Starting phenix.real_space_refine on Fri Dec 27 08:35:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ctj_26992/12_2024/8ctj_26992.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ctj_26992/12_2024/8ctj_26992.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ctj_26992/12_2024/8ctj_26992.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ctj_26992/12_2024/8ctj_26992.map" model { file = "/net/cci-nas-00/data/ceres_data/8ctj_26992/12_2024/8ctj_26992.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ctj_26992/12_2024/8ctj_26992.cif" } resolution = 4.74 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= 0.005 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 18 5.16 5 C 2202 2.51 5 N 529 2.21 5 O 562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3312 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3286 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 27 Time building chain proxies: 2.58, per 1000 atoms: 0.78 Number of scatterers: 3312 At special positions: 0 Unit cell: (55.75, 57.98, 105.925, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 1 15.00 O 562 8.00 N 529 7.00 C 2202 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 128 " distance=2.04 Simple disulfide: pdb=" SG CYS A 89 " - pdb=" SG CYS A 431 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 339.6 milliseconds 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 3 sheets defined 59.6% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.776A pdb=" N TYR A 94 " --> pdb=" O TYR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 100 through 110 removed outlier: 4.056A pdb=" N GLU A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 133 removed outlier: 3.745A pdb=" N LEU A 131 " --> pdb=" O ASN A 127 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A 132 " --> pdb=" O CYS A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 251 removed outlier: 3.647A pdb=" N MET A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 228 " --> pdb=" O TYR A 224 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N CYS A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR A 251 " --> pdb=" O TRP A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 285 removed outlier: 3.586A pdb=" N PHE A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 317 removed outlier: 3.642A pdb=" N LEU A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 353 removed outlier: 4.554A pdb=" N MET A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 393 removed outlier: 4.074A pdb=" N PHE A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) Proline residue: A 366 - end of helix Processing helix chain 'A' and resid 394 through 428 removed outlier: 3.747A pdb=" N ARG A 427 " --> pdb=" O THR A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 460 Processing helix chain 'A' and resid 465 through 471 removed outlier: 4.007A pdb=" N PHE A 471 " --> pdb=" O GLN A 467 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45 Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 59 Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 59 228 hydrogen bonds defined for protein. 663 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: 0.86 Time building geometry restraints manager: 1.03 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: 977 1.34 - 1.47: 929 1.47 - 1.60: 1461 1.60 - 1.73: 1 1.73 - 1.86: 30 Bond restraints: 3398 Sorted by residual: bond pdb=" O4P PEE A 601 " pdb=" P PEE A 601 " ideal model delta sigma weight residual 1.653 1.776 -0.123 2.00e-02 2.50e+03 3.81e+01 bond pdb=" C1 PEE A 601 " pdb=" C2 PEE A 601 " ideal model delta sigma weight residual 1.519 1.555 -0.036 2.00e-02 2.50e+03 3.19e+00 bond pdb=" CA ASP A 75 " pdb=" CB ASP A 75 " ideal model delta sigma weight residual 1.531 1.577 -0.047 3.12e-02 1.03e+03 2.25e+00 bond pdb=" CB CYS A 74 " pdb=" SG CYS A 74 " ideal model delta sigma weight residual 1.808 1.855 -0.047 3.30e-02 9.18e+02 2.05e+00 bond pdb=" C2 PEE A 601 " pdb=" C3 PEE A 601 " ideal model delta sigma weight residual 1.512 1.540 -0.028 2.00e-02 2.50e+03 2.03e+00 ... (remaining 3393 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 4511 2.78 - 5.57: 71 5.57 - 8.35: 20 8.35 - 11.14: 0 11.14 - 13.92: 1 Bond angle restraints: 4603 Sorted by residual: angle pdb=" O1P PEE A 601 " pdb=" P PEE A 601 " pdb=" O2P PEE A 601 " ideal model delta sigma weight residual 119.43 133.35 -13.92 3.00e+00 1.11e-01 2.15e+01 angle pdb=" CA LYS A 213 " pdb=" CB LYS A 213 " pdb=" CG LYS A 213 " ideal model delta sigma weight residual 114.10 121.83 -7.73 2.00e+00 2.50e-01 1.49e+01 angle pdb=" N GLN A 135 " pdb=" CA GLN A 135 " pdb=" C GLN A 135 " ideal model delta sigma weight residual 110.44 106.16 4.28 1.20e+00 6.94e-01 1.27e+01 angle pdb=" CA TRP A 252 " pdb=" CB TRP A 252 " pdb=" CG TRP A 252 " ideal model delta sigma weight residual 113.60 120.05 -6.45 1.90e+00 2.77e-01 1.15e+01 angle pdb=" CA MET A 231 " pdb=" CB MET A 231 " pdb=" CG MET A 231 " ideal model delta sigma weight residual 114.10 120.85 -6.75 2.00e+00 2.50e-01 1.14e+01 ... (remaining 4598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.18: 1924 29.18 - 58.35: 50 58.35 - 87.53: 6 87.53 - 116.71: 0 116.71 - 145.89: 2 Dihedral angle restraints: 1982 sinusoidal: 805 harmonic: 1177 Sorted by residual: dihedral pdb=" CB CYS A 89 " pdb=" SG CYS A 89 " pdb=" SG CYS A 431 " pdb=" CB CYS A 431 " ideal model delta sinusoidal sigma weight residual 93.00 144.73 -51.73 1 1.00e+01 1.00e-02 3.65e+01 dihedral pdb=" O2 PEE A 601 " pdb=" C1 PEE A 601 " pdb=" C2 PEE A 601 " pdb=" O3P PEE A 601 " ideal model delta sinusoidal sigma weight residual -59.96 85.93 -145.89 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" C3 PEE A 601 " pdb=" C1 PEE A 601 " pdb=" C2 PEE A 601 " pdb=" O3P PEE A 601 " ideal model delta sinusoidal sigma weight residual 62.73 -156.57 -140.70 1 3.00e+01 1.11e-03 1.89e+01 ... (remaining 1979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 459 0.077 - 0.155: 54 0.155 - 0.232: 6 0.232 - 0.309: 0 0.309 - 0.387: 1 Chirality restraints: 520 Sorted by residual: chirality pdb=" C2 PEE A 601 " pdb=" C1 PEE A 601 " pdb=" C3 PEE A 601 " pdb=" O2 PEE A 601 " both_signs ideal model delta sigma weight residual False -2.33 -2.71 0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CB ILE A 44 " pdb=" CA ILE A 44 " pdb=" CG1 ILE A 44 " pdb=" CG2 ILE A 44 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB THR A 405 " pdb=" CA THR A 405 " pdb=" OG1 THR A 405 " pdb=" CG2 THR A 405 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 517 not shown) Planarity restraints: 551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 371 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.62e+00 pdb=" CG ASP A 371 " -0.041 2.00e-02 2.50e+03 pdb=" OD1 ASP A 371 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP A 371 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 135 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C GLN A 135 " -0.038 2.00e-02 2.50e+03 pdb=" O GLN A 135 " 0.015 2.00e-02 2.50e+03 pdb=" N THR A 136 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 404 " -0.010 2.00e-02 2.50e+03 1.54e-02 4.17e+00 pdb=" CG PHE A 404 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 404 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 404 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 404 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 404 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 404 " 0.001 2.00e-02 2.50e+03 ... (remaining 548 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 536 2.77 - 3.30: 3273 3.30 - 3.83: 5397 3.83 - 4.37: 5945 4.37 - 4.90: 10260 Nonbonded interactions: 25411 Sorted by model distance: nonbonded pdb=" O TYR A 340 " pdb=" OG SER A 344 " model vdw 2.233 3.040 nonbonded pdb=" OG SER A 77 " pdb=" O SER A 191 " model vdw 2.233 3.040 nonbonded pdb=" O ILE A 419 " pdb=" OG1 THR A 423 " model vdw 2.276 3.040 nonbonded pdb=" O ASN A 200 " pdb=" OG SER A 203 " model vdw 2.312 3.040 nonbonded pdb=" O SER A 399 " pdb=" ND1 HIS A 403 " model vdw 2.381 3.120 ... (remaining 25406 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 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: 0.260 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.520 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4996 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 3398 Z= 0.264 Angle : 0.917 13.923 4603 Z= 0.487 Chirality : 0.051 0.387 520 Planarity : 0.006 0.052 551 Dihedral : 14.667 145.887 1214 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: -0.72 (0.41), residues: 395 helix: 0.26 (0.32), residues: 229 sheet: -1.55 (0.73), residues: 47 loop : -1.24 (0.56), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 244 HIS 0.001 0.000 HIS A 43 PHE 0.035 0.003 PHE A 379 TYR 0.018 0.003 TYR A 277 ARG 0.010 0.001 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.1993 (mtt) cc_final: 0.1692 (mtt) REVERT: A 227 MET cc_start: 0.8191 (tmm) cc_final: 0.7913 (tmm) REVERT: A 270 MET cc_start: 0.4612 (mmt) cc_final: 0.3946 (mmt) REVERT: A 386 MET cc_start: 0.8365 (tpp) cc_final: 0.7971 (tpp) REVERT: A 438 LEU cc_start: 0.6769 (mp) cc_final: 0.6373 (tp) REVERT: A 440 VAL cc_start: 0.9073 (t) cc_final: 0.8753 (p) REVERT: A 453 LEU cc_start: 0.8336 (mt) cc_final: 0.8123 (mt) REVERT: A 457 MET cc_start: 0.5495 (mtm) cc_final: 0.4779 (ptp) REVERT: A 467 GLN cc_start: 0.8176 (tt0) cc_final: 0.7943 (tt0) REVERT: A 468 ARG cc_start: 0.8817 (mtm180) cc_final: 0.7808 (mmm160) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1994 time to fit residues: 25.6156 Evaluate side-chains 87 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 135 GLN A 143 HIS A 356 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5498 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3398 Z= 0.254 Angle : 0.753 12.307 4603 Z= 0.387 Chirality : 0.045 0.189 520 Planarity : 0.006 0.055 551 Dihedral : 11.655 134.008 453 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % 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: -0.07 (0.41), residues: 395 helix: 0.89 (0.32), residues: 236 sheet: -1.32 (0.74), residues: 47 loop : -1.33 (0.55), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 252 HIS 0.012 0.004 HIS A 43 PHE 0.027 0.003 PHE A 276 TYR 0.014 0.002 TYR A 52 ARG 0.013 0.001 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7018 (mmmt) cc_final: 0.6769 (mppt) REVERT: A 80 ILE cc_start: 0.8229 (mt) cc_final: 0.7188 (mt) REVERT: A 91 ASN cc_start: 0.7246 (m-40) cc_final: 0.6620 (p0) REVERT: A 132 PHE cc_start: 0.6243 (t80) cc_final: 0.5979 (t80) REVERT: A 206 PHE cc_start: 0.6878 (m-80) cc_final: 0.6400 (m-80) REVERT: A 227 MET cc_start: 0.8367 (tmm) cc_final: 0.8000 (tmm) REVERT: A 386 MET cc_start: 0.8286 (tpp) cc_final: 0.7914 (tpp) REVERT: A 387 LYS cc_start: 0.8962 (tptt) cc_final: 0.8546 (ttmt) REVERT: A 438 LEU cc_start: 0.7914 (mp) cc_final: 0.7255 (tp) REVERT: A 453 LEU cc_start: 0.8297 (mt) cc_final: 0.8010 (mt) REVERT: A 457 MET cc_start: 0.6286 (mtm) cc_final: 0.5591 (ptp) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1851 time to fit residues: 23.5063 Evaluate side-chains 91 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 143 HIS A 187 HIS ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5829 moved from start: 0.7392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3398 Z= 0.303 Angle : 0.809 13.743 4603 Z= 0.419 Chirality : 0.047 0.174 520 Planarity : 0.006 0.040 551 Dihedral : 11.737 124.322 453 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.28 % Allowed : 6.46 % Favored : 93.26 % 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: -0.34 (0.40), residues: 395 helix: 0.69 (0.33), residues: 218 sheet: -1.31 (0.64), residues: 54 loop : -1.22 (0.55), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 252 HIS 0.011 0.003 HIS A 187 PHE 0.016 0.003 PHE A 404 TYR 0.032 0.003 TYR A 94 ARG 0.011 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.8328 (mt) cc_final: 0.8087 (mp) REVERT: A 61 ARG cc_start: 0.8592 (mtp-110) cc_final: 0.8240 (mtp-110) REVERT: A 80 ILE cc_start: 0.8406 (mt) cc_final: 0.7651 (mt) REVERT: A 119 GLN cc_start: 0.7217 (pt0) cc_final: 0.6615 (pt0) REVERT: A 143 HIS cc_start: 0.6771 (m170) cc_final: 0.6485 (m-70) REVERT: A 227 MET cc_start: 0.8617 (tmm) cc_final: 0.8169 (tmm) REVERT: A 288 GLU cc_start: 0.6085 (tt0) cc_final: 0.5703 (tt0) REVERT: A 298 GLU cc_start: 0.8097 (tp30) cc_final: 0.7774 (tp30) REVERT: A 386 MET cc_start: 0.8614 (tpp) cc_final: 0.8204 (tpp) REVERT: A 387 LYS cc_start: 0.8918 (tptt) cc_final: 0.8539 (tttp) REVERT: A 408 LEU cc_start: 0.8395 (mt) cc_final: 0.8131 (mt) REVERT: A 424 MET cc_start: 0.7304 (mmp) cc_final: 0.7092 (mpp) REVERT: A 435 TRP cc_start: 0.8089 (p-90) cc_final: 0.7122 (p-90) REVERT: A 437 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7248 (mm-30) REVERT: A 457 MET cc_start: 0.6602 (mtm) cc_final: 0.5755 (ttm) outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.1615 time to fit residues: 21.5408 Evaluate side-chains 92 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 135 GLN ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5898 moved from start: 0.8681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3398 Z= 0.259 Angle : 0.711 12.135 4603 Z= 0.369 Chirality : 0.044 0.240 520 Planarity : 0.005 0.045 551 Dihedral : 10.797 114.896 453 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % 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: -0.21 (0.41), residues: 395 helix: 0.98 (0.34), residues: 218 sheet: -1.42 (0.72), residues: 49 loop : -1.48 (0.50), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 82 HIS 0.007 0.002 HIS A 187 PHE 0.017 0.002 PHE A 364 TYR 0.021 0.002 TYR A 94 ARG 0.005 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ILE cc_start: 0.8355 (mt) cc_final: 0.7512 (mt) REVERT: A 84 LEU cc_start: 0.8524 (tp) cc_final: 0.8202 (tp) REVERT: A 95 ASN cc_start: 0.9303 (m-40) cc_final: 0.9019 (m110) REVERT: A 227 MET cc_start: 0.8769 (tmm) cc_final: 0.8276 (tmm) REVERT: A 259 GLN cc_start: 0.8217 (mp10) cc_final: 0.7959 (mp10) REVERT: A 270 MET cc_start: 0.5650 (mmp) cc_final: 0.5359 (mmp) REVERT: A 298 GLU cc_start: 0.8146 (tp30) cc_final: 0.7811 (tp30) REVERT: A 386 MET cc_start: 0.8658 (tpp) cc_final: 0.8222 (tpp) REVERT: A 387 LYS cc_start: 0.8968 (tptt) cc_final: 0.8514 (tttp) REVERT: A 424 MET cc_start: 0.6989 (mmp) cc_final: 0.6706 (mmm) REVERT: A 434 ASP cc_start: 0.5070 (t0) cc_final: 0.4802 (t0) REVERT: A 448 LEU cc_start: 0.9441 (pp) cc_final: 0.9126 (pp) REVERT: A 451 MET cc_start: 0.7813 (mtt) cc_final: 0.7220 (mtt) REVERT: A 453 LEU cc_start: 0.8321 (mt) cc_final: 0.8017 (mt) REVERT: A 457 MET cc_start: 0.6745 (mtm) cc_final: 0.6144 (mtm) REVERT: A 459 LEU cc_start: 0.7143 (mt) cc_final: 0.6776 (mt) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1651 time to fit residues: 22.1608 Evaluate side-chains 103 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 356 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6030 moved from start: 1.0347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3398 Z= 0.302 Angle : 0.783 12.445 4603 Z= 0.409 Chirality : 0.046 0.157 520 Planarity : 0.006 0.057 551 Dihedral : 11.154 115.439 453 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.40), residues: 395 helix: 0.42 (0.33), residues: 218 sheet: -1.27 (0.73), residues: 44 loop : -1.62 (0.50), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 82 HIS 0.010 0.003 HIS A 187 PHE 0.022 0.003 PHE A 184 TYR 0.029 0.003 TYR A 94 ARG 0.007 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8006 (mmmt) cc_final: 0.7660 (mmmt) REVERT: A 80 ILE cc_start: 0.8355 (mt) cc_final: 0.7443 (mt) REVERT: A 84 LEU cc_start: 0.8610 (tp) cc_final: 0.8111 (tp) REVERT: A 95 ASN cc_start: 0.9129 (m-40) cc_final: 0.8918 (m110) REVERT: A 119 GLN cc_start: 0.7700 (pt0) cc_final: 0.7274 (pt0) REVERT: A 184 PHE cc_start: 0.9085 (t80) cc_final: 0.8800 (t80) REVERT: A 220 THR cc_start: 0.7819 (p) cc_final: 0.7574 (p) REVERT: A 222 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8257 (mp0) REVERT: A 227 MET cc_start: 0.8617 (tmm) cc_final: 0.8269 (tmm) REVERT: A 298 GLU cc_start: 0.8142 (tp30) cc_final: 0.7699 (tp30) REVERT: A 386 MET cc_start: 0.8744 (tpp) cc_final: 0.8308 (tpp) REVERT: A 387 LYS cc_start: 0.8900 (tptt) cc_final: 0.8406 (tttp) REVERT: A 397 LYS cc_start: 0.8934 (ptpp) cc_final: 0.8420 (ptmt) REVERT: A 401 TYR cc_start: 0.9166 (m-10) cc_final: 0.8899 (m-10) REVERT: A 438 LEU cc_start: 0.8685 (mp) cc_final: 0.8234 (mm) REVERT: A 448 LEU cc_start: 0.9476 (pp) cc_final: 0.9179 (pp) REVERT: A 451 MET cc_start: 0.8013 (mtt) cc_final: 0.7316 (mtt) REVERT: A 453 LEU cc_start: 0.8396 (mt) cc_final: 0.8145 (mt) REVERT: A 457 MET cc_start: 0.6958 (mtm) cc_final: 0.6350 (mtm) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1574 time to fit residues: 22.3648 Evaluate side-chains 101 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.0060 chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 0.2980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 356 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5907 moved from start: 1.0565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3398 Z= 0.168 Angle : 0.647 9.209 4603 Z= 0.335 Chirality : 0.043 0.153 520 Planarity : 0.004 0.046 551 Dihedral : 10.465 107.383 453 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % 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 (0.42), residues: 395 helix: 1.36 (0.34), residues: 218 sheet: -1.55 (0.62), residues: 57 loop : -1.45 (0.56), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 177 HIS 0.004 0.001 HIS A 43 PHE 0.035 0.002 PHE A 240 TYR 0.014 0.001 TYR A 182 ARG 0.002 0.000 ARG A 427 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ILE cc_start: 0.8469 (mt) cc_final: 0.7820 (mt) REVERT: A 95 ASN cc_start: 0.9139 (m-40) cc_final: 0.8829 (m110) REVERT: A 119 GLN cc_start: 0.7548 (pt0) cc_final: 0.7035 (pt0) REVERT: A 178 GLN cc_start: 0.7243 (tm-30) cc_final: 0.6997 (tm-30) REVERT: A 206 PHE cc_start: 0.8100 (m-80) cc_final: 0.6988 (m-80) REVERT: A 227 MET cc_start: 0.8557 (tmm) cc_final: 0.8083 (tmm) REVERT: A 231 MET cc_start: 0.6998 (tpp) cc_final: 0.6366 (tpp) REVERT: A 298 GLU cc_start: 0.8049 (tp30) cc_final: 0.7525 (tp30) REVERT: A 386 MET cc_start: 0.8694 (tpp) cc_final: 0.8239 (tpp) REVERT: A 397 LYS cc_start: 0.9026 (ptpp) cc_final: 0.8434 (pttt) REVERT: A 401 TYR cc_start: 0.8955 (m-10) cc_final: 0.8752 (m-10) REVERT: A 436 ARG cc_start: 0.8050 (mmm-85) cc_final: 0.7481 (mmm-85) REVERT: A 451 MET cc_start: 0.7794 (mtt) cc_final: 0.7152 (mtt) REVERT: A 453 LEU cc_start: 0.8525 (mt) cc_final: 0.8281 (mt) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1631 time to fit residues: 23.3651 Evaluate side-chains 98 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 24 optimal weight: 0.0980 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.1980 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 356 GLN A 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5891 moved from start: 1.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3398 Z= 0.167 Angle : 0.665 8.849 4603 Z= 0.338 Chirality : 0.043 0.161 520 Planarity : 0.004 0.045 551 Dihedral : 9.978 100.629 453 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % 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: 0.39 (0.42), residues: 395 helix: 1.59 (0.34), residues: 218 sheet: -1.44 (0.64), residues: 57 loop : -1.30 (0.57), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 82 HIS 0.005 0.001 HIS A 43 PHE 0.028 0.002 PHE A 240 TYR 0.020 0.002 TYR A 118 ARG 0.002 0.000 ARG A 427 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7573 (p0) cc_final: 0.6965 (p0) REVERT: A 80 ILE cc_start: 0.8504 (mt) cc_final: 0.7975 (mt) REVERT: A 95 ASN cc_start: 0.9051 (m-40) cc_final: 0.8812 (m110) REVERT: A 178 GLN cc_start: 0.7324 (tm-30) cc_final: 0.6399 (tm-30) REVERT: A 182 TYR cc_start: 0.6455 (m-10) cc_final: 0.5812 (m-10) REVERT: A 227 MET cc_start: 0.8447 (tmm) cc_final: 0.8047 (tmm) REVERT: A 233 MET cc_start: 0.8277 (ttm) cc_final: 0.7873 (tpp) REVERT: A 298 GLU cc_start: 0.8071 (tp30) cc_final: 0.7556 (tp30) REVERT: A 386 MET cc_start: 0.8760 (tpp) cc_final: 0.8284 (tpp) REVERT: A 397 LYS cc_start: 0.9009 (ptpp) cc_final: 0.8420 (pttt) REVERT: A 408 LEU cc_start: 0.8313 (mt) cc_final: 0.8104 (mt) REVERT: A 436 ARG cc_start: 0.8013 (mmm-85) cc_final: 0.7588 (mmm-85) REVERT: A 448 LEU cc_start: 0.9490 (pp) cc_final: 0.9271 (pp) REVERT: A 451 MET cc_start: 0.7910 (mtt) cc_final: 0.7292 (mtt) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1636 time to fit residues: 23.8134 Evaluate side-chains 104 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 356 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5970 moved from start: 1.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3398 Z= 0.190 Angle : 0.673 9.101 4603 Z= 0.347 Chirality : 0.043 0.183 520 Planarity : 0.004 0.039 551 Dihedral : 9.658 93.377 453 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: 0.30 (0.42), residues: 395 helix: 1.47 (0.34), residues: 218 sheet: -1.31 (0.73), residues: 49 loop : -1.36 (0.54), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 82 HIS 0.007 0.002 HIS A 43 PHE 0.028 0.002 PHE A 240 TYR 0.018 0.002 TYR A 182 ARG 0.002 0.000 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ILE cc_start: 0.8550 (mt) cc_final: 0.8057 (mt) REVERT: A 95 ASN cc_start: 0.8998 (m-40) cc_final: 0.8665 (m110) REVERT: A 227 MET cc_start: 0.8434 (tmm) cc_final: 0.8096 (tmm) REVERT: A 233 MET cc_start: 0.8200 (ttm) cc_final: 0.7808 (tpp) REVERT: A 270 MET cc_start: 0.4947 (mmp) cc_final: 0.4711 (mmp) REVERT: A 288 GLU cc_start: 0.5935 (tt0) cc_final: 0.5459 (tt0) REVERT: A 298 GLU cc_start: 0.8044 (tp30) cc_final: 0.7380 (tp30) REVERT: A 386 MET cc_start: 0.8875 (tpp) cc_final: 0.8430 (tpp) REVERT: A 387 LYS cc_start: 0.8846 (tptt) cc_final: 0.8418 (tttp) REVERT: A 436 ARG cc_start: 0.7912 (mmm-85) cc_final: 0.7474 (mmm-85) REVERT: A 451 MET cc_start: 0.7876 (mtt) cc_final: 0.7282 (mtt) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1673 time to fit residues: 23.5573 Evaluate side-chains 98 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.0050 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 31 optimal weight: 0.0570 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 overall best weight: 0.4512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 356 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5932 moved from start: 1.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3398 Z= 0.164 Angle : 0.648 8.686 4603 Z= 0.330 Chirality : 0.042 0.184 520 Planarity : 0.004 0.039 551 Dihedral : 8.651 89.848 453 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: 0.49 (0.43), residues: 395 helix: 1.64 (0.34), residues: 219 sheet: -1.18 (0.74), residues: 49 loop : -1.38 (0.54), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 82 HIS 0.006 0.002 HIS A 43 PHE 0.025 0.002 PHE A 240 TYR 0.017 0.002 TYR A 118 ARG 0.005 0.001 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 TYR cc_start: 0.7532 (m-80) cc_final: 0.7316 (m-80) REVERT: A 61 ARG cc_start: 0.7944 (mtp180) cc_final: 0.7419 (mmm160) REVERT: A 80 ILE cc_start: 0.8625 (mt) cc_final: 0.8200 (mt) REVERT: A 91 ASN cc_start: 0.7845 (m-40) cc_final: 0.7443 (m-40) REVERT: A 95 ASN cc_start: 0.9099 (m-40) cc_final: 0.8405 (m-40) REVERT: A 110 GLU cc_start: 0.6879 (pp20) cc_final: 0.6236 (mm-30) REVERT: A 119 GLN cc_start: 0.7711 (pt0) cc_final: 0.7484 (pt0) REVERT: A 182 TYR cc_start: 0.6340 (m-10) cc_final: 0.5903 (m-10) REVERT: A 227 MET cc_start: 0.8421 (tmm) cc_final: 0.7984 (tmm) REVERT: A 233 MET cc_start: 0.8147 (ttm) cc_final: 0.7944 (tpp) REVERT: A 270 MET cc_start: 0.4759 (mmp) cc_final: 0.4527 (mmt) REVERT: A 288 GLU cc_start: 0.5807 (tt0) cc_final: 0.5301 (tt0) REVERT: A 298 GLU cc_start: 0.8243 (tp30) cc_final: 0.7749 (tp30) REVERT: A 386 MET cc_start: 0.8634 (tpp) cc_final: 0.8204 (tpp) REVERT: A 436 ARG cc_start: 0.7971 (mmm-85) cc_final: 0.7566 (mmm-85) REVERT: A 451 MET cc_start: 0.7891 (mtt) cc_final: 0.7285 (mtt) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1477 time to fit residues: 20.9725 Evaluate side-chains 103 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 13 optimal weight: 0.4980 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 0.0670 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 356 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5938 moved from start: 1.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3398 Z= 0.170 Angle : 0.646 8.102 4603 Z= 0.333 Chirality : 0.043 0.191 520 Planarity : 0.004 0.037 551 Dihedral : 8.042 89.557 453 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.43), residues: 395 helix: 1.64 (0.34), residues: 219 sheet: -1.19 (0.74), residues: 49 loop : -1.40 (0.54), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 82 HIS 0.006 0.001 HIS A 43 PHE 0.025 0.002 PHE A 240 TYR 0.021 0.002 TYR A 94 ARG 0.004 0.000 ARG A 392 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ILE cc_start: 0.8659 (mt) cc_final: 0.8225 (mt) REVERT: A 91 ASN cc_start: 0.7611 (m-40) cc_final: 0.7159 (m-40) REVERT: A 95 ASN cc_start: 0.9305 (m-40) cc_final: 0.8712 (m110) REVERT: A 110 GLU cc_start: 0.6952 (pp20) cc_final: 0.6204 (mm-30) REVERT: A 182 TYR cc_start: 0.6679 (m-10) cc_final: 0.5946 (m-80) REVERT: A 206 PHE cc_start: 0.8071 (m-80) cc_final: 0.7034 (m-80) REVERT: A 221 LEU cc_start: 0.9094 (mt) cc_final: 0.8890 (mt) REVERT: A 227 MET cc_start: 0.8391 (tmm) cc_final: 0.7860 (tmm) REVERT: A 233 MET cc_start: 0.8127 (ttm) cc_final: 0.7878 (tpp) REVERT: A 265 VAL cc_start: 0.8117 (t) cc_final: 0.7909 (t) REVERT: A 288 GLU cc_start: 0.5813 (tt0) cc_final: 0.5323 (tt0) REVERT: A 298 GLU cc_start: 0.8202 (tp30) cc_final: 0.7955 (tp30) REVERT: A 386 MET cc_start: 0.8728 (tpp) cc_final: 0.8274 (tpp) REVERT: A 436 ARG cc_start: 0.7938 (mmm-85) cc_final: 0.7518 (mmm-85) REVERT: A 451 MET cc_start: 0.7883 (mtt) cc_final: 0.7272 (mtt) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1456 time to fit residues: 19.6929 Evaluate side-chains 99 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 39 optimal weight: 3.9990 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 135 GLN A 356 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.197506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.172130 restraints weight = 6106.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.178246 restraints weight = 3714.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.182517 restraints weight = 2460.422| |-----------------------------------------------------------------------------| r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6043 moved from start: 1.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3398 Z= 0.184 Angle : 0.669 8.217 4603 Z= 0.346 Chirality : 0.043 0.202 520 Planarity : 0.005 0.049 551 Dihedral : 7.615 90.543 453 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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: 0.42 (0.43), residues: 395 helix: 1.51 (0.34), residues: 219 sheet: -1.20 (0.74), residues: 49 loop : -1.25 (0.55), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 82 HIS 0.006 0.001 HIS A 43 PHE 0.025 0.002 PHE A 240 TYR 0.021 0.002 TYR A 94 ARG 0.007 0.001 ARG A 351 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1133.34 seconds wall clock time: 21 minutes 9.07 seconds (1269.07 seconds total)