Starting phenix.real_space_refine on Fri Sep 11 08:33:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pla_13486/09_2026/7pla_13486_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pla_13486/09_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_13486/09_2026/7pla_13486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pla_13486/09_2026/7pla_13486.map" model { file = "/net/cci-nas-00/data/ceres_data/7pla_13486/09_2026/7pla_13486_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pla_13486/09_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-2.2.1-6174/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: 2.16, per 1000 atoms: 0.25 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: 0.84 Conformation dependent library (CDL) restraints added in 154.8 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: 1.26 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: 2.07 Time building geometry restraints manager: 1.09 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 1.20e-02 6.94e+03 1.75e+01 bond pdb=" O3' G B 40 " pdb=" P A B 41 " ideal model delta sigma weight residual 1.607 1.559 0.048 1.20e-02 6.94e+03 1.63e+01 bond pdb=" O3' A B 229 " pdb=" P G B 230 " ideal model delta sigma weight residual 1.607 1.560 0.047 1.20e-02 6.94e+03 1.54e+01 bond pdb=" O3' U B 90 " pdb=" P C B 91 " ideal model delta sigma weight residual 1.607 1.563 0.044 1.20e-02 6.94e+03 1.36e+01 bond pdb=" O3' G B 135 " pdb=" P G B 136 " ideal model delta sigma weight residual 1.607 1.565 0.042 1.20e-02 6.94e+03 1.22e+01 ... (remaining 9369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 12888 1.89 - 3.79: 782 3.79 - 5.68: 134 5.68 - 7.57: 21 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=" C2' U B 48 " pdb=" C1' U B 48 " pdb=" N1 U B 48 " ideal model delta sigma weight residual 112.00 118.58 -6.58 1.10e+00 8.26e-01 3.58e+01 angle pdb=" N LYS A 407 " pdb=" CA LYS A 407 " pdb=" C LYS A 407 " ideal model delta sigma weight residual 112.38 118.50 -6.12 1.22e+00 6.72e-01 2.52e+01 angle pdb=" C2' U B 60 " pdb=" C1' U B 60 " pdb=" N1 U B 60 " ideal model delta sigma weight residual 112.00 117.25 -5.25 1.10e+00 8.26e-01 2.28e+01 angle pdb=" C2' C B 21 " pdb=" C1' C B 21 " pdb=" N1 C B 21 " ideal model delta sigma weight residual 112.00 117.12 -5.12 1.10e+00 8.26e-01 2.17e+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: 1502 0.116 - 0.232: 203 0.232 - 0.347: 15 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.480 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.570 ------------------------------------------------------------------------------- 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 : 0.008 0.050 9374 Z= 0.553 Angle : 1.012 9.466 13832 Z= 0.731 Chirality : 0.080 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 0.00756 / 0.55 ( 9374) covalent geometry : angle 1.01170 / 0.73 (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 : 0.215 Fit side-chains REVERT: A 81 MET cc_start: 0.8943 (tpt) cc_final: 0.8504 (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: 0.1255 time to fit residues: 2.3998 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 : 0.210 ------------------------------------------------------------------------------- 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: 30.0000 chunk 53 optimal weight: 40.0000 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: 20.0000 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 40.0000 chunk 45 optimal weight: 50.0000 chunk 27 optimal weight: 4.9990 overall best weight: 7.7790 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.064293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.046046 restraints weight = 47573.056| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 3.26 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1593 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= 0.284 Angle : 0.780 9.888 13832 Z= 0.433 Chirality : 0.053 0.403 1724 Planarity : 0.005 0.038 870 Dihedral : 26.840 179.962 4135 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.30 % Allowed : 5.18 % Favored : 93.52 % 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: 0.05 (0.41), residues: 429 helix: 1.26 (0.32), residues: 234 sheet: -1.56 (0.58), residues: 70 loop : -1.22 (0.58), residues: 125 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 0.008 0.002 PHE A 313 TRP 0.011 0.002 TRP A 94 HIS 0.005 0.001 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.28 ( 9374) covalent geometry : angle 0.77988 / 0.43 (13832) hydrogen bonds : bond 0.07265 / 4.73 ( 426) hydrogen bonds : angle 4.39025 / 3.14 ( 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 16 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 11 time to evaluate : 0.210 Fit side-chains REVERT: A 35 LEU cc_start: 0.9409 (mt) cc_final: 0.9198 (mt) REVERT: A 81 MET cc_start: 0.8906 (tpt) cc_final: 0.8614 (tpt) REVERT: A 347 PHE cc_start: 0.8550 (m-80) cc_final: 0.7772 (m-80) outliers start: 5 outliers final: 3 residues processed: 16 average time/residue: 0.1113 time to fit residues: 2.6357 Evaluate side-chains 13 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 376 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 23 optimal weight: 10.0000 chunk 65 optimal weight: 60.0000 chunk 50 optimal weight: 30.0000 chunk 40 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 60 optimal weight: 30.0000 chunk 19 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 = 0.3816 r_free = 0.3816 target = 0.064892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.046655 restraints weight = 47799.691| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.20 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9374 Z= 0.209 Angle : 0.612 7.303 13832 Z= 0.354 Chirality : 0.044 0.331 1724 Planarity : 0.005 0.035 870 Dihedral : 26.433 179.925 4135 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.30 % Allowed : 8.55 % 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: 0.28 (0.42), residues: 429 helix: 1.73 (0.34), residues: 227 sheet: -1.87 (0.53), residues: 86 loop : -1.15 (0.62), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 300 TYR 0.013 0.002 TYR A 89 PHE 0.008 0.002 PHE A 325 TRP 0.011 0.002 TRP A 94 HIS 0.003 0.001 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.21 ( 9374) covalent geometry : angle 0.61151 / 0.35 (13832) hydrogen bonds : bond 0.06135 / 4.04 ( 426) hydrogen bonds : angle 3.99364 / 2.85 ( 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 16 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 11 time to evaluate : 0.251 Fit side-chains REVERT: A 17 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7411 (mtm180) REVERT: A 81 MET cc_start: 0.8718 (tpt) cc_final: 0.8434 (tpt) outliers start: 5 outliers final: 2 residues processed: 15 average time/residue: 0.1390 time to fit residues: 2.9563 Evaluate side-chains 12 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 9 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 90 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: 7.9990 chunk 30 optimal weight: 20.0000 chunk 48 optimal weight: 30.0000 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 46 optimal weight: 40.0000 chunk 29 optimal weight: 0.8980 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 446 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.064354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.046030 restraints weight = 48813.059| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 3.19 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2564 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= 0.220 Angle : 0.627 9.832 13832 Z= 0.352 Chirality : 0.044 0.304 1724 Planarity : 0.005 0.035 870 Dihedral : 26.164 179.689 4135 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.11 % Allowed : 6.99 % Favored : 89.90 % 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: 0.45 (0.42), residues: 429 helix: 1.84 (0.34), residues: 228 sheet: -1.69 (0.54), residues: 84 loop : -1.17 (0.60), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 421 TYR 0.011 0.002 TYR A 374 PHE 0.008 0.001 PHE A 285 TRP 0.011 0.002 TRP A 94 HIS 0.003 0.001 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.22 ( 9374) covalent geometry : angle 0.62740 / 0.35 (13832) hydrogen bonds : bond 0.06155 / 4.00 ( 426) hydrogen bonds : angle 3.86289 / 2.74 ( 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 23 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 11 time to evaluate : 0.214 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 21 average time/residue: 0.1161 time to fit residues: 3.4967 Evaluate side-chains 14 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 9 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG 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 376 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 50.0000 chunk 39 optimal weight: 2.9990 chunk 64 optimal weight: 50.0000 chunk 23 optimal weight: 0.0000 chunk 1 optimal weight: 5.9990 chunk 56 optimal weight: 30.0000 chunk 47 optimal weight: 30.0000 chunk 17 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.7790 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.065495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.047292 restraints weight = 48936.351| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 3.32 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9374 Z= 0.125 Angle : 0.519 7.177 13832 Z= 0.307 Chirality : 0.038 0.315 1724 Planarity : 0.004 0.030 870 Dihedral : 26.109 179.510 4135 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.07 % Allowed : 10.36 % Favored : 87.56 % 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: 0.73 (0.42), residues: 429 helix: 2.14 (0.34), residues: 230 sheet: -1.61 (0.52), residues: 85 loop : -1.22 (0.61), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 492 TYR 0.021 0.001 TYR A 474 PHE 0.011 0.001 PHE A 328 TRP 0.009 0.002 TRP A 356 HIS 0.002 0.001 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.13 ( 9374) covalent geometry : angle 0.51913 / 0.31 (13832) hydrogen bonds : bond 0.05362 / 3.52 ( 426) hydrogen bonds : angle 3.59098 / 2.53 ( 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 18 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 10 time to evaluate : 0.210 Fit side-chains REVERT: A 17 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7104 (mtm180) REVERT: A 405 MET cc_start: 0.7681 (ppp) cc_final: 0.6809 (ppp) outliers start: 8 outliers final: 7 residues processed: 16 average time/residue: 0.1305 time to fit residues: 2.9190 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 : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG 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 368 LEU Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 608 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 4 optimal weight: 30.0000 chunk 57 optimal weight: 30.0000 chunk 28 optimal weight: 3.9990 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: 30.0000 chunk 65 optimal weight: 50.0000 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 overall best weight: 11.3996 ------------------------------------------------------------------------------- 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 = 0.3807 r_free = 0.3807 target = 0.063964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.045551 restraints weight = 48931.082| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.31 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 9374 Z= 0.366 Angle : 0.758 8.328 13832 Z= 0.404 Chirality : 0.051 0.308 1724 Planarity : 0.005 0.034 870 Dihedral : 25.973 179.520 4135 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.63 % Allowed : 10.36 % Favored : 86.01 % 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: 1.51 (0.33), residues: 229 sheet: -1.92 (0.53), residues: 84 loop : -1.16 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 320 TYR 0.013 0.002 TYR A 374 PHE 0.009 0.002 PHE A 325 TRP 0.013 0.003 TRP A 94 HIS 0.005 0.001 HIS A 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00691 / 0.37 ( 9374) covalent geometry : angle 0.75752 / 0.40 (13832) hydrogen bonds : bond 0.07310 / 4.72 ( 426) hydrogen bonds : angle 3.99679 / 2.81 ( 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 24 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 10 time to evaluate : 0.224 Fit side-chains REVERT: A 405 MET cc_start: 0.7818 (ppp) cc_final: 0.7298 (ppp) REVERT: A 570 TYR cc_start: 0.8141 (t80) cc_final: 0.7717 (t80) outliers start: 14 outliers final: 9 residues processed: 22 average time/residue: 0.1066 time to fit residues: 3.3349 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 : 0.247 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 55 optimal weight: 40.0000 chunk 58 optimal weight: 50.0000 chunk 34 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 63 optimal weight: 20.0000 chunk 52 optimal weight: 40.0000 chunk 27 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.3969 r_free = 0.3969 target = 0.068620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.051094 restraints weight = 50394.275| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.11 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9374 Z= 0.142 Angle : 0.546 7.310 13832 Z= 0.314 Chirality : 0.039 0.309 1724 Planarity : 0.004 0.030 870 Dihedral : 26.017 179.472 4135 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.07 % Allowed : 12.18 % Favored : 85.75 % 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 are not related in a simple way. whole: 0.60 (0.42), residues: 429 helix: 2.05 (0.34), residues: 230 sheet: -1.72 (0.52), residues: 86 loop : -1.24 (0.62), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 525 TYR 0.016 0.001 TYR A 474 PHE 0.010 0.001 PHE A 328 TRP 0.008 0.001 TRP A 366 HIS 0.002 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 ( 9374) covalent geometry : angle 0.54641 / 0.31 (13832) hydrogen bonds : bond 0.05422 / 3.55 ( 426) hydrogen bonds : angle 3.61197 / 2.55 ( 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 18 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 10 time to evaluate : 0.192 Fit side-chains REVERT: A 405 MET cc_start: 0.7934 (ppp) cc_final: 0.7448 (ppp) outliers start: 8 outliers final: 6 residues processed: 15 average time/residue: 0.1094 time to fit residues: 2.4589 Evaluate side-chains 16 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 10 time to evaluate : 0.204 ------------------------------------------------------------------------------- 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 355 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 CYS 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: 40.0000 chunk 50 optimal weight: 40.0000 chunk 35 optimal weight: 7.9990 chunk 46 optimal weight: 30.0000 chunk 33 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 56 optimal weight: 30.0000 chunk 48 optimal weight: 30.0000 chunk 3 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 57 optimal weight: 30.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.065280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.047265 restraints weight = 48603.114| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 3.21 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9374 Z= 0.237 Angle : 0.611 7.720 13832 Z= 0.340 Chirality : 0.043 0.311 1724 Planarity : 0.005 0.033 870 Dihedral : 25.887 179.302 4135 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.59 % Allowed : 11.66 % Favored : 85.75 % 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 are not related in a simple way. whole: 0.54 (0.42), residues: 429 helix: 1.92 (0.33), residues: 230 sheet: -1.68 (0.53), residues: 83 loop : -1.16 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 17 TYR 0.011 0.002 TYR A 474 PHE 0.008 0.001 PHE A 325 TRP 0.009 0.002 TRP A 94 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.24 ( 9374) covalent geometry : angle 0.61065 / 0.34 (13832) hydrogen bonds : bond 0.06163 / 3.99 ( 426) hydrogen bonds : angle 3.72158 / 2.63 ( 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 20 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 10 time to evaluate : 0.164 Fit side-chains REVERT: A 405 MET cc_start: 0.7852 (ppp) cc_final: 0.7413 (ppp) REVERT: A 570 TYR cc_start: 0.8177 (t80) cc_final: 0.7745 (t80) outliers start: 10 outliers final: 9 residues processed: 19 average time/residue: 0.0904 time to fit residues: 2.5787 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 : 0.136 ------------------------------------------------------------------------------- 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 461 VAL 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: 0.8980 chunk 36 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 20.0000 chunk 48 optimal weight: 30.0000 chunk 60 optimal weight: 30.0000 chunk 19 optimal weight: 30.0000 chunk 44 optimal weight: 30.0000 overall best weight: 5.1790 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.068467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.050171 restraints weight = 52878.306| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 3.38 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3263 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= 0.187 Angle : 0.550 7.426 13832 Z= 0.315 Chirality : 0.039 0.310 1724 Planarity : 0.004 0.032 870 Dihedral : 25.847 179.283 4135 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.59 % Allowed : 11.92 % 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: 0.67 (0.42), residues: 429 helix: 2.08 (0.34), residues: 230 sheet: -1.67 (0.52), residues: 84 loop : -1.21 (0.61), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 17 TYR 0.013 0.002 TYR A 474 PHE 0.008 0.001 PHE A 285 TRP 0.009 0.002 TRP A 94 HIS 0.003 0.001 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.19 ( 9374) covalent geometry : angle 0.54998 / 0.31 (13832) hydrogen bonds : bond 0.05614 / 3.66 ( 426) hydrogen bonds : angle 3.62595 / 2.56 ( 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 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 Fit side-chains REVERT: A 20 LEU cc_start: 0.9412 (tp) cc_final: 0.9159 (tt) REVERT: A 405 MET cc_start: 0.7775 (ppp) cc_final: 0.7375 (ppp) outliers start: 10 outliers final: 10 residues processed: 19 average time/residue: 0.0974 time to fit residues: 2.7906 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 : 0.195 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 54 optimal weight: 30.0000 chunk 59 optimal weight: 50.0000 chunk 17 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 46 optimal weight: 40.0000 chunk 10 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.065337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.047358 restraints weight = 48772.980| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 3.15 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9374 Z= 0.192 Angle : 0.559 7.393 13832 Z= 0.318 Chirality : 0.040 0.312 1724 Planarity : 0.004 0.032 870 Dihedral : 25.784 179.191 4135 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.85 % Allowed : 11.66 % 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: 0.68 (0.42), residues: 429 helix: 2.05 (0.34), residues: 230 sheet: -1.60 (0.52), residues: 82 loop : -1.17 (0.60), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 17 TYR 0.012 0.002 TYR A 474 PHE 0.008 0.001 PHE A 285 TRP 0.009 0.002 TRP A 94 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.19 ( 9374) covalent geometry : angle 0.55912 / 0.32 (13832) hydrogen bonds : bond 0.05808 / 3.78 ( 426) hydrogen bonds : angle 3.62152 / 2.56 ( 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 23 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 12 time to evaluate : 0.204 Fit side-chains REVERT: A 405 MET cc_start: 0.7821 (ppp) cc_final: 0.7427 (ppp) REVERT: A 570 TYR cc_start: 0.8163 (t80) cc_final: 0.7712 (t80) outliers start: 11 outliers final: 10 residues processed: 22 average time/residue: 0.0926 time to fit residues: 3.1105 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 : 0.171 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 54 optimal weight: 30.0000 chunk 36 optimal weight: 5.9990 chunk 45 optimal weight: 50.0000 chunk 13 optimal weight: 8.9990 chunk 48 optimal weight: 30.0000 chunk 31 optimal weight: 10.0000 chunk 52 optimal weight: 50.0000 chunk 49 optimal weight: 30.0000 chunk 57 optimal weight: 30.0000 chunk 2 optimal weight: 7.9990 overall best weight: 7.5992 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.065961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.047787 restraints weight = 51118.636| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 3.29 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9374 Z= 0.259 Angle : 0.619 8.084 13832 Z= 0.344 Chirality : 0.043 0.309 1724 Planarity : 0.005 0.033 870 Dihedral : 25.766 178.814 4135 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.11 % Allowed : 11.92 % 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: 0.47 (0.42), residues: 429 helix: 1.85 (0.33), residues: 230 sheet: -1.67 (0.54), residues: 83 loop : -1.19 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 17 TYR 0.011 0.002 TYR A 316 PHE 0.009 0.001 PHE A 325 TRP 0.012 0.002 TRP A 94 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.26 ( 9374) covalent geometry : angle 0.61933 / 0.34 (13832) hydrogen bonds : bond 0.06369 / 4.16 ( 426) hydrogen bonds : angle 3.78395 / 2.67 ( 1009) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1816.12 seconds wall clock time: 32 minutes 4.51 seconds (1924.51 seconds total)