Starting phenix.real_space_refine on Fri Apr 5 23:52:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8scz_40347/04_2024/8scz_40347_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8scz_40347/04_2024/8scz_40347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8scz_40347/04_2024/8scz_40347.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8scz_40347/04_2024/8scz_40347.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8scz_40347/04_2024/8scz_40347_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8scz_40347/04_2024/8scz_40347_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 62 5.49 5 S 31 5.16 5 C 3853 2.51 5 N 1092 2.21 5 O 1372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A ASP 372": "OD1" <-> "OD2" Residue "A ASP 435": "OD1" <-> "OD2" Residue "A TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 565": "OD1" <-> "OD2" Residue "A GLU 591": "OE1" <-> "OE2" Residue "A GLU 607": "OE1" <-> "OE2" Residue "A GLU 612": "OE1" <-> "OE2" Residue "A ASP 690": "OD1" <-> "OD2" Residue "A ASP 836": "OD1" <-> "OD2" Residue "A GLU 883": "OE1" <-> "OE2" Residue "A TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6411 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5123 Classifications: {'peptide': 635} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 27, 'TRANS': 607} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1287 Unusual residues: {'GTP': 1} Classifications: {'RNA': 59, 'undetermined': 1} Modifications used: {'rna3p_pur': 29, 'rna3p_pyr': 30} Link IDs: {'rna3p': 58, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" G B 2 " Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4191 SG CYS A 810 60.315 59.247 80.471 1.00 37.82 S ATOM 4217 SG CYS A 813 62.572 62.668 80.179 1.00 49.69 S ATOM 4630 SG CYS A 864 59.188 62.171 82.238 1.00 46.29 S ATOM 4669 SG CYS A 869 59.417 62.787 78.708 1.00 0.00 S Time building chain proxies: 4.19, per 1000 atoms: 0.65 Number of scatterers: 6411 At special positions: 0 Unit cell: (100.392, 91.848, 111.072, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 31 16.00 P 62 15.00 O 1372 8.00 N 1092 7.00 C 3853 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.04 Conformation dependent library (CDL) restraints added in 937.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 813 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " Number of angles added : 6 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1220 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 5 sheets defined 42.7% alpha, 8.3% beta 29 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 2.93 Creating SS restraints... Processing helix chain 'A' and resid 245 through 256 Proline residue: A 253 - end of helix removed outlier: 3.984A pdb=" N LYS A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 283 Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 334 through 339 Processing helix chain 'A' and resid 348 through 357 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 374 through 376 No H-bonds generated for 'chain 'A' and resid 374 through 376' Processing helix chain 'A' and resid 382 through 394 Processing helix chain 'A' and resid 420 through 433 Processing helix chain 'A' and resid 470 through 488 removed outlier: 3.864A pdb=" N ARG A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 496 No H-bonds generated for 'chain 'A' and resid 493 through 496' Processing helix chain 'A' and resid 507 through 522 removed outlier: 4.325A pdb=" N VAL A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 557 Processing helix chain 'A' and resid 560 through 575 Processing helix chain 'A' and resid 581 through 601 removed outlier: 3.986A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A 599 " --> pdb=" O GLN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 624 Processing helix chain 'A' and resid 638 through 647 removed outlier: 3.822A pdb=" N ALA A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 644 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 770 Processing helix chain 'A' and resid 773 through 793 Processing helix chain 'A' and resid 889 through 891 No H-bonds generated for 'chain 'A' and resid 889 through 891' Processing sheet with id= A, first strand: chain 'A' and resid 294 through 296 removed outlier: 5.946A pdb=" N GLN A 404 " --> pdb=" O MET A 369 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N PHE A 371 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ILE A 406 " --> pdb=" O PHE A 371 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 458 through 462 removed outlier: 6.962A pdb=" N CYS A 738 " --> pdb=" O PHE A 459 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ARG A 461 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU A 740 " --> pdb=" O ARG A 461 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 902 through 904 removed outlier: 3.888A pdb=" N CYS A 818 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 823 through 825 Processing sheet with id= E, first strand: chain 'A' and resid 842 through 846 removed outlier: 6.747A pdb=" N HIS A 876 " --> pdb=" O ARG A 859 " (cutoff:3.500A) 213 hydrogen bonds defined for protein. 627 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 75 hydrogen bonds 150 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1771 1.34 - 1.46: 1611 1.46 - 1.58: 3116 1.58 - 1.70: 122 1.70 - 1.82: 43 Bond restraints: 6663 Sorted by residual: bond pdb=" C VAL A 332 " pdb=" N PRO A 333 " ideal model delta sigma weight residual 1.332 1.361 -0.029 1.32e-02 5.74e+03 4.94e+00 bond pdb=" CB PRO A 626 " pdb=" CG PRO A 626 " ideal model delta sigma weight residual 1.492 1.600 -0.108 5.00e-02 4.00e+02 4.66e+00 bond pdb=" C ILE A 300 " pdb=" N PRO A 301 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.32e+00 bond pdb=" CB PHE A 388 " pdb=" CG PHE A 388 " ideal model delta sigma weight residual 1.502 1.541 -0.039 2.30e-02 1.89e+03 2.88e+00 bond pdb=" C ILE A 884 " pdb=" N PRO A 885 " ideal model delta sigma weight residual 1.331 1.351 -0.020 1.20e-02 6.94e+03 2.69e+00 ... (remaining 6658 not shown) Histogram of bond angle deviations from ideal: 99.11 - 106.11: 435 106.11 - 113.10: 3647 113.10 - 120.10: 2490 120.10 - 127.09: 2537 127.09 - 134.09: 174 Bond angle restraints: 9283 Sorted by residual: angle pdb=" C GLU A 330 " pdb=" N ASN A 331 " pdb=" CA ASN A 331 " ideal model delta sigma weight residual 121.54 130.32 -8.78 1.91e+00 2.74e-01 2.11e+01 angle pdb=" CA PRO A 626 " pdb=" N PRO A 626 " pdb=" CD PRO A 626 " ideal model delta sigma weight residual 112.00 107.07 4.93 1.40e+00 5.10e-01 1.24e+01 angle pdb=" C GLN A 299 " pdb=" N ILE A 300 " pdb=" CA ILE A 300 " ideal model delta sigma weight residual 120.33 123.08 -2.75 8.00e-01 1.56e+00 1.18e+01 angle pdb=" CA TYR A 390 " pdb=" CB TYR A 390 " pdb=" CG TYR A 390 " ideal model delta sigma weight residual 113.90 119.94 -6.04 1.80e+00 3.09e-01 1.13e+01 angle pdb=" CA ILE A 300 " pdb=" C ILE A 300 " pdb=" N PRO A 301 " ideal model delta sigma weight residual 120.83 122.88 -2.05 6.10e-01 2.69e+00 1.13e+01 ... (remaining 9278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.40: 3489 18.40 - 36.81: 413 36.81 - 55.21: 141 55.21 - 73.61: 84 73.61 - 92.01: 12 Dihedral angle restraints: 4139 sinusoidal: 2267 harmonic: 1872 Sorted by residual: dihedral pdb=" C8 GTP B 1 " pdb=" C1' GTP B 1 " pdb=" N9 GTP B 1 " pdb=" O4' GTP B 1 " ideal model delta sinusoidal sigma weight residual 104.59 13.48 91.11 1 2.00e+01 2.50e-03 2.45e+01 dihedral pdb=" CA GLU A 373 " pdb=" C GLU A 373 " pdb=" N CYS A 374 " pdb=" CA CYS A 374 " ideal model delta harmonic sigma weight residual -180.00 -159.83 -20.17 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLN A 404 " pdb=" C GLN A 404 " pdb=" N VAL A 405 " pdb=" CA VAL A 405 " ideal model delta harmonic sigma weight residual 180.00 -162.43 -17.57 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 4136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 810 0.044 - 0.088: 198 0.088 - 0.132: 60 0.132 - 0.175: 12 0.175 - 0.219: 3 Chirality restraints: 1083 Sorted by residual: chirality pdb=" CB ILE A 693 " pdb=" CA ILE A 693 " pdb=" CG1 ILE A 693 " pdb=" CG2 ILE A 693 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB VAL A 877 " pdb=" CA VAL A 877 " pdb=" CG1 VAL A 877 " pdb=" CG2 VAL A 877 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CG LEU A 552 " pdb=" CB LEU A 552 " pdb=" CD1 LEU A 552 " pdb=" CD2 LEU A 552 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 8.86e-01 ... (remaining 1080 not shown) Planarity restraints: 962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 342 " -0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C ASP A 342 " 0.066 2.00e-02 2.50e+03 pdb=" O ASP A 342 " -0.025 2.00e-02 2.50e+03 pdb=" N ILE A 343 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 800 " -0.061 5.00e-02 4.00e+02 9.40e-02 1.41e+01 pdb=" N PRO A 801 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO A 801 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 801 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 390 " 0.016 2.00e-02 2.50e+03 2.14e-02 9.17e+00 pdb=" CG TYR A 390 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR A 390 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR A 390 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR A 390 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 390 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 390 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 390 " 0.000 2.00e-02 2.50e+03 ... (remaining 959 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 22 2.45 - 3.06: 3592 3.06 - 3.67: 10467 3.67 - 4.29: 14954 4.29 - 4.90: 23696 Nonbonded interactions: 52731 Sorted by model distance: nonbonded pdb=" OH TYR A 246 " pdb=" CD1 LEU A 449 " model vdw 1.836 3.460 nonbonded pdb=" CE1 PHE A 460 " pdb=" CD2 LEU A 740 " model vdw 2.268 3.760 nonbonded pdb=" O GLN A 457 " pdb=" CD2 PHE A 459 " model vdw 2.285 3.340 nonbonded pdb=" O GLN A 511 " pdb=" OG1 THR A 515 " model vdw 2.304 2.440 nonbonded pdb=" O GLU A 583 " pdb=" OG1 THR A 587 " model vdw 2.315 2.440 ... (remaining 52726 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.880 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 24.570 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 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 : 0.004 0.108 6663 Z= 0.251 Angle : 0.819 9.946 9283 Z= 0.427 Chirality : 0.044 0.219 1083 Planarity : 0.006 0.094 962 Dihedral : 19.405 92.015 2919 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.22 % Favored : 93.62 % Rotamer: Outliers : 0.35 % Allowed : 27.32 % Favored : 72.33 % 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: -2.21 (0.29), residues: 627 helix: -0.88 (0.27), residues: 279 sheet: -2.03 (0.58), residues: 74 loop : -1.81 (0.32), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 908 HIS 0.005 0.001 HIS A 375 PHE 0.032 0.002 PHE A 388 TYR 0.052 0.003 TYR A 390 ARG 0.008 0.001 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.627 Fit side-chains REVERT: A 279 GLU cc_start: 0.7272 (mm-30) cc_final: 0.7025 (mm-30) REVERT: A 469 ASP cc_start: 0.6996 (p0) cc_final: 0.6607 (p0) outliers start: 2 outliers final: 1 residues processed: 70 average time/residue: 0.1601 time to fit residues: 15.8718 Evaluate side-chains 58 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 800 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 0.0000 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN A 573 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6663 Z= 0.162 Angle : 0.491 6.821 9283 Z= 0.245 Chirality : 0.035 0.137 1083 Planarity : 0.004 0.051 962 Dihedral : 17.388 92.617 1614 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.26 % Favored : 94.58 % Rotamer: Outliers : 3.15 % Allowed : 26.62 % Favored : 70.23 % 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: -1.21 (0.32), residues: 627 helix: 0.37 (0.30), residues: 285 sheet: -2.47 (0.55), residues: 81 loop : -1.49 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 908 HIS 0.003 0.001 HIS A 375 PHE 0.013 0.001 PHE A 856 TYR 0.024 0.002 TYR A 390 ARG 0.002 0.000 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 68 time to evaluate : 0.632 Fit side-chains REVERT: A 469 ASP cc_start: 0.7070 (p0) cc_final: 0.6689 (p0) REVERT: A 547 LYS cc_start: 0.7840 (mmtm) cc_final: 0.7604 (mmtm) REVERT: A 760 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7475 (ptm) outliers start: 18 outliers final: 10 residues processed: 78 average time/residue: 0.1694 time to fit residues: 18.5086 Evaluate side-chains 72 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 843 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 62 optimal weight: 0.2980 chunk 67 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6663 Z= 0.159 Angle : 0.484 6.941 9283 Z= 0.239 Chirality : 0.036 0.155 1083 Planarity : 0.003 0.045 962 Dihedral : 17.290 91.345 1613 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.78 % Favored : 95.06 % Rotamer: Outliers : 3.50 % Allowed : 25.74 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.33), residues: 627 helix: 1.05 (0.31), residues: 284 sheet: -2.44 (0.56), residues: 79 loop : -1.36 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 908 HIS 0.002 0.000 HIS A 375 PHE 0.011 0.001 PHE A 856 TYR 0.021 0.001 TYR A 390 ARG 0.002 0.000 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 67 time to evaluate : 0.638 Fit side-chains REVERT: A 469 ASP cc_start: 0.7101 (p0) cc_final: 0.6742 (p0) REVERT: A 547 LYS cc_start: 0.7805 (mmtm) cc_final: 0.7490 (mmtm) REVERT: A 760 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7531 (ptm) outliers start: 20 outliers final: 14 residues processed: 78 average time/residue: 0.1928 time to fit residues: 21.1781 Evaluate side-chains 78 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 63 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 843 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 4.9990 chunk 6 optimal weight: 0.4980 chunk 29 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 62 optimal weight: 0.0170 chunk 66 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 55 optimal weight: 0.2980 chunk 37 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6663 Z= 0.131 Angle : 0.458 6.777 9283 Z= 0.226 Chirality : 0.035 0.128 1083 Planarity : 0.003 0.042 962 Dihedral : 17.242 89.598 1613 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.42 % Favored : 94.42 % Rotamer: Outliers : 4.55 % Allowed : 24.87 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.34), residues: 627 helix: 1.44 (0.32), residues: 285 sheet: -2.45 (0.56), residues: 79 loop : -1.19 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 646 HIS 0.002 0.000 HIS A 557 PHE 0.013 0.001 PHE A 882 TYR 0.018 0.001 TYR A 390 ARG 0.002 0.000 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 70 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 469 ASP cc_start: 0.7013 (p0) cc_final: 0.6669 (p0) REVERT: A 479 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7690 (mtm) REVERT: A 547 LYS cc_start: 0.7728 (mmtm) cc_final: 0.7441 (mmtm) REVERT: A 760 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7481 (ptm) outliers start: 26 outliers final: 15 residues processed: 89 average time/residue: 0.1652 time to fit residues: 20.5018 Evaluate side-chains 81 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 64 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 16 optimal weight: 0.0980 chunk 22 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6663 Z= 0.195 Angle : 0.503 8.582 9283 Z= 0.247 Chirality : 0.036 0.163 1083 Planarity : 0.003 0.041 962 Dihedral : 17.242 94.988 1613 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.90 % Favored : 93.94 % Rotamer: Outliers : 4.03 % Allowed : 26.80 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.34), residues: 627 helix: 1.53 (0.32), residues: 281 sheet: -2.52 (0.57), residues: 79 loop : -1.10 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 908 HIS 0.004 0.001 HIS A 281 PHE 0.015 0.001 PHE A 371 TYR 0.019 0.001 TYR A 390 ARG 0.002 0.000 ARG A 824 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 65 time to evaluate : 0.666 Fit side-chains REVERT: A 469 ASP cc_start: 0.7044 (p0) cc_final: 0.6676 (p0) REVERT: A 479 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7774 (mtp) REVERT: A 547 LYS cc_start: 0.7593 (mmtm) cc_final: 0.7146 (mmtm) outliers start: 23 outliers final: 19 residues processed: 79 average time/residue: 0.1817 time to fit residues: 19.5935 Evaluate side-chains 81 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 61 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 843 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 55 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6663 Z= 0.174 Angle : 0.486 7.088 9283 Z= 0.240 Chirality : 0.036 0.141 1083 Planarity : 0.003 0.041 962 Dihedral : 17.269 92.369 1613 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.58 % Favored : 94.26 % Rotamer: Outliers : 4.20 % Allowed : 27.50 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.35), residues: 627 helix: 1.68 (0.32), residues: 280 sheet: -2.42 (0.59), residues: 72 loop : -1.17 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 908 HIS 0.002 0.000 HIS A 280 PHE 0.012 0.001 PHE A 371 TYR 0.018 0.001 TYR A 390 ARG 0.001 0.000 ARG A 546 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 63 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 469 ASP cc_start: 0.6994 (p0) cc_final: 0.6695 (p0) REVERT: A 479 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7664 (mtm) REVERT: A 547 LYS cc_start: 0.7553 (mmtm) cc_final: 0.7100 (mmtm) REVERT: A 851 LYS cc_start: 0.5918 (tptp) cc_final: 0.4448 (ttpt) outliers start: 24 outliers final: 19 residues processed: 78 average time/residue: 0.1657 time to fit residues: 18.1666 Evaluate side-chains 78 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 58 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 843 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 56 optimal weight: 0.0020 chunk 66 optimal weight: 20.0000 chunk 41 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6663 Z= 0.154 Angle : 0.474 6.922 9283 Z= 0.235 Chirality : 0.035 0.141 1083 Planarity : 0.003 0.040 962 Dihedral : 17.283 91.800 1613 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 4.38 % Allowed : 26.97 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.35), residues: 627 helix: 1.82 (0.32), residues: 280 sheet: -2.37 (0.60), residues: 72 loop : -1.13 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 908 HIS 0.001 0.000 HIS A 281 PHE 0.010 0.001 PHE A 371 TYR 0.030 0.001 TYR A 390 ARG 0.002 0.000 ARG A 824 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 59 time to evaluate : 0.582 Fit side-chains REVERT: A 469 ASP cc_start: 0.6993 (p0) cc_final: 0.6731 (p0) REVERT: A 479 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7598 (mtm) REVERT: A 547 LYS cc_start: 0.7511 (mmtm) cc_final: 0.7058 (mmtm) outliers start: 25 outliers final: 20 residues processed: 75 average time/residue: 0.1460 time to fit residues: 16.1943 Evaluate side-chains 77 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 56 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 843 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6663 Z= 0.190 Angle : 0.505 9.714 9283 Z= 0.249 Chirality : 0.036 0.150 1083 Planarity : 0.003 0.040 962 Dihedral : 17.293 93.628 1613 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.20 % Allowed : 27.50 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.35), residues: 627 helix: 1.79 (0.32), residues: 280 sheet: -2.52 (0.59), residues: 72 loop : -1.12 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 873 HIS 0.002 0.001 HIS A 871 PHE 0.012 0.001 PHE A 371 TYR 0.029 0.001 TYR A 390 ARG 0.002 0.000 ARG A 824 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 60 time to evaluate : 0.646 Fit side-chains REVERT: A 337 ILE cc_start: 0.7438 (mt) cc_final: 0.7215 (mt) REVERT: A 469 ASP cc_start: 0.7018 (p0) cc_final: 0.6738 (p0) REVERT: A 479 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7685 (mtm) REVERT: A 547 LYS cc_start: 0.7495 (mmtm) cc_final: 0.7016 (mmtm) outliers start: 24 outliers final: 20 residues processed: 75 average time/residue: 0.1454 time to fit residues: 15.9600 Evaluate side-chains 79 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 58 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 843 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 65 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6663 Z= 0.165 Angle : 0.479 6.933 9283 Z= 0.238 Chirality : 0.036 0.140 1083 Planarity : 0.003 0.040 962 Dihedral : 17.307 91.881 1613 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.85 % Allowed : 28.02 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.35), residues: 627 helix: 1.86 (0.32), residues: 280 sheet: -2.43 (0.60), residues: 72 loop : -1.12 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 873 HIS 0.001 0.000 HIS A 281 PHE 0.034 0.001 PHE A 388 TYR 0.027 0.001 TYR A 390 ARG 0.001 0.000 ARG A 791 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 58 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: A 469 ASP cc_start: 0.6966 (p0) cc_final: 0.6701 (p0) REVERT: A 479 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7787 (mtm) REVERT: A 547 LYS cc_start: 0.7492 (mmtm) cc_final: 0.7025 (mmtm) outliers start: 22 outliers final: 19 residues processed: 71 average time/residue: 0.1543 time to fit residues: 15.7434 Evaluate side-chains 76 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 56 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 843 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 16 optimal weight: 0.1980 chunk 50 optimal weight: 0.0980 chunk 8 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6663 Z= 0.259 Angle : 0.564 10.374 9283 Z= 0.278 Chirality : 0.038 0.169 1083 Planarity : 0.004 0.040 962 Dihedral : 17.377 96.829 1613 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 4.03 % Allowed : 28.02 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.34), residues: 627 helix: 1.42 (0.31), residues: 281 sheet: -2.70 (0.57), residues: 74 loop : -1.09 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 908 HIS 0.003 0.001 HIS A 871 PHE 0.015 0.002 PHE A 371 TYR 0.030 0.002 TYR A 390 ARG 0.003 0.000 ARG A 824 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 63 time to evaluate : 0.619 Fit side-chains REVERT: A 469 ASP cc_start: 0.7036 (p0) cc_final: 0.6791 (p0) REVERT: A 479 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7976 (mtm) REVERT: A 547 LYS cc_start: 0.7533 (mmtm) cc_final: 0.7029 (mmtm) outliers start: 23 outliers final: 21 residues processed: 77 average time/residue: 0.1358 time to fit residues: 15.3116 Evaluate side-chains 81 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 59 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 843 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 0.0870 chunk 54 optimal weight: 0.2980 chunk 22 optimal weight: 8.9990 chunk 56 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.228516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.190285 restraints weight = 6396.846| |-----------------------------------------------------------------------------| r_work (start): 0.4188 rms_B_bonded: 1.36 r_work: 0.3969 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6663 Z= 0.140 Angle : 0.489 9.986 9283 Z= 0.241 Chirality : 0.036 0.127 1083 Planarity : 0.003 0.039 962 Dihedral : 17.370 88.925 1613 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.15 % Allowed : 29.60 % Favored : 67.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.35), residues: 627 helix: 1.74 (0.32), residues: 282 sheet: -2.42 (0.59), residues: 74 loop : -1.05 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 873 HIS 0.004 0.001 HIS A 375 PHE 0.010 0.001 PHE A 882 TYR 0.023 0.001 TYR A 390 ARG 0.002 0.000 ARG A 811 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1516.63 seconds wall clock time: 28 minutes 29.29 seconds (1709.29 seconds total)