Starting phenix.real_space_refine on Fri Dec 27 06:52:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y6l_33643/12_2024/7y6l_33643.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y6l_33643/12_2024/7y6l_33643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y6l_33643/12_2024/7y6l_33643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y6l_33643/12_2024/7y6l_33643.map" model { file = "/net/cci-nas-00/data/ceres_data/7y6l_33643/12_2024/7y6l_33643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y6l_33643/12_2024/7y6l_33643.cif" } resolution = 3.5 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 2115 2.51 5 N 556 2.21 5 O 621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3308 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1519 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "H" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 953 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 822 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "A" 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: 2.51, per 1000 atoms: 0.76 Number of scatterers: 3308 At special positions: 0 Unit cell: (101.967, 72.952, 66.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 621 8.00 N 556 7.00 C 2115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 A1301 " - " ASN A 343 " Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 397.4 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 7 sheets defined 8.5% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.140A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.722A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.063A pdb=" N LEU H 18 " --> pdb=" O TRP H 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.324A pdb=" N TRP H 33 " --> pdb=" O ILE H 99 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP H 57 " --> pdb=" O HIS H 52 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.795A pdb=" N CYS H 96 " --> pdb=" O TRP H 112 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TRP H 112 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG H 98 " --> pdb=" O HIS H 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.450A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) 113 hydrogen bonds defined for protein. 261 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: 0.84 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1037 1.35 - 1.48: 969 1.48 - 1.60: 1371 1.60 - 1.73: 0 1.73 - 1.85: 20 Bond restraints: 3397 Sorted by residual: bond pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " ideal model delta sigma weight residual 1.808 1.850 -0.042 3.30e-02 9.18e+02 1.65e+00 bond pdb=" CB VAL A 350 " pdb=" CG1 VAL A 350 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.34e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.429 -0.023 2.00e-02 2.50e+03 1.34e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.12e+00 bond pdb=" C3 NAG A1301 " pdb=" O3 NAG A1301 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 9.63e-01 ... (remaining 3392 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 4543 1.74 - 3.48: 67 3.48 - 5.22: 5 5.22 - 6.97: 2 6.97 - 8.71: 1 Bond angle restraints: 4618 Sorted by residual: angle pdb=" CA CYS A 432 " pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 114.40 123.11 -8.71 2.30e+00 1.89e-01 1.43e+01 angle pdb=" C LYS L 50 " pdb=" N ALA L 51 " pdb=" CA ALA L 51 " ideal model delta sigma weight residual 121.54 126.98 -5.44 1.91e+00 2.74e-01 8.11e+00 angle pdb=" C VAL A 350 " pdb=" CA VAL A 350 " pdb=" CB VAL A 350 " ideal model delta sigma weight residual 112.26 109.09 3.17 1.62e+00 3.81e-01 3.83e+00 angle pdb=" N VAL A 350 " pdb=" CA VAL A 350 " pdb=" C VAL A 350 " ideal model delta sigma weight residual 111.09 113.30 -2.21 1.25e+00 6.40e-01 3.14e+00 angle pdb=" CA TYR L 91 " pdb=" CB TYR L 91 " pdb=" CG TYR L 91 " ideal model delta sigma weight residual 113.90 117.09 -3.19 1.80e+00 3.09e-01 3.13e+00 ... (remaining 4613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 1741 17.68 - 35.37: 211 35.37 - 53.05: 44 53.05 - 70.73: 8 70.73 - 88.42: 2 Dihedral angle restraints: 2006 sinusoidal: 785 harmonic: 1221 Sorted by residual: dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual 93.00 47.13 45.87 1 1.00e+01 1.00e-02 2.92e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 50.37 42.63 1 1.00e+01 1.00e-02 2.54e+01 dihedral pdb=" CA CYS A 432 " pdb=" C CYS A 432 " pdb=" N VAL A 433 " pdb=" CA VAL A 433 " ideal model delta harmonic sigma weight residual -180.00 -163.73 -16.27 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 2003 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 337 0.039 - 0.079: 113 0.079 - 0.118: 46 0.118 - 0.157: 2 0.157 - 0.197: 1 Chirality restraints: 499 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 496 not shown) Planarity restraints: 587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 383 " 0.034 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO A 384 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 384 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 384 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 76 " 0.006 2.00e-02 2.50e+03 1.27e-02 1.62e+00 pdb=" C ILE H 76 " -0.022 2.00e-02 2.50e+03 pdb=" O ILE H 76 " 0.008 2.00e-02 2.50e+03 pdb=" N THR H 77 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 511 " 0.005 2.00e-02 2.50e+03 1.04e-02 1.08e+00 pdb=" C VAL A 511 " -0.018 2.00e-02 2.50e+03 pdb=" O VAL A 511 " 0.007 2.00e-02 2.50e+03 pdb=" N VAL A 512 " 0.006 2.00e-02 2.50e+03 ... (remaining 584 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 255 2.74 - 3.28: 3095 3.28 - 3.82: 5294 3.82 - 4.36: 6181 4.36 - 4.90: 11199 Nonbonded interactions: 26024 Sorted by model distance: nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.198 3.040 nonbonded pdb=" OD2 ASP A 398 " pdb=" OH TYR A 423 " model vdw 2.223 3.040 nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.240 3.040 nonbonded pdb=" O SER A 443 " pdb=" NH1 ARG H 59 " model vdw 2.251 3.120 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.296 3.040 ... (remaining 26019 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.560 Find NCS groups from input model: 0.030 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 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 0.042 3397 Z= 0.231 Angle : 0.540 8.708 4618 Z= 0.286 Chirality : 0.045 0.197 499 Planarity : 0.004 0.052 586 Dihedral : 15.592 88.416 1214 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.56 % Allowed : 24.79 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.30 (0.42), residues: 416 helix: -3.39 (0.77), residues: 27 sheet: 0.90 (0.45), residues: 153 loop : -0.53 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.002 0.001 HIS H 110 PHE 0.011 0.001 PHE A 392 TYR 0.015 0.001 TYR L 91 ARG 0.004 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.377 Fit side-chains REVERT: A 357 ARG cc_start: 0.7266 (ttt-90) cc_final: 0.6858 (ttm-80) REVERT: A 403 ARG cc_start: 0.7775 (ttp80) cc_final: 0.7560 (mtp180) REVERT: A 471 GLU cc_start: 0.6768 (mm-30) cc_final: 0.6402 (mm-30) REVERT: H 17 SER cc_start: 0.8227 (m) cc_final: 0.7955 (p) REVERT: H 19 MET cc_start: 0.7052 (ttm) cc_final: 0.6608 (ttp) REVERT: H 21 SER cc_start: 0.7327 (p) cc_final: 0.7057 (t) REVERT: L 69 THR cc_start: 0.7509 (p) cc_final: 0.7144 (m) outliers start: 2 outliers final: 2 residues processed: 52 average time/residue: 0.1594 time to fit residues: 10.3154 Evaluate side-chains 39 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 105 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 23 optimal weight: 0.1980 chunk 37 optimal weight: 5.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN H 67 HIS L 6 GLN L 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 3397 Z= 0.149 Angle : 0.506 7.824 4618 Z= 0.269 Chirality : 0.045 0.200 499 Planarity : 0.004 0.041 586 Dihedral : 5.331 55.637 488 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.79 % Allowed : 23.10 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.09 (0.42), residues: 416 helix: -2.75 (0.87), residues: 27 sheet: 0.98 (0.45), residues: 156 loop : -0.43 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 33 HIS 0.003 0.001 HIS H 110 PHE 0.007 0.001 PHE A 392 TYR 0.010 0.001 TYR L 91 ARG 0.003 0.000 ARG H 59 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 38 time to evaluate : 0.357 Fit side-chains REVERT: A 357 ARG cc_start: 0.7205 (ttt-90) cc_final: 0.6752 (ttm-80) REVERT: A 462 LYS cc_start: 0.6857 (OUTLIER) cc_final: 0.6247 (mmtm) REVERT: A 471 GLU cc_start: 0.6755 (mm-30) cc_final: 0.6468 (mm-30) REVERT: H 17 SER cc_start: 0.8191 (m) cc_final: 0.7975 (p) REVERT: H 19 MET cc_start: 0.7054 (ttm) cc_final: 0.6673 (ttp) REVERT: H 21 SER cc_start: 0.7333 (p) cc_final: 0.7094 (t) REVERT: H 91 THR cc_start: 0.7572 (OUTLIER) cc_final: 0.7348 (t) REVERT: L 5 THR cc_start: 0.7388 (m) cc_final: 0.6644 (t) outliers start: 17 outliers final: 11 residues processed: 54 average time/residue: 0.1692 time to fit residues: 11.5569 Evaluate side-chains 47 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 0.0070 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 0.0070 chunk 12 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.9418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3397 Z= 0.165 Angle : 0.495 7.931 4618 Z= 0.261 Chirality : 0.045 0.194 499 Planarity : 0.003 0.037 586 Dihedral : 4.670 33.927 487 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.79 % Allowed : 23.94 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.42), residues: 416 helix: -2.52 (0.91), residues: 27 sheet: 1.10 (0.45), residues: 151 loop : -0.48 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 33 HIS 0.003 0.001 HIS H 110 PHE 0.007 0.001 PHE A 347 TYR 0.011 0.001 TYR L 91 ARG 0.002 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 34 time to evaluate : 0.356 Fit side-chains REVERT: A 357 ARG cc_start: 0.7215 (ttt-90) cc_final: 0.6788 (ttm-80) REVERT: A 462 LYS cc_start: 0.6877 (OUTLIER) cc_final: 0.6301 (mmtm) REVERT: A 471 GLU cc_start: 0.6759 (mm-30) cc_final: 0.6463 (mm-30) REVERT: H 10 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.4946 (mp0) REVERT: H 19 MET cc_start: 0.7220 (ttm) cc_final: 0.6828 (ttp) REVERT: H 91 THR cc_start: 0.7471 (OUTLIER) cc_final: 0.7238 (t) outliers start: 17 outliers final: 11 residues processed: 50 average time/residue: 0.1310 time to fit residues: 8.4750 Evaluate side-chains 45 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 31 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3397 Z= 0.159 Angle : 0.492 7.875 4618 Z= 0.257 Chirality : 0.045 0.195 499 Planarity : 0.003 0.034 586 Dihedral : 4.521 31.993 486 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 6.48 % Allowed : 22.82 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.42), residues: 416 helix: -2.27 (0.97), residues: 27 sheet: 1.14 (0.45), residues: 150 loop : -0.45 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 33 HIS 0.002 0.000 HIS H 110 PHE 0.009 0.001 PHE L 71 TYR 0.011 0.001 TYR L 91 ARG 0.001 0.000 ARG H 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 32 time to evaluate : 0.434 Fit side-chains REVERT: A 357 ARG cc_start: 0.7188 (ttt-90) cc_final: 0.6795 (ttm-80) REVERT: A 462 LYS cc_start: 0.6878 (OUTLIER) cc_final: 0.6309 (mmtm) REVERT: H 10 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.4829 (mp0) REVERT: H 19 MET cc_start: 0.7163 (ttm) cc_final: 0.6750 (ttp) REVERT: H 91 THR cc_start: 0.7466 (OUTLIER) cc_final: 0.7241 (t) outliers start: 23 outliers final: 13 residues processed: 54 average time/residue: 0.1471 time to fit residues: 9.9812 Evaluate side-chains 47 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 31 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 20 optimal weight: 0.0270 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 0.0030 chunk 7 optimal weight: 0.9990 overall best weight: 0.5850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3397 Z= 0.131 Angle : 0.479 7.320 4618 Z= 0.251 Chirality : 0.044 0.192 499 Planarity : 0.003 0.032 586 Dihedral : 4.372 30.187 486 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.92 % Allowed : 21.69 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.19 (0.43), residues: 416 helix: -1.45 (1.29), residues: 19 sheet: 0.93 (0.44), residues: 158 loop : -0.26 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 33 HIS 0.002 0.000 HIS H 110 PHE 0.006 0.001 PHE A 392 TYR 0.008 0.001 TYR L 91 ARG 0.004 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 32 time to evaluate : 0.350 Fit side-chains REVERT: A 357 ARG cc_start: 0.7162 (ttt-90) cc_final: 0.6667 (ttm-80) REVERT: A 396 TYR cc_start: 0.7438 (m-80) cc_final: 0.7236 (m-80) REVERT: A 462 LYS cc_start: 0.6896 (OUTLIER) cc_final: 0.6307 (mmtm) REVERT: H 10 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.4806 (mp0) REVERT: H 19 MET cc_start: 0.7190 (ttm) cc_final: 0.6768 (ttp) REVERT: H 91 THR cc_start: 0.7441 (OUTLIER) cc_final: 0.7220 (t) outliers start: 21 outliers final: 17 residues processed: 52 average time/residue: 0.1373 time to fit residues: 9.2453 Evaluate side-chains 51 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 31 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 20.0000 chunk 18 optimal weight: 0.0670 chunk 3 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.1980 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3397 Z= 0.133 Angle : 0.472 7.141 4618 Z= 0.247 Chirality : 0.044 0.190 499 Planarity : 0.003 0.030 586 Dihedral : 4.289 28.533 486 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 6.48 % Allowed : 21.13 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.24 (0.43), residues: 416 helix: -1.29 (1.34), residues: 19 sheet: 0.97 (0.44), residues: 158 loop : -0.24 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 353 HIS 0.001 0.000 HIS H 110 PHE 0.006 0.001 PHE A 392 TYR 0.008 0.001 TYR L 91 ARG 0.003 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 33 time to evaluate : 0.357 Fit side-chains REVERT: A 357 ARG cc_start: 0.7141 (ttt-90) cc_final: 0.6569 (ttm-80) REVERT: A 396 TYR cc_start: 0.7410 (m-80) cc_final: 0.7048 (m-80) REVERT: A 462 LYS cc_start: 0.6926 (OUTLIER) cc_final: 0.6334 (mmtm) REVERT: H 10 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.4792 (mp0) REVERT: H 19 MET cc_start: 0.7175 (ttm) cc_final: 0.6742 (ttp) REVERT: H 91 THR cc_start: 0.7440 (OUTLIER) cc_final: 0.7220 (t) REVERT: H 93 MET cc_start: 0.7619 (tpt) cc_final: 0.6998 (tpt) outliers start: 23 outliers final: 18 residues processed: 54 average time/residue: 0.1400 time to fit residues: 9.7264 Evaluate side-chains 54 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 33 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 0.0470 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3397 Z= 0.176 Angle : 0.501 7.986 4618 Z= 0.259 Chirality : 0.045 0.198 499 Planarity : 0.003 0.030 586 Dihedral : 4.463 29.969 486 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 6.48 % Allowed : 20.85 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.22 (0.42), residues: 416 helix: -1.33 (1.32), residues: 19 sheet: 1.16 (0.44), residues: 151 loop : -0.37 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.002 0.001 HIS H 110 PHE 0.011 0.001 PHE H 109 TYR 0.011 0.001 TYR L 91 ARG 0.003 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 34 time to evaluate : 0.357 Fit side-chains REVERT: A 357 ARG cc_start: 0.7145 (ttt-90) cc_final: 0.6746 (ttm-80) REVERT: A 462 LYS cc_start: 0.6945 (OUTLIER) cc_final: 0.6316 (mmtm) REVERT: H 10 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.4833 (mp0) REVERT: H 19 MET cc_start: 0.7263 (ttm) cc_final: 0.6834 (ttp) REVERT: H 39 GLN cc_start: 0.6948 (OUTLIER) cc_final: 0.6561 (tt0) REVERT: H 91 THR cc_start: 0.7486 (OUTLIER) cc_final: 0.7263 (t) REVERT: H 93 MET cc_start: 0.7597 (tpt) cc_final: 0.6909 (tpt) REVERT: L 88 CYS cc_start: 0.8443 (p) cc_final: 0.8067 (p) outliers start: 23 outliers final: 18 residues processed: 56 average time/residue: 0.1329 time to fit residues: 9.5147 Evaluate side-chains 54 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 32 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 0.0270 chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3397 Z= 0.137 Angle : 0.480 7.412 4618 Z= 0.250 Chirality : 0.045 0.258 499 Planarity : 0.003 0.029 586 Dihedral : 4.639 37.218 486 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.92 % Allowed : 21.69 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.29 (0.43), residues: 416 helix: -1.22 (1.36), residues: 19 sheet: 1.03 (0.44), residues: 158 loop : -0.23 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 353 HIS 0.002 0.000 HIS H 110 PHE 0.007 0.001 PHE H 109 TYR 0.009 0.001 TYR L 91 ARG 0.003 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 34 time to evaluate : 0.379 Fit side-chains REVERT: A 357 ARG cc_start: 0.7129 (ttt-90) cc_final: 0.6750 (ttm-80) REVERT: A 462 LYS cc_start: 0.6942 (OUTLIER) cc_final: 0.6311 (mmtm) REVERT: H 10 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.4848 (mp0) REVERT: H 19 MET cc_start: 0.7209 (ttm) cc_final: 0.6797 (ttp) REVERT: H 91 THR cc_start: 0.7451 (OUTLIER) cc_final: 0.7233 (t) REVERT: H 97 THR cc_start: 0.9270 (m) cc_final: 0.9020 (p) REVERT: L 88 CYS cc_start: 0.8451 (p) cc_final: 0.8074 (p) outliers start: 21 outliers final: 16 residues processed: 54 average time/residue: 0.1478 time to fit residues: 10.0465 Evaluate side-chains 49 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 30 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 0.0670 chunk 27 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3397 Z= 0.204 Angle : 0.529 8.488 4618 Z= 0.275 Chirality : 0.046 0.211 499 Planarity : 0.003 0.028 586 Dihedral : 5.079 43.648 486 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 7.04 % Allowed : 20.85 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.24 (0.42), residues: 416 helix: -1.22 (1.35), residues: 19 sheet: 1.17 (0.44), residues: 151 loop : -0.36 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.002 0.001 HIS H 110 PHE 0.008 0.001 PHE H 109 TYR 0.012 0.001 TYR L 91 ARG 0.003 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 32 time to evaluate : 0.369 Fit side-chains REVERT: A 357 ARG cc_start: 0.7176 (ttt-90) cc_final: 0.6818 (ttm-80) REVERT: A 462 LYS cc_start: 0.6945 (OUTLIER) cc_final: 0.6314 (mmtm) REVERT: H 10 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.4731 (mp0) REVERT: H 19 MET cc_start: 0.7276 (ttm) cc_final: 0.6885 (ttp) REVERT: H 39 GLN cc_start: 0.6929 (OUTLIER) cc_final: 0.6555 (tt0) REVERT: H 91 THR cc_start: 0.7553 (OUTLIER) cc_final: 0.7324 (t) outliers start: 25 outliers final: 18 residues processed: 54 average time/residue: 0.1441 time to fit residues: 9.9634 Evaluate side-chains 53 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 31 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3397 Z= 0.274 Angle : 0.593 9.804 4618 Z= 0.308 Chirality : 0.048 0.205 499 Planarity : 0.004 0.029 586 Dihedral : 5.848 51.136 486 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 6.20 % Allowed : 21.69 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.02 (0.42), residues: 416 helix: -1.51 (1.26), residues: 19 sheet: 1.00 (0.43), residues: 151 loop : -0.49 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.001 HIS H 110 PHE 0.016 0.002 PHE A 342 TYR 0.016 0.002 TYR L 91 ARG 0.003 0.000 ARG A 454 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 34 time to evaluate : 0.370 Fit side-chains REVERT: A 357 ARG cc_start: 0.7204 (ttt-90) cc_final: 0.6892 (ttm-80) REVERT: A 462 LYS cc_start: 0.6922 (OUTLIER) cc_final: 0.6426 (mmtt) REVERT: H 10 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.4838 (mp0) REVERT: H 19 MET cc_start: 0.7265 (ttm) cc_final: 0.6855 (ttp) REVERT: H 39 GLN cc_start: 0.6956 (OUTLIER) cc_final: 0.6576 (tt0) REVERT: H 91 THR cc_start: 0.7689 (OUTLIER) cc_final: 0.7434 (t) outliers start: 22 outliers final: 17 residues processed: 53 average time/residue: 0.1369 time to fit residues: 9.4626 Evaluate side-chains 55 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 34 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.164028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.132913 restraints weight = 3550.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.134543 restraints weight = 2903.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.135403 restraints weight = 2553.197| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 3397 Z= 0.286 Angle : 0.599 10.209 4618 Z= 0.312 Chirality : 0.048 0.207 499 Planarity : 0.004 0.032 586 Dihedral : 5.657 45.755 486 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 6.48 % Allowed : 21.13 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.41), residues: 416 helix: -2.48 (0.91), residues: 27 sheet: 0.74 (0.42), residues: 153 loop : -0.55 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.003 0.001 HIS H 110 PHE 0.010 0.002 PHE H 109 TYR 0.016 0.002 TYR L 91 ARG 0.003 0.001 ARG A 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1124.07 seconds wall clock time: 21 minutes 28.51 seconds (1288.51 seconds total)