: 1.05 (0.26), residues: 395 sheet: 0.51 (0.79), residues: 43 loop : 0.33 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.016 0.001 PHE A 314 TYR 0.020 0.001 TYR A 183 ARG 0.006 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.8335 (ttp) cc_final: 0.8124 (ttm) REVERT: A 79 GLN cc_start: 0.7526 (tp40) cc_final: 0.7087 (tp-100) REVERT: A 98 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.7106 (tt0) REVERT: A 171 GLU cc_start: 0.7365 (mp0) cc_final: 0.7078 (mp0) REVERT: A 406 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8097 (mm-30) REVERT: A 470 LYS cc_start: 0.8004 (mtmm) cc_final: 0.7712 (mtmp) REVERT: A 578 ASN cc_start: 0.7884 (OUTLIER) cc_final: 0.7598 (p0) REVERT: B 494 SER cc_start: 0.8454 (m) cc_final: 0.8161 (t) outliers start: 16 outliers final: 11 residues processed: 106 average time/residue: 1.1856 time to fit residues: 132.6034 Evaluate side-chains 104 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 483 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.0870 chunk 71 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 175 GLN A 322 ASN A 325 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6641 Z= 0.159 Angle : 0.499 6.991 9025 Z= 0.259 Chirality : 0.041 0.139 938 Planarity : 0.004 0.036 1172 Dihedral : 4.155 20.036 890 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.15 % Allowed : 17.93 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.02 (0.29), residues: 789 helix: 1.15 (0.26), residues: 394 sheet: 0.52 (0.79), residues: 43 loop : 0.31 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.015 0.001 PHE A 314 TYR 0.021 0.001 TYR A 183 ARG 0.011 0.000 ARG A 600 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.812 Fit side-chains revert: symmetry clash REVERT: A 79 GLN cc_start: 0.7519 (tp40) cc_final: 0.7089 (tp-100) REVERT: A 470 LYS cc_start: 0.8001 (mtmm) cc_final: 0.7710 (mtmp) REVERT: A 578 ASN cc_start: 0.7887 (OUTLIER) cc_final: 0.7604 (p0) REVERT: B 494 SER cc_start: 0.8445 (m) cc_final: 0.8156 (t) outliers start: 15 outliers final: 11 residues processed: 100 average time/residue: 1.1181 time to fit residues: 118.2971 Evaluate side-chains 100 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 483 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.1980 chunk 41 optimal weight: 3.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.151758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.118475 restraints weight = 7258.957| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.80 r_work: 0.3160 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6641 Z= 0.227 Angle : 0.541 6.915 9025 Z= 0.280 Chirality : 0.042 0.149 938 Planarity : 0.004 0.036 1172 Dihedral : 4.303 20.027 890 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.30 % Allowed : 18.36 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.88 (0.29), residues: 789 helix: 1.02 (0.26), residues: 398 sheet: 0.50 (0.79), residues: 43 loop : 0.25 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.007 0.001 HIS A 241 PHE 0.013 0.001 PHE A 32 TYR 0.020 0.002 TYR A 385 ARG 0.004 0.000 ARG A 340 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3062.02 seconds wall clock time: 55 minutes 14.11 seconds (3314.11 seconds total)