Starting phenix.real_space_refine on Thu Jul 2 12:20:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pla_13486/07_2026/7pla_13486_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pla_13486/07_2026/7pla_13486.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pla_13486/07_2026/7pla_13486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pla_13486/07_2026/7pla_13486.map" model { file = "/net/cci-nas-00/data/ceres_data/7pla_13486/07_2026/7pla_13486_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pla_13486/07_2026/7pla_13486_neut.cif" } resolution = 3.04 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= 0.005 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: 5 Type Number sf(0) Gaussians P 243 5.49 5 S 11 5.16 5 C 4560 2.51 5 N 1555 2.21 5 O 2332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8701 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3533 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 420} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 4619 Classifications: {'RNA': 217} Modifications used: {'rna2p_pur': 18, 'rna2p_pyr': 18, 'rna3p_pur': 92, 'rna3p_pyr': 89} Link IDs: {'rna2p': 36, 'rna3p': 180} Chain breaks: 3 Chain: "C" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 339 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "D" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 210 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.47, per 1000 atoms: 0.17 Number of scatterers: 8701 At special positions: 0 Unit cell: (99.84, 92.8, 116.48, 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 11 16.00 P 243 15.00 O 2332 8.00 N 1555 7.00 C 4560 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.64 Conformation dependent library (CDL) restraints added in 123.8 milliseconds 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 826 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 2 sheets defined 56.5% alpha, 15.3% beta 89 base pairs and 155 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 13 through 42 Proline residue: A 30 - end of helix removed outlier: 3.709A pdb=" N ASN A 33 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLN A 41 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N HIS A 42 " --> pdb=" O GLN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 69 removed outlier: 3.779A pdb=" N GLN A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) Proline residue: A 65 - end of helix removed outlier: 4.414A pdb=" N THR A 68 " --> pdb=" O GLN A 64 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASP A 69 " --> pdb=" O PRO A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 92 removed outlier: 3.593A pdb=" N MET A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE A 84 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 339 removed outlier: 4.048A pdb=" N PHE A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 347 removed outlier: 3.604A pdb=" N LEU A 346 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 343 through 347' Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 407 Processing helix chain 'A' and resid 413 through 430 removed outlier: 4.096A pdb=" N ASN A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'A' and resid 485 through 506 removed outlier: 3.591A pdb=" N GLN A 506 " --> pdb=" O ARG A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 538 removed outlier: 3.661A pdb=" N ALA A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 551 Processing helix chain 'A' and resid 552 through 567 Processing helix chain 'A' and resid 570 through 585 Processing helix chain 'A' and resid 591 through 605 Processing helix chain 'A' and resid 618 through 636 removed outlier: 3.830A pdb=" N THR A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 283 through 285 removed outlier: 6.708A pdb=" N LEU A 349 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ASP A 378 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN A 351 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU A 371 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 10 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LEU A 301 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 471 through 475 removed outlier: 6.835A pdb=" N VAL A 463 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N TYR A 474 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL A 461 " --> pdb=" O TYR A 474 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N SER A 445 " --> pdb=" O ALA A 540 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N SER A 542 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE A 447 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N VAL A 544 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A 449 " --> pdb=" O VAL A 544 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N VAL A 451 " --> pdb=" O PRO A 546 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL A 607 " --> pdb=" O GLY A 541 " (cutoff:3.500A) 202 hydrogen bonds defined for protein. 597 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 224 hydrogen bonds 412 hydrogen bond angles 0 basepair planarities 89 basepair parallelities 155 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 958 1.32 - 1.44: 3816 1.44 - 1.56: 4107 1.56 - 1.69: 477 1.69 - 1.81: 16 Bond restraints: 9374 Sorted by residual: bond pdb=" O3' G B 230 " pdb=" P G B 231 " ideal model delta sigma weight residual 1.607 1.557 0.050 1.50e-02 4.44e+03 1.12e+01 bond pdb=" N GLY A 359 " pdb=" CA GLY A 359 " ideal model delta sigma weight residual 1.445 1.477 -0.032 9.90e-03 1.02e+04 1.06e+01 bond pdb=" O3' G B 40 " pdb=" P A B 41 " ideal model delta sigma weight residual 1.607 1.559 0.048 1.50e-02 4.44e+03 1.04e+01 bond pdb=" C PRO A 365 " pdb=" O PRO A 365 " ideal model delta sigma weight residual 1.238 1.195 0.043 1.36e-02 5.41e+03 9.91e+00 bond pdb=" O3' A B 229 " pdb=" P G B 230 " ideal model delta sigma weight residual 1.607 1.560 0.047 1.50e-02 4.44e+03 9.85e+00 ... (remaining 9369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 12722 1.89 - 3.79: 892 3.79 - 5.68: 188 5.68 - 7.57: 23 7.57 - 9.47: 7 Bond angle restraints: 13832 Sorted by residual: angle pdb=" N ASN A 367 " pdb=" CA ASN A 367 " pdb=" C ASN A 367 " ideal model delta sigma weight residual 111.75 103.96 7.79 1.28e+00 6.10e-01 3.71e+01 angle pdb=" O3' A B 130 " pdb=" C3' A B 130 " pdb=" C2' A B 130 " ideal model delta sigma weight residual 109.50 117.81 -8.31 1.50e+00 4.44e-01 3.07e+01 angle pdb=" O3' G B 86 " pdb=" C3' G B 86 " pdb=" C2' G B 86 " ideal model delta sigma weight residual 109.50 101.27 8.23 1.50e+00 4.44e-01 3.01e+01 angle pdb=" O3' U B 98 " pdb=" C3' U B 98 " pdb=" C2' U B 98 " ideal model delta sigma weight residual 109.50 117.71 -8.21 1.50e+00 4.44e-01 3.00e+01 angle pdb=" C4' G B 230 " pdb=" C3' G B 230 " pdb=" O3' G B 230 " ideal model delta sigma weight residual 113.00 104.98 8.02 1.50e+00 4.44e-01 2.86e+01 ... (remaining 13827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 5020 35.80 - 71.59: 744 71.59 - 107.39: 75 107.39 - 143.19: 3 143.19 - 178.99: 9 Dihedral angle restraints: 5851 sinusoidal: 4577 harmonic: 1274 Sorted by residual: dihedral pdb=" O4' U B 84 " pdb=" C1' U B 84 " pdb=" N1 U B 84 " pdb=" C2 U B 84 " ideal model delta sinusoidal sigma weight residual 200.00 25.83 174.17 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" C5' U B 98 " pdb=" C4' U B 98 " pdb=" C3' U B 98 " pdb=" O3' U B 98 " ideal model delta sinusoidal sigma weight residual 147.00 87.55 59.45 1 8.00e+00 1.56e-02 7.37e+01 dihedral pdb=" O4' U B 8 " pdb=" C1' U B 8 " pdb=" N1 U B 8 " pdb=" C2 U B 8 " ideal model delta sinusoidal sigma weight residual -160.00 -34.81 -125.19 1 1.50e+01 4.44e-03 6.73e+01 ... (remaining 5848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 1361 0.116 - 0.232: 343 0.232 - 0.347: 16 0.347 - 0.463: 2 0.463 - 0.579: 2 Chirality restraints: 1724 Sorted by residual: chirality pdb=" P G B 174 " pdb=" OP1 G B 174 " pdb=" OP2 G B 174 " pdb=" O5' G B 174 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.58 2.00e-01 2.50e+01 8.38e+00 chirality pdb=" P G B 221 " pdb=" OP1 G B 221 " pdb=" OP2 G B 221 " pdb=" O5' G B 221 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.47e+00 chirality pdb=" C3' A B 130 " pdb=" C4' A B 130 " pdb=" O3' A B 130 " pdb=" C2' A B 130 " both_signs ideal model delta sigma weight residual False -2.74 -2.37 -0.37 2.00e-01 2.50e+01 3.51e+00 ... (remaining 1721 not shown) Planarity restraints: 870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U B 101 " -0.045 2.00e-02 2.50e+03 2.37e-02 1.26e+01 pdb=" N1 U B 101 " 0.051 2.00e-02 2.50e+03 pdb=" C2 U B 101 " 0.009 2.00e-02 2.50e+03 pdb=" O2 U B 101 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U B 101 " -0.004 2.00e-02 2.50e+03 pdb=" C4 U B 101 " -0.014 2.00e-02 2.50e+03 pdb=" O4 U B 101 " -0.007 2.00e-02 2.50e+03 pdb=" C5 U B 101 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U B 101 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 45 " -0.032 2.00e-02 2.50e+03 1.81e-02 7.38e+00 pdb=" N1 U B 45 " 0.040 2.00e-02 2.50e+03 pdb=" C2 U B 45 " 0.007 2.00e-02 2.50e+03 pdb=" O2 U B 45 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U B 45 " -0.007 2.00e-02 2.50e+03 pdb=" C4 U B 45 " -0.008 2.00e-02 2.50e+03 pdb=" O4 U B 45 " -0.002 2.00e-02 2.50e+03 pdb=" C5 U B 45 " -0.007 2.00e-02 2.50e+03 pdb=" C6 U B 45 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 44 " -0.029 2.00e-02 2.50e+03 1.56e-02 5.50e+00 pdb=" N1 U B 44 " 0.035 2.00e-02 2.50e+03 pdb=" C2 U B 44 " 0.005 2.00e-02 2.50e+03 pdb=" O2 U B 44 " -0.001 2.00e-02 2.50e+03 pdb=" N3 U B 44 " 0.000 2.00e-02 2.50e+03 pdb=" C4 U B 44 " -0.004 2.00e-02 2.50e+03 pdb=" O4 U B 44 " -0.008 2.00e-02 2.50e+03 pdb=" C5 U B 44 " -0.003 2.00e-02 2.50e+03 pdb=" C6 U B 44 " 0.005 2.00e-02 2.50e+03 ... (remaining 867 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1367 2.75 - 3.29: 7522 3.29 - 3.83: 18158 3.83 - 4.36: 22029 4.36 - 4.90: 28991 Nonbonded interactions: 78067 Sorted by model distance: nonbonded pdb=" OG SER A 424 " pdb=" NH1 ARG A 428 " model vdw 2.216 3.120 nonbonded pdb=" OG SER A 77 " pdb=" C5' DG D 16 " model vdw 2.234 3.440 nonbonded pdb=" O GLY A 454 " pdb=" OH TYR A 590 " model vdw 2.257 3.040 nonbonded pdb=" O TRP A 293 " pdb=" NE2 GLN A 332 " model vdw 2.258 3.120 nonbonded pdb=" NZ LYS A 547 " pdb=" OE1 GLU A 610 " model vdw 2.284 3.120 ... (remaining 78062 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.430 Find NCS groups from input model: 0.020 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6116 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 : 0.007 0.050 9374 Z= 0.488 Angle : 1.080 9.466 13832 Z= 0.757 Chirality : 0.092 0.579 1724 Planarity : 0.005 0.031 870 Dihedral : 26.236 178.987 5025 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.26 % Allowed : 0.52 % Favored : 99.22 % 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 are not related in a simple way. whole: -0.03 (0.41), residues: 429 helix: 1.11 (0.34), residues: 231 sheet: -1.19 (0.63), residues: 70 loop : -1.32 (0.56), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 17 TYR 0.011 0.001 TYR A 474 PHE 0.017 0.002 PHE A 347 TRP 0.026 0.002 TRP A 94 HIS 0.009 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00748 / 0.49 ( 9374) covalent geometry : angle 1.08040 / 0.76 (13832) hydrogen bonds : bond 0.15814 / 10.08 ( 426) hydrogen bonds : angle 9.28498 / 6.75 ( 1009) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.175 Fit side-chains REVERT: A 81 MET cc_start: 0.8943 (tpt) cc_final: 0.8503 (tpp) REVERT: A 347 PHE cc_start: 0.8227 (m-80) cc_final: 0.7981 (m-80) outliers start: 1 outliers final: 0 residues processed: 13 average time/residue: 0.0853 time to fit residues: 1.6685 Evaluate side-chains 11 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 20.0000 chunk 53 optimal weight: 30.0000 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 50.0000 chunk 62 optimal weight: 40.0000 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 40.0000 chunk 27 optimal weight: 4.9990 overall best weight: 5.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.064807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.046611 restraints weight = 47301.392| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.36 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9374 Z= 0.244 Angle : 0.653 8.481 13832 Z= 0.398 Chirality : 0.044 0.258 1724 Planarity : 0.005 0.034 870 Dihedral : 27.094 179.303 4135 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.04 % Allowed : 4.40 % Favored : 94.56 % 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 are not related in a simple way. whole: 0.18 (0.41), residues: 429 helix: 1.41 (0.33), residues: 232 sheet: -1.44 (0.58), residues: 70 loop : -1.27 (0.57), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 300 TYR 0.010 0.002 TYR A 474 PHE 0.007 0.001 PHE A 325 TRP 0.011 0.002 TRP A 94 HIS 0.004 0.001 HIS A 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.24 ( 9374) covalent geometry : angle 0.65322 / 0.40 (13832) hydrogen bonds : bond 0.06892 / 4.49 ( 426) hydrogen bonds : angle 4.43768 / 3.19 ( 1009) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 13 time to evaluate : 0.138 Fit side-chains REVERT: A 35 LEU cc_start: 0.9409 (mt) cc_final: 0.9199 (mt) REVERT: A 81 MET cc_start: 0.8884 (tpt) cc_final: 0.8582 (tpt) REVERT: A 347 PHE cc_start: 0.8489 (m-80) cc_final: 0.7967 (m-80) outliers start: 4 outliers final: 2 residues processed: 16 average time/residue: 0.0721 time to fit residues: 1.7461 Evaluate side-chains 13 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 11 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 376 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 23 optimal weight: 8.9990 chunk 65 optimal weight: 60.0000 chunk 50 optimal weight: 30.0000 chunk 40 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 21 optimal weight: 30.0000 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 60 optimal weight: 30.0000 chunk 19 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.064000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.045674 restraints weight = 47937.701| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.32 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9374 Z= 0.255 Angle : 0.627 7.839 13832 Z= 0.374 Chirality : 0.043 0.272 1724 Planarity : 0.005 0.036 870 Dihedral : 26.573 178.709 4135 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.07 % Allowed : 7.77 % Favored : 90.16 % 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 are not related in a simple way. whole: 0.26 (0.42), residues: 429 helix: 1.66 (0.33), residues: 227 sheet: -1.76 (0.54), residues: 80 loop : -1.21 (0.60), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 300 TYR 0.021 0.003 TYR A 89 PHE 0.011 0.002 PHE A 401 TRP 0.017 0.002 TRP A 94 HIS 0.005 0.002 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.25 ( 9374) covalent geometry : angle 0.62719 / 0.37 (13832) hydrogen bonds : bond 0.06164 / 3.99 ( 426) hydrogen bonds : angle 3.98721 / 2.82 ( 1009) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 9 time to evaluate : 0.174 Fit side-chains REVERT: A 81 MET cc_start: 0.8723 (tpt) cc_final: 0.8422 (tpt) outliers start: 8 outliers final: 4 residues processed: 16 average time/residue: 0.1172 time to fit residues: 2.5167 Evaluate side-chains 12 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 8 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 376 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 46 optimal weight: 30.0000 chunk 29 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.064492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.046256 restraints weight = 48546.805| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.27 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9374 Z= 0.172 Angle : 0.545 9.001 13832 Z= 0.327 Chirality : 0.039 0.281 1724 Planarity : 0.005 0.088 870 Dihedral : 26.389 179.259 4135 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.81 % Allowed : 8.81 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.42), residues: 429 helix: 1.98 (0.34), residues: 228 sheet: -1.80 (0.51), residues: 87 loop : -1.23 (0.62), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 421 TYR 0.011 0.001 TYR A 474 PHE 0.009 0.001 PHE A 328 TRP 0.010 0.001 TRP A 94 HIS 0.002 0.001 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.17 ( 9374) covalent geometry : angle 0.54489 / 0.33 (13832) hydrogen bonds : bond 0.05475 / 3.59 ( 426) hydrogen bonds : angle 3.76787 / 2.67 ( 1009) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 11 time to evaluate : 0.137 Fit side-chains REVERT: A 81 MET cc_start: 0.8656 (tpt) cc_final: 0.8413 (tpt) REVERT: A 405 MET cc_start: 0.7710 (ppp) cc_final: 0.6919 (ppp) outliers start: 7 outliers final: 6 residues processed: 16 average time/residue: 0.0688 time to fit residues: 1.7600 Evaluate side-chains 15 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 9 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 608 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 40.0000 chunk 39 optimal weight: 3.9990 chunk 64 optimal weight: 50.0000 chunk 23 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 17 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 367 ASN A 379 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.064384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.045999 restraints weight = 48467.047| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.28 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9374 Z= 0.216 Angle : 0.556 7.573 13832 Z= 0.334 Chirality : 0.039 0.281 1724 Planarity : 0.005 0.072 870 Dihedral : 26.191 179.166 4135 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.11 % Allowed : 9.07 % Favored : 87.82 % 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 are not related in a simple way. whole: 0.55 (0.41), residues: 429 helix: 1.94 (0.33), residues: 230 sheet: -1.58 (0.52), residues: 84 loop : -1.27 (0.61), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 17 TYR 0.018 0.002 TYR A 474 PHE 0.008 0.001 PHE A 325 TRP 0.010 0.002 TRP A 356 HIS 0.004 0.001 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.22 ( 9374) covalent geometry : angle 0.55585 / 0.33 (13832) hydrogen bonds : bond 0.05605 / 3.64 ( 426) hydrogen bonds : angle 3.71167 / 2.61 ( 1009) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 10 time to evaluate : 0.158 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 19 average time/residue: 0.0770 time to fit residues: 2.2138 Evaluate side-chains 15 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 10 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 4 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 28 optimal weight: 0.6980 chunk 49 optimal weight: 30.0000 chunk 30 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 55 optimal weight: 40.0000 chunk 44 optimal weight: 20.0000 chunk 65 optimal weight: 60.0000 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 overall best weight: 8.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 379 ASN A 446 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.064273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.046009 restraints weight = 48990.738| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 3.39 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 9374 Z= 0.311 Angle : 0.627 8.029 13832 Z= 0.368 Chirality : 0.042 0.260 1724 Planarity : 0.005 0.062 870 Dihedral : 26.123 179.126 4135 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.37 % Allowed : 9.84 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.41), residues: 429 helix: 1.59 (0.33), residues: 227 sheet: -1.97 (0.52), residues: 84 loop : -1.29 (0.59), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 17 TYR 0.012 0.002 TYR A 374 PHE 0.010 0.002 PHE A 281 TRP 0.014 0.002 TRP A 94 HIS 0.005 0.001 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.31 ( 9374) covalent geometry : angle 0.62705 / 0.37 (13832) hydrogen bonds : bond 0.06553 / 4.24 ( 426) hydrogen bonds : angle 3.93284 / 2.77 ( 1009) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 10 time to evaluate : 0.150 Fit side-chains REVERT: A 527 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8263 (mp) REVERT: A 570 TYR cc_start: 0.8138 (t80) cc_final: 0.7702 (t80) outliers start: 13 outliers final: 8 residues processed: 21 average time/residue: 0.0598 time to fit residues: 1.9991 Evaluate side-chains 19 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 10 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 608 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 29 optimal weight: 3.9990 chunk 55 optimal weight: 30.0000 chunk 58 optimal weight: 50.0000 chunk 34 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 63 optimal weight: 20.0000 chunk 52 optimal weight: 30.0000 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.065839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.048016 restraints weight = 49369.182| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 3.17 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9374 Z= 0.164 Angle : 0.523 7.459 13832 Z= 0.314 Chirality : 0.037 0.285 1724 Planarity : 0.004 0.038 870 Dihedral : 26.130 179.093 4135 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.11 % Allowed : 11.40 % Favored : 85.49 % 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 are not related in a simple way. whole: 0.46 (0.42), residues: 429 helix: 1.93 (0.34), residues: 228 sheet: -1.77 (0.52), residues: 85 loop : -1.25 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 17 TYR 0.018 0.002 TYR A 474 PHE 0.010 0.001 PHE A 328 TRP 0.009 0.001 TRP A 94 HIS 0.002 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.16 ( 9374) covalent geometry : angle 0.52340 / 0.31 (13832) hydrogen bonds : bond 0.05296 / 3.48 ( 426) hydrogen bonds : angle 3.64615 / 2.57 ( 1009) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 10 time to evaluate : 0.203 Fit side-chains REVERT: A 405 MET cc_start: 0.7779 (ppp) cc_final: 0.7281 (ppp) outliers start: 12 outliers final: 8 residues processed: 19 average time/residue: 0.0731 time to fit residues: 2.1557 Evaluate side-chains 18 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 10 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 608 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 4 optimal weight: 20.0000 chunk 50 optimal weight: 30.0000 chunk 35 optimal weight: 5.9990 chunk 46 optimal weight: 30.0000 chunk 33 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 57 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.068296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.049927 restraints weight = 52843.573| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.44 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9374 Z= 0.198 Angle : 0.536 7.521 13832 Z= 0.320 Chirality : 0.038 0.278 1724 Planarity : 0.004 0.035 870 Dihedral : 26.031 179.194 4135 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.11 % Allowed : 12.18 % Favored : 84.72 % 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 are not related in a simple way. whole: 0.47 (0.42), residues: 429 helix: 1.93 (0.34), residues: 228 sheet: -1.72 (0.52), residues: 84 loop : -1.26 (0.60), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 17 TYR 0.013 0.002 TYR A 474 PHE 0.008 0.001 PHE A 285 TRP 0.010 0.002 TRP A 94 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.20 ( 9374) covalent geometry : angle 0.53632 / 0.32 (13832) hydrogen bonds : bond 0.05506 / 3.58 ( 426) hydrogen bonds : angle 3.65636 / 2.58 ( 1009) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 9 time to evaluate : 0.123 Fit side-chains REVERT: A 405 MET cc_start: 0.7825 (ppp) cc_final: 0.7365 (ppp) outliers start: 12 outliers final: 12 residues processed: 20 average time/residue: 0.0701 time to fit residues: 2.1246 Evaluate side-chains 21 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 9 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 608 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 30 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 19 optimal weight: 30.0000 chunk 44 optimal weight: 20.0000 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.067769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.050291 restraints weight = 50222.224| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 3.18 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 9374 Z= 0.236 Angle : 0.571 8.351 13832 Z= 0.336 Chirality : 0.039 0.270 1724 Planarity : 0.005 0.035 870 Dihedral : 25.963 179.141 4135 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.37 % Allowed : 11.66 % Favored : 84.97 % 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 are not related in a simple way. whole: 0.38 (0.41), residues: 429 helix: 1.81 (0.34), residues: 228 sheet: -1.78 (0.52), residues: 83 loop : -1.21 (0.60), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 17 TYR 0.011 0.002 TYR A 474 PHE 0.008 0.001 PHE A 325 TRP 0.011 0.002 TRP A 94 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.24 ( 9374) covalent geometry : angle 0.57147 / 0.34 (13832) hydrogen bonds : bond 0.05790 / 3.76 ( 426) hydrogen bonds : angle 3.72658 / 2.63 ( 1009) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 10 time to evaluate : 0.124 Fit side-chains REVERT: A 81 MET cc_start: 0.9092 (mpp) cc_final: 0.8808 (pmm) REVERT: A 405 MET cc_start: 0.8005 (ppp) cc_final: 0.7564 (ppp) REVERT: A 570 TYR cc_start: 0.8161 (t80) cc_final: 0.7719 (t80) outliers start: 13 outliers final: 11 residues processed: 22 average time/residue: 0.0706 time to fit residues: 2.3562 Evaluate side-chains 21 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 10 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 608 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 59 optimal weight: 40.0000 chunk 17 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 46 optimal weight: 30.0000 chunk 10 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.068088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.050700 restraints weight = 50281.537| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 3.12 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9374 Z= 0.188 Angle : 0.529 7.389 13832 Z= 0.315 Chirality : 0.037 0.272 1724 Planarity : 0.004 0.033 870 Dihedral : 25.907 179.068 4135 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.37 % Allowed : 11.92 % Favored : 84.72 % 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 are not related in a simple way. whole: 0.57 (0.42), residues: 429 helix: 1.95 (0.34), residues: 228 sheet: -1.60 (0.52), residues: 82 loop : -1.18 (0.60), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 17 TYR 0.013 0.001 TYR A 474 PHE 0.006 0.001 PHE A 325 TRP 0.010 0.002 TRP A 94 HIS 0.002 0.001 HIS A 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.19 ( 9374) covalent geometry : angle 0.52915 / 0.31 (13832) hydrogen bonds : bond 0.05390 / 3.51 ( 426) hydrogen bonds : angle 3.61565 / 2.55 ( 1009) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 11 time to evaluate : 0.125 Fit side-chains REVERT: A 405 MET cc_start: 0.7961 (ppp) cc_final: 0.7539 (ppp) outliers start: 13 outliers final: 10 residues processed: 21 average time/residue: 0.0756 time to fit residues: 2.4343 Evaluate side-chains 20 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 10 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 608 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 8.9990 chunk 54 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 chunk 45 optimal weight: 50.0000 chunk 13 optimal weight: 8.9990 chunk 48 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 52 optimal weight: 40.0000 chunk 49 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.067730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.049395 restraints weight = 53176.503| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 3.55 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9374 Z= 0.285 Angle : 0.595 7.805 13832 Z= 0.348 Chirality : 0.040 0.258 1724 Planarity : 0.005 0.037 870 Dihedral : 25.840 179.965 4135 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.11 % Allowed : 12.44 % Favored : 84.46 % 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 are not related in a simple way. whole: 0.25 (0.41), residues: 429 helix: 1.62 (0.33), residues: 228 sheet: -1.65 (0.55), residues: 83 loop : -1.22 (0.59), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 17 TYR 0.010 0.002 TYR A 374 PHE 0.009 0.002 PHE A 325 TRP 0.013 0.002 TRP A 94 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.29 ( 9374) covalent geometry : angle 0.59508 / 0.35 (13832) hydrogen bonds : bond 0.06178 / 4.01 ( 426) hydrogen bonds : angle 3.76963 / 2.66 ( 1009) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1413.00 seconds wall clock time: 25 minutes 4.65 seconds (1504.65 seconds total)