Starting phenix.real_space_refine on Fri Aug 22 18:17:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9euq_19980/08_2025/9euq_19980.cif Found real_map, /net/cci-nas-00/data/ceres_data/9euq_19980/08_2025/9euq_19980.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9euq_19980/08_2025/9euq_19980.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9euq_19980/08_2025/9euq_19980.map" model { file = "/net/cci-nas-00/data/ceres_data/9euq_19980/08_2025/9euq_19980.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9euq_19980/08_2025/9euq_19980.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.013 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: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 33 5.16 5 Be 1 3.05 5 C 4269 2.51 5 N 1110 2.21 5 O 1276 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6693 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 880, 6688 Classifications: {'peptide': 880} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 29, 'TRANS': 850} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' MG': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.76, per 1000 atoms: 0.26 Number of scatterers: 6693 At special positions: 0 Unit cell: (69.696, 91.52, 128.128, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 33 16.00 Mg 1 11.99 F 3 9.00 O 1276 8.00 N 1110 7.00 C 4269 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 359.1 milliseconds Enol-peptide restraints added in 1.4 microseconds 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1632 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 5 sheets defined 56.0% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 23 through 33 Processing helix chain 'A' and resid 46 through 55 Processing helix chain 'A' and resid 57 through 74 Processing helix chain 'A' and resid 75 through 102 Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 183 through 187 removed outlier: 3.892A pdb=" N ARG A 187 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 212 Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 230 through 264 Processing helix chain 'A' and resid 270 through 290 Processing helix chain 'A' and resid 293 through 311 Processing helix chain 'A' and resid 319 through 327 removed outlier: 4.567A pdb=" N GLU A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 379 Processing helix chain 'A' and resid 394 through 407 removed outlier: 3.570A pdb=" N VAL A 398 " --> pdb=" O ASP A 394 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 407 " --> pdb=" O PHE A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 418 removed outlier: 3.834A pdb=" N ILE A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 458 Processing helix chain 'A' and resid 472 through 488 Processing helix chain 'A' and resid 528 through 541 removed outlier: 4.026A pdb=" N TYR A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA A 533 " --> pdb=" O GLU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 563 Processing helix chain 'A' and resid 575 through 581 Processing helix chain 'A' and resid 582 through 589 Processing helix chain 'A' and resid 600 through 614 Processing helix chain 'A' and resid 626 through 634 removed outlier: 4.339A pdb=" N ALA A 630 " --> pdb=" O ASN A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 651 Processing helix chain 'A' and resid 660 through 701 removed outlier: 4.031A pdb=" N VAL A 664 " --> pdb=" O PHE A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 718 Processing helix chain 'A' and resid 720 through 729 Processing helix chain 'A' and resid 752 through 777 Processing helix chain 'A' and resid 779 through 802 removed outlier: 4.151A pdb=" N THR A 799 " --> pdb=" O ARG A 795 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N PHE A 800 " --> pdb=" O THR A 796 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA A 801 " --> pdb=" O LEU A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 813 Processing helix chain 'A' and resid 817 through 835 Processing helix chain 'A' and resid 850 through 879 Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 127 removed outlier: 4.273A pdb=" N LYS A 116 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N VAL A 136 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 196 " --> pdb=" O ASP A 160 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS A 158 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY A 200 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N SER A 156 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLY A 202 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N SER A 154 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N PHE A 204 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE A 152 " --> pdb=" O PHE A 204 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N VAL A 206 " --> pdb=" O ARG A 150 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ARG A 150 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU A 157 " --> pdb=" O LYS A 173 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 127 removed outlier: 4.273A pdb=" N LYS A 116 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N VAL A 136 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 196 " --> pdb=" O ASP A 160 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS A 158 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY A 200 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N SER A 156 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLY A 202 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N SER A 154 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N PHE A 204 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE A 152 " --> pdb=" O PHE A 204 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N VAL A 206 " --> pdb=" O ARG A 150 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ARG A 150 " --> pdb=" O VAL A 206 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 314 through 316 removed outlier: 6.596A pdb=" N GLY A 637 " --> pdb=" O MET A 653 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LEU A 655 " --> pdb=" O GLY A 637 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA A 639 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N MET A 620 " --> pdb=" O VAL A 638 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N MET A 640 " --> pdb=" O MET A 620 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 330 through 333 removed outlier: 6.226A pdb=" N ILE A 331 " --> pdb=" O VAL A 546 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ILE A 548 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N THR A 333 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N TYR A 596 " --> pdb=" O THR A 545 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N MET A 547 " --> pdb=" O TYR A 596 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 349 through 350 removed outlier: 4.179A pdb=" N GLY A 519 " --> pdb=" O TYR A 495 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY A 496 " --> pdb=" O THR A 447 " (cutoff:3.500A) 400 hydrogen bonds defined for protein. 1167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.28 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2205 1.34 - 1.46: 1369 1.46 - 1.58: 3154 1.58 - 1.70: 0 1.70 - 1.82: 61 Bond restraints: 6789 Sorted by residual: bond pdb=" N VAL A 516 " pdb=" CA VAL A 516 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.61e+00 bond pdb=" N ILE A 515 " pdb=" CA ILE A 515 " ideal model delta sigma weight residual 1.460 1.496 -0.035 1.30e-02 5.92e+03 7.39e+00 bond pdb=" N PHE A 843 " pdb=" CA PHE A 843 " ideal model delta sigma weight residual 1.457 1.487 -0.029 1.10e-02 8.26e+03 7.16e+00 bond pdb=" N GLU A 167 " pdb=" CA GLU A 167 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.21e-02 6.83e+03 6.96e+00 bond pdb=" N LEU A 478 " pdb=" CA LEU A 478 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.35e+00 ... (remaining 6784 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 9070 2.28 - 4.57: 97 4.57 - 6.85: 14 6.85 - 9.14: 4 9.14 - 11.42: 1 Bond angle restraints: 9186 Sorted by residual: angle pdb=" CB MET A 782 " pdb=" CG MET A 782 " pdb=" SD MET A 782 " ideal model delta sigma weight residual 112.70 124.12 -11.42 3.00e+00 1.11e-01 1.45e+01 angle pdb=" CA LYS A 356 " pdb=" CB LYS A 356 " pdb=" CG LYS A 356 " ideal model delta sigma weight residual 114.10 121.57 -7.47 2.00e+00 2.50e-01 1.39e+01 angle pdb=" C LEU A 104 " pdb=" N ASP A 105 " pdb=" CA ASP A 105 " ideal model delta sigma weight residual 121.54 128.46 -6.92 1.91e+00 2.74e-01 1.31e+01 angle pdb=" N ILE A 515 " pdb=" CA ILE A 515 " pdb=" C ILE A 515 " ideal model delta sigma weight residual 113.22 109.00 4.22 1.23e+00 6.61e-01 1.18e+01 angle pdb=" C LYS A 43 " pdb=" N LYS A 44 " pdb=" CA LYS A 44 " ideal model delta sigma weight residual 121.54 127.58 -6.04 1.91e+00 2.74e-01 1.00e+01 ... (remaining 9181 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 3504 17.88 - 35.76: 467 35.76 - 53.63: 120 53.63 - 71.51: 36 71.51 - 89.39: 9 Dihedral angle restraints: 4136 sinusoidal: 1609 harmonic: 2527 Sorted by residual: dihedral pdb=" CA ASP A 135 " pdb=" CB ASP A 135 " pdb=" CG ASP A 135 " pdb=" OD1 ASP A 135 " ideal model delta sinusoidal sigma weight residual -30.00 -83.49 53.49 1 2.00e+01 2.50e-03 9.72e+00 dihedral pdb=" CB LYS A 540 " pdb=" CG LYS A 540 " pdb=" CD LYS A 540 " pdb=" CE LYS A 540 " ideal model delta sinusoidal sigma weight residual -180.00 -120.61 -59.39 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N GLU A 583 " pdb=" CA GLU A 583 " pdb=" CB GLU A 583 " pdb=" CG GLU A 583 " ideal model delta sinusoidal sigma weight residual -60.00 -119.26 59.26 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 4133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 736 0.034 - 0.068: 250 0.068 - 0.102: 81 0.102 - 0.136: 25 0.136 - 0.170: 7 Chirality restraints: 1099 Sorted by residual: chirality pdb=" CA GLU A 167 " pdb=" N GLU A 167 " pdb=" C GLU A 167 " pdb=" CB GLU A 167 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.19e-01 chirality pdb=" CB ILE A 401 " pdb=" CA ILE A 401 " pdb=" CG1 ILE A 401 " pdb=" CG2 ILE A 401 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.88e-01 chirality pdb=" CG LEU A 379 " pdb=" CB LEU A 379 " pdb=" CD1 LEU A 379 " pdb=" CD2 LEU A 379 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.35e-01 ... (remaining 1096 not shown) Planarity restraints: 1174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 132 " 0.026 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO A 133 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 133 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 133 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 843 " 0.007 2.00e-02 2.50e+03 1.36e-02 1.84e+00 pdb=" C PHE A 843 " -0.023 2.00e-02 2.50e+03 pdb=" O PHE A 843 " 0.009 2.00e-02 2.50e+03 pdb=" N SER A 844 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 230 " -0.021 5.00e-02 4.00e+02 3.19e-02 1.63e+00 pdb=" N PRO A 231 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 231 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 231 " -0.018 5.00e-02 4.00e+02 ... (remaining 1171 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 94 2.60 - 3.18: 5973 3.18 - 3.75: 11733 3.75 - 4.33: 15139 4.33 - 4.90: 25419 Nonbonded interactions: 58358 Sorted by model distance: nonbonded pdb=" OD2 ASP A 334 " pdb="MG MG A 901 " model vdw 2.026 2.170 nonbonded pdb=" OD1 ASP A 623 " pdb="MG MG A 901 " model vdw 2.060 2.170 nonbonded pdb=" O THR A 336 " pdb="MG MG A 901 " model vdw 2.109 2.170 nonbonded pdb=" O ARG A 108 " pdb=" OG SER A 111 " model vdw 2.209 3.040 nonbonded pdb=" O LEU A 236 " pdb=" OG SER A 240 " model vdw 2.222 3.040 ... (remaining 58353 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.700 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: 0.020 Set scattering table: 0.020 Process input model: 7.560 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:5.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 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 : 0.006 0.463 6790 Z= 0.580 Angle : 0.581 11.422 9186 Z= 0.304 Chirality : 0.041 0.170 1099 Planarity : 0.003 0.045 1174 Dihedral : 18.086 89.391 2504 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.56 % Allowed : 36.73 % Favored : 62.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.29), residues: 878 helix: 1.63 (0.24), residues: 487 sheet: -0.65 (0.61), residues: 75 loop : -1.27 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 108 TYR 0.013 0.001 TYR A 831 PHE 0.007 0.001 PHE A 843 TRP 0.015 0.001 TRP A 703 HIS 0.001 0.000 HIS A 592 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 6789) covalent geometry : angle 0.58111 ( 9186) hydrogen bonds : bond 0.12795 ( 384) hydrogen bonds : angle 5.47938 ( 1167) Misc. bond : bond 0.46264 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 109 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.8420 (ptm) cc_final: 0.8120 (ttp) REVERT: A 226 GLU cc_start: 0.7430 (tt0) cc_final: 0.6834 (tt0) REVERT: A 271 MET cc_start: 0.7004 (tpt) cc_final: 0.4723 (pmm) REVERT: A 292 GLU cc_start: 0.8475 (mp0) cc_final: 0.8005 (mp0) REVERT: A 462 PHE cc_start: 0.8124 (t80) cc_final: 0.7902 (t80) REVERT: A 480 GLU cc_start: 0.8929 (tt0) cc_final: 0.8601 (tp30) REVERT: A 487 ASN cc_start: 0.8387 (m-40) cc_final: 0.7490 (t0) outliers start: 4 outliers final: 1 residues processed: 113 average time/residue: 0.3900 time to fit residues: 47.1264 Evaluate side-chains 97 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 707 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.166241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.121341 restraints weight = 8261.566| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.01 r_work: 0.3393 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6790 Z= 0.152 Angle : 0.561 7.509 9186 Z= 0.282 Chirality : 0.042 0.136 1099 Planarity : 0.004 0.047 1174 Dihedral : 4.127 37.196 931 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 5.73 % Allowed : 31.28 % Favored : 62.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.29), residues: 878 helix: 1.65 (0.24), residues: 484 sheet: -0.80 (0.61), residues: 81 loop : -1.33 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 108 TYR 0.015 0.001 TYR A 831 PHE 0.009 0.001 PHE A 685 TRP 0.014 0.002 TRP A 48 HIS 0.002 0.000 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 6789) covalent geometry : angle 0.56078 ( 9186) hydrogen bonds : bond 0.04128 ( 384) hydrogen bonds : angle 4.40670 ( 1167) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 104 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: A 163 MET cc_start: 0.8409 (ptm) cc_final: 0.8159 (ttp) REVERT: A 196 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7757 (tt) REVERT: A 226 GLU cc_start: 0.7393 (tt0) cc_final: 0.6827 (tt0) REVERT: A 292 GLU cc_start: 0.8569 (mp0) cc_final: 0.7969 (mp0) REVERT: A 375 HIS cc_start: 0.8398 (m-70) cc_final: 0.8195 (m90) REVERT: A 462 PHE cc_start: 0.7865 (t80) cc_final: 0.7607 (t80) REVERT: A 480 GLU cc_start: 0.8923 (tt0) cc_final: 0.8593 (tp30) REVERT: A 484 GLU cc_start: 0.7952 (tp30) cc_final: 0.7289 (tp30) REVERT: A 487 ASN cc_start: 0.8407 (m-40) cc_final: 0.7539 (t0) REVERT: A 613 LYS cc_start: 0.8623 (tttm) cc_final: 0.8418 (ttpp) REVERT: A 640 MET cc_start: 0.8930 (mmm) cc_final: 0.8311 (mmt) outliers start: 41 outliers final: 13 residues processed: 132 average time/residue: 0.4062 time to fit residues: 57.6360 Evaluate side-chains 110 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 673 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 42 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 62 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 35 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 576 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.166895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.122099 restraints weight = 8183.915| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.99 r_work: 0.3426 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6790 Z= 0.135 Angle : 0.545 8.628 9186 Z= 0.271 Chirality : 0.042 0.175 1099 Planarity : 0.004 0.050 1174 Dihedral : 3.874 22.224 929 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 5.45 % Allowed : 32.12 % Favored : 62.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.29), residues: 878 helix: 1.72 (0.23), residues: 483 sheet: -0.56 (0.68), residues: 65 loop : -1.38 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 150 TYR 0.013 0.001 TYR A 831 PHE 0.008 0.001 PHE A 239 TRP 0.011 0.001 TRP A 703 HIS 0.001 0.000 HIS A 552 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 6789) covalent geometry : angle 0.54548 ( 9186) hydrogen bonds : bond 0.03846 ( 384) hydrogen bonds : angle 4.19393 ( 1167) Misc. bond : bond 0.00031 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 108 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8196 (mt) cc_final: 0.7786 (mp) REVERT: A 153 GLU cc_start: 0.8126 (tt0) cc_final: 0.7450 (tm-30) REVERT: A 163 MET cc_start: 0.8345 (ptm) cc_final: 0.8072 (ttp) REVERT: A 189 ASN cc_start: 0.9046 (p0) cc_final: 0.8750 (p0) REVERT: A 196 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7602 (tt) REVERT: A 226 GLU cc_start: 0.7336 (tt0) cc_final: 0.6929 (tt0) REVERT: A 292 GLU cc_start: 0.8542 (mp0) cc_final: 0.8037 (mp0) REVERT: A 375 HIS cc_start: 0.8336 (m-70) cc_final: 0.8076 (m90) REVERT: A 462 PHE cc_start: 0.7780 (t80) cc_final: 0.7521 (t80) REVERT: A 480 GLU cc_start: 0.8915 (tt0) cc_final: 0.8569 (tp30) REVERT: A 487 ASN cc_start: 0.8381 (m-40) cc_final: 0.7513 (t0) REVERT: A 523 MET cc_start: 0.8714 (ttm) cc_final: 0.8450 (mtm) REVERT: A 640 MET cc_start: 0.8868 (mmm) cc_final: 0.8469 (mmt) outliers start: 39 outliers final: 16 residues processed: 133 average time/residue: 0.3619 time to fit residues: 51.7232 Evaluate side-chains 117 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 783 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 37 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 2 optimal weight: 0.0470 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.164445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.119080 restraints weight = 8359.207| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.02 r_work: 0.3368 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6790 Z= 0.180 Angle : 0.584 9.400 9186 Z= 0.289 Chirality : 0.043 0.185 1099 Planarity : 0.004 0.049 1174 Dihedral : 3.927 22.289 929 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 6.15 % Allowed : 32.40 % Favored : 61.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.28), residues: 878 helix: 1.61 (0.23), residues: 483 sheet: -0.71 (0.67), residues: 65 loop : -1.39 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 108 TYR 0.014 0.001 TYR A 831 PHE 0.009 0.001 PHE A 239 TRP 0.011 0.002 TRP A 703 HIS 0.001 0.000 HIS A 127 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 6789) covalent geometry : angle 0.58432 ( 9186) hydrogen bonds : bond 0.04036 ( 384) hydrogen bonds : angle 4.28597 ( 1167) Misc. bond : bond 0.00086 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 109 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8640 (tptt) REVERT: A 43 LYS cc_start: 0.8265 (mptt) cc_final: 0.7926 (tppt) REVERT: A 153 GLU cc_start: 0.8152 (tt0) cc_final: 0.7397 (tm-30) REVERT: A 167 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.7079 (mt-10) REVERT: A 196 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7681 (tt) REVERT: A 226 GLU cc_start: 0.7514 (tt0) cc_final: 0.6927 (tt0) REVERT: A 292 GLU cc_start: 0.8624 (mp0) cc_final: 0.8186 (mp0) REVERT: A 375 HIS cc_start: 0.8386 (m-70) cc_final: 0.8120 (m90) REVERT: A 462 PHE cc_start: 0.7855 (t80) cc_final: 0.7595 (t80) REVERT: A 480 GLU cc_start: 0.8938 (tt0) cc_final: 0.8625 (tp30) REVERT: A 484 GLU cc_start: 0.7982 (tp30) cc_final: 0.7266 (tp30) REVERT: A 487 ASN cc_start: 0.8430 (m-40) cc_final: 0.7566 (t0) REVERT: A 523 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8535 (mtm) REVERT: A 583 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7978 (mm-30) REVERT: A 613 LYS cc_start: 0.8712 (tttm) cc_final: 0.8470 (ttpp) outliers start: 44 outliers final: 18 residues processed: 139 average time/residue: 0.3883 time to fit residues: 57.9589 Evaluate side-chains 119 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.163797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.119017 restraints weight = 8418.407| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.00 r_work: 0.3379 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6790 Z= 0.161 Angle : 0.597 11.624 9186 Z= 0.288 Chirality : 0.042 0.192 1099 Planarity : 0.004 0.051 1174 Dihedral : 3.943 22.010 929 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 5.59 % Allowed : 33.66 % Favored : 60.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.28), residues: 878 helix: 1.61 (0.23), residues: 483 sheet: -0.96 (0.66), residues: 65 loop : -1.37 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 108 TYR 0.014 0.001 TYR A 349 PHE 0.008 0.001 PHE A 685 TRP 0.017 0.002 TRP A 48 HIS 0.001 0.000 HIS A 552 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 6789) covalent geometry : angle 0.59672 ( 9186) hydrogen bonds : bond 0.03926 ( 384) hydrogen bonds : angle 4.23319 ( 1167) Misc. bond : bond 0.00056 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 107 time to evaluate : 0.198 Fit side-chains REVERT: A 29 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8656 (tptt) REVERT: A 43 LYS cc_start: 0.8309 (mptt) cc_final: 0.8014 (tppt) REVERT: A 153 GLU cc_start: 0.8112 (tt0) cc_final: 0.7294 (tm-30) REVERT: A 163 MET cc_start: 0.8494 (ptm) cc_final: 0.8282 (ttp) REVERT: A 167 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6807 (mt-10) REVERT: A 196 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7599 (tt) REVERT: A 226 GLU cc_start: 0.7463 (tt0) cc_final: 0.6894 (tt0) REVERT: A 292 GLU cc_start: 0.8626 (mp0) cc_final: 0.8152 (mp0) REVERT: A 375 HIS cc_start: 0.8377 (m-70) cc_final: 0.8117 (m90) REVERT: A 462 PHE cc_start: 0.7752 (t80) cc_final: 0.7482 (t80) REVERT: A 480 GLU cc_start: 0.8920 (tt0) cc_final: 0.8601 (tp30) REVERT: A 484 GLU cc_start: 0.7968 (tp30) cc_final: 0.7275 (tp30) REVERT: A 487 ASN cc_start: 0.8416 (m-40) cc_final: 0.7546 (t0) REVERT: A 523 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8433 (mtm) outliers start: 40 outliers final: 17 residues processed: 131 average time/residue: 0.3997 time to fit residues: 56.4316 Evaluate side-chains 120 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 80 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 576 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.164522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.119873 restraints weight = 8459.154| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.00 r_work: 0.3373 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6790 Z= 0.169 Angle : 0.597 11.468 9186 Z= 0.290 Chirality : 0.043 0.199 1099 Planarity : 0.004 0.052 1174 Dihedral : 3.980 23.160 929 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 6.84 % Allowed : 33.10 % Favored : 60.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.28), residues: 878 helix: 1.56 (0.23), residues: 483 sheet: -1.06 (0.66), residues: 65 loop : -1.35 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 108 TYR 0.014 0.001 TYR A 831 PHE 0.009 0.001 PHE A 685 TRP 0.022 0.002 TRP A 48 HIS 0.001 0.000 HIS A 552 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 6789) covalent geometry : angle 0.59739 ( 9186) hydrogen bonds : bond 0.03976 ( 384) hydrogen bonds : angle 4.25652 ( 1167) Misc. bond : bond 0.00059 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 105 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8697 (tptt) REVERT: A 43 LYS cc_start: 0.8338 (mptt) cc_final: 0.8050 (tppt) REVERT: A 153 GLU cc_start: 0.8160 (tt0) cc_final: 0.7380 (tm-30) REVERT: A 163 MET cc_start: 0.8403 (ptm) cc_final: 0.8171 (ttp) REVERT: A 196 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7667 (tt) REVERT: A 226 GLU cc_start: 0.7491 (tt0) cc_final: 0.6920 (tt0) REVERT: A 234 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7583 (ttm-80) REVERT: A 292 GLU cc_start: 0.8601 (mp0) cc_final: 0.8181 (mp0) REVERT: A 375 HIS cc_start: 0.8427 (m-70) cc_final: 0.8176 (m90) REVERT: A 460 TYR cc_start: 0.7269 (m-80) cc_final: 0.7034 (m-80) REVERT: A 462 PHE cc_start: 0.7778 (t80) cc_final: 0.7479 (t80) REVERT: A 484 GLU cc_start: 0.8003 (tp30) cc_final: 0.7325 (tp30) REVERT: A 487 ASN cc_start: 0.8418 (m-40) cc_final: 0.7558 (t0) REVERT: A 523 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8507 (mtm) REVERT: A 583 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7977 (mm-30) REVERT: A 880 LYS cc_start: 0.5594 (OUTLIER) cc_final: 0.3902 (tptt) outliers start: 49 outliers final: 20 residues processed: 139 average time/residue: 0.4012 time to fit residues: 59.8312 Evaluate side-chains 128 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 234 ARG Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 880 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 68 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 51 optimal weight: 10.0000 chunk 20 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 64 optimal weight: 0.0170 chunk 85 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 576 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.166278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.122180 restraints weight = 8295.783| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.03 r_work: 0.3407 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6790 Z= 0.131 Angle : 0.599 11.918 9186 Z= 0.287 Chirality : 0.042 0.175 1099 Planarity : 0.004 0.053 1174 Dihedral : 3.915 22.494 929 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 5.31 % Allowed : 34.50 % Favored : 60.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.29), residues: 878 helix: 1.71 (0.23), residues: 483 sheet: -0.92 (0.68), residues: 65 loop : -1.32 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 108 TYR 0.012 0.001 TYR A 831 PHE 0.009 0.001 PHE A 455 TRP 0.026 0.002 TRP A 48 HIS 0.001 0.000 HIS A 552 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 6789) covalent geometry : angle 0.59936 ( 9186) hydrogen bonds : bond 0.03738 ( 384) hydrogen bonds : angle 4.12967 ( 1167) Misc. bond : bond 0.00030 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 108 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8659 (tptt) REVERT: A 43 LYS cc_start: 0.8362 (mptt) cc_final: 0.7991 (tppt) REVERT: A 153 GLU cc_start: 0.8073 (tt0) cc_final: 0.7367 (tm-30) REVERT: A 189 ASN cc_start: 0.9067 (p0) cc_final: 0.8777 (p0) REVERT: A 196 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7627 (tt) REVERT: A 226 GLU cc_start: 0.7458 (tt0) cc_final: 0.6915 (tt0) REVERT: A 234 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7509 (ttm-80) REVERT: A 292 GLU cc_start: 0.8534 (mp0) cc_final: 0.8190 (mp0) REVERT: A 375 HIS cc_start: 0.8380 (m-70) cc_final: 0.8146 (m90) REVERT: A 460 TYR cc_start: 0.7262 (m-80) cc_final: 0.7029 (m-80) REVERT: A 462 PHE cc_start: 0.7796 (t80) cc_final: 0.7416 (t80) REVERT: A 480 GLU cc_start: 0.8919 (tt0) cc_final: 0.8605 (tp30) REVERT: A 484 GLU cc_start: 0.7979 (tp30) cc_final: 0.7301 (tp30) REVERT: A 487 ASN cc_start: 0.8394 (m-40) cc_final: 0.7513 (t0) REVERT: A 497 TYR cc_start: 0.7694 (p90) cc_final: 0.7214 (p90) REVERT: A 523 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8421 (mtm) REVERT: A 583 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7959 (mm-30) REVERT: A 880 LYS cc_start: 0.5506 (OUTLIER) cc_final: 0.3810 (tptt) outliers start: 38 outliers final: 15 residues processed: 134 average time/residue: 0.4436 time to fit residues: 63.6692 Evaluate side-chains 121 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 234 ARG Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 880 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 32 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.161617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.116910 restraints weight = 8380.684| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.99 r_work: 0.3368 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6790 Z= 0.209 Angle : 0.646 11.126 9186 Z= 0.312 Chirality : 0.044 0.182 1099 Planarity : 0.004 0.054 1174 Dihedral : 4.015 22.888 929 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 5.59 % Allowed : 34.36 % Favored : 60.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.28), residues: 878 helix: 1.50 (0.23), residues: 483 sheet: -1.04 (0.69), residues: 63 loop : -1.35 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 108 TYR 0.016 0.002 TYR A 831 PHE 0.013 0.001 PHE A 674 TRP 0.027 0.003 TRP A 48 HIS 0.001 0.000 HIS A 127 Details of bonding type rmsd covalent geometry : bond 0.00492 ( 6789) covalent geometry : angle 0.64591 ( 9186) hydrogen bonds : bond 0.04109 ( 384) hydrogen bonds : angle 4.32859 ( 1167) Misc. bond : bond 0.00083 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 104 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 2 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7688 (tm-30) REVERT: A 29 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8669 (tptt) REVERT: A 43 LYS cc_start: 0.8317 (mptt) cc_final: 0.7925 (tppt) REVERT: A 45 ASP cc_start: 0.7911 (m-30) cc_final: 0.7603 (m-30) REVERT: A 153 GLU cc_start: 0.8155 (tt0) cc_final: 0.7365 (tm-30) REVERT: A 167 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.7050 (mt-10) REVERT: A 196 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7676 (tt) REVERT: A 226 GLU cc_start: 0.7551 (tt0) cc_final: 0.6951 (tt0) REVERT: A 234 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7581 (ttm-80) REVERT: A 292 GLU cc_start: 0.8666 (mp0) cc_final: 0.8205 (mp0) REVERT: A 375 HIS cc_start: 0.8426 (m-70) cc_final: 0.8176 (m90) REVERT: A 462 PHE cc_start: 0.7960 (t80) cc_final: 0.7580 (t80) REVERT: A 480 GLU cc_start: 0.8916 (tt0) cc_final: 0.8613 (tp30) REVERT: A 484 GLU cc_start: 0.7998 (tp30) cc_final: 0.7323 (tp30) REVERT: A 487 ASN cc_start: 0.8411 (m-40) cc_final: 0.7566 (t0) REVERT: A 497 TYR cc_start: 0.7747 (p90) cc_final: 0.7471 (p90) REVERT: A 523 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8554 (mtm) REVERT: A 583 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7964 (mm-30) REVERT: A 880 LYS cc_start: 0.5618 (OUTLIER) cc_final: 0.3827 (tptt) outliers start: 40 outliers final: 19 residues processed: 131 average time/residue: 0.4431 time to fit residues: 62.1405 Evaluate side-chains 128 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 234 ARG Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 880 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 83 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 64 optimal weight: 0.2980 chunk 65 optimal weight: 0.6980 chunk 4 optimal weight: 0.0370 chunk 19 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.166272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.122570 restraints weight = 8465.966| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.00 r_work: 0.3427 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6790 Z= 0.132 Angle : 0.627 11.200 9186 Z= 0.298 Chirality : 0.042 0.178 1099 Planarity : 0.004 0.055 1174 Dihedral : 3.933 22.379 929 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.87 % Favored : 96.01 % Rotamer: Outliers : 3.91 % Allowed : 36.17 % Favored : 59.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.29), residues: 878 helix: 1.66 (0.23), residues: 489 sheet: -0.59 (0.75), residues: 56 loop : -1.32 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 108 TYR 0.013 0.001 TYR A 460 PHE 0.008 0.001 PHE A 685 TRP 0.033 0.003 TRP A 48 HIS 0.001 0.000 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 6789) covalent geometry : angle 0.62746 ( 9186) hydrogen bonds : bond 0.03730 ( 384) hydrogen bonds : angle 4.12613 ( 1167) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8703 (tptt) REVERT: A 43 LYS cc_start: 0.8342 (mptt) cc_final: 0.7938 (tppt) REVERT: A 153 GLU cc_start: 0.8048 (tt0) cc_final: 0.7369 (tm-30) REVERT: A 167 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6725 (mt-10) REVERT: A 189 ASN cc_start: 0.9162 (p0) cc_final: 0.8953 (p0) REVERT: A 226 GLU cc_start: 0.7352 (tt0) cc_final: 0.6839 (tt0) REVERT: A 234 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7507 (ttm-80) REVERT: A 292 GLU cc_start: 0.8532 (mp0) cc_final: 0.8045 (mp0) REVERT: A 375 HIS cc_start: 0.8348 (m-70) cc_final: 0.8115 (m90) REVERT: A 462 PHE cc_start: 0.7838 (t80) cc_final: 0.7524 (t80) REVERT: A 470 MET cc_start: 0.2223 (ppp) cc_final: 0.0886 (ptt) REVERT: A 480 GLU cc_start: 0.8925 (tt0) cc_final: 0.8596 (tp30) REVERT: A 484 GLU cc_start: 0.8014 (tp30) cc_final: 0.7291 (OUTLIER) REVERT: A 487 ASN cc_start: 0.8358 (m-40) cc_final: 0.7511 (t0) REVERT: A 497 TYR cc_start: 0.7703 (p90) cc_final: 0.7481 (p90) REVERT: A 523 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8384 (mtm) REVERT: A 583 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7953 (mm-30) REVERT: A 729 MET cc_start: 0.7932 (mmt) cc_final: 0.7725 (mmp) REVERT: A 880 LYS cc_start: 0.5502 (OUTLIER) cc_final: 0.3710 (tptt) outliers start: 28 outliers final: 16 residues processed: 120 average time/residue: 0.4206 time to fit residues: 54.0304 Evaluate side-chains 118 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 234 ARG Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 880 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 45 optimal weight: 0.0870 chunk 27 optimal weight: 0.9980 chunk 75 optimal weight: 0.0770 chunk 59 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.165689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.121903 restraints weight = 8386.670| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.99 r_work: 0.3406 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6790 Z= 0.142 Angle : 0.628 11.937 9186 Z= 0.300 Chirality : 0.042 0.171 1099 Planarity : 0.004 0.058 1174 Dihedral : 3.908 22.603 929 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.44 % Favored : 95.44 % Rotamer: Outliers : 4.05 % Allowed : 36.31 % Favored : 59.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.29), residues: 878 helix: 1.67 (0.23), residues: 489 sheet: -0.69 (0.74), residues: 58 loop : -1.33 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 108 TYR 0.014 0.001 TYR A 831 PHE 0.008 0.001 PHE A 685 TRP 0.038 0.003 TRP A 48 HIS 0.001 0.000 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 6789) covalent geometry : angle 0.62817 ( 9186) hydrogen bonds : bond 0.03754 ( 384) hydrogen bonds : angle 4.11716 ( 1167) Misc. bond : bond 0.00044 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8678 (tptt) REVERT: A 43 LYS cc_start: 0.8365 (mptt) cc_final: 0.7968 (tppt) REVERT: A 153 GLU cc_start: 0.7965 (tt0) cc_final: 0.7365 (tm-30) REVERT: A 226 GLU cc_start: 0.7343 (tt0) cc_final: 0.6855 (tt0) REVERT: A 234 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7550 (ttm-80) REVERT: A 292 GLU cc_start: 0.8536 (mp0) cc_final: 0.8180 (mp0) REVERT: A 375 HIS cc_start: 0.8365 (m-70) cc_final: 0.8131 (m90) REVERT: A 462 PHE cc_start: 0.7839 (t80) cc_final: 0.7499 (t80) REVERT: A 470 MET cc_start: 0.2192 (ppp) cc_final: 0.0930 (ptt) REVERT: A 480 GLU cc_start: 0.8942 (tt0) cc_final: 0.8648 (tp30) REVERT: A 484 GLU cc_start: 0.8030 (tp30) cc_final: 0.7393 (tp30) REVERT: A 487 ASN cc_start: 0.8376 (m-40) cc_final: 0.7577 (t0) REVERT: A 497 TYR cc_start: 0.7726 (p90) cc_final: 0.7272 (p90) REVERT: A 523 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8458 (mtm) REVERT: A 583 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.8004 (mm-30) REVERT: A 880 LYS cc_start: 0.5579 (OUTLIER) cc_final: 0.3745 (tptt) outliers start: 29 outliers final: 17 residues processed: 119 average time/residue: 0.4227 time to fit residues: 53.6090 Evaluate side-chains 117 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 234 ARG Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 880 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.164994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.120156 restraints weight = 8298.448| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.02 r_work: 0.3387 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6790 Z= 0.175 Angle : 0.648 12.258 9186 Z= 0.311 Chirality : 0.044 0.227 1099 Planarity : 0.004 0.060 1174 Dihedral : 3.992 22.403 929 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.21 % Favored : 95.67 % Rotamer: Outliers : 4.33 % Allowed : 35.47 % Favored : 60.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.29), residues: 878 helix: 1.56 (0.23), residues: 489 sheet: -0.78 (0.68), residues: 71 loop : -1.31 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 108 TYR 0.014 0.001 TYR A 831 PHE 0.010 0.001 PHE A 674 TRP 0.040 0.003 TRP A 48 HIS 0.001 0.000 HIS A 552 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 6789) covalent geometry : angle 0.64778 ( 9186) hydrogen bonds : bond 0.03955 ( 384) hydrogen bonds : angle 4.22320 ( 1167) Misc. bond : bond 0.00065 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2694.27 seconds wall clock time: 46 minutes 40.94 seconds (2800.94 seconds total)