Starting phenix.real_space_refine on Tue Mar 3 20:54:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pla_13486/03_2026/7pla_13486_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pla_13486/03_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_13486/03_2026/7pla_13486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pla_13486/03_2026/7pla_13486.map" model { file = "/net/cci-nas-00/data/ceres_data/7pla_13486/03_2026/7pla_13486_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pla_13486/03_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-5986/lib/python3.9/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: 2.17, 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: 0.93 Conformation dependent library (CDL) restraints added in 142.0 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: 1.82 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: 2.34 Time building geometry restraints manager: 1.06 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 - 1.74: 12548 1.74 - 3.47: 994 3.47 - 5.21: 249 5.21 - 6.94: 30 6.94 - 8.68: 11 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: 1363 0.116 - 0.232: 343 0.232 - 0.347: 14 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: 2.630 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: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.950 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5863 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= 0.455 Angle : 1.084 8.680 13832 Z= 0.712 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 covalent geometry : bond 0.00755 ( 9374) covalent geometry : angle 1.08407 (13832) hydrogen bonds : bond 0.15814 ( 426) hydrogen bonds : angle 9.28498 ( 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 : 0.193 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: 0.1269 time to fit residues: 2.3535 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 : 0.172 ------------------------------------------------------------------------------- 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: 10.0000 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.064076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.045753 restraints weight = 48165.235| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 3.30 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9374 Z= 0.261 Angle : 0.707 7.271 13832 Z= 0.363 Chirality : 0.039 0.265 1724 Planarity : 0.005 0.033 870 Dihedral : 26.542 178.431 4135 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.04 % Allowed : 6.22 % Favored : 92.75 % 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: 0.26 (0.41), residues: 429 helix: 1.62 (0.33), residues: 227 sheet: -1.70 (0.55), residues: 79 loop : -1.17 (0.60), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 300 TYR 0.013 0.002 TYR A 80 PHE 0.010 0.002 PHE A 313 TRP 0.016 0.002 TRP A 366 HIS 0.004 0.001 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00528 ( 9374) covalent geometry : angle 0.70725 (13832) hydrogen bonds : bond 0.05364 ( 426) hydrogen bonds : angle 4.03556 ( 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 : 0.183 Fit side-chains revert: symmetry clash REVERT: A 35 LEU cc_start: 0.9387 (mt) cc_final: 0.9179 (mt) REVERT: A 81 MET cc_start: 0.8722 (tpt) cc_final: 0.8477 (tpt) REVERT: A 347 PHE cc_start: 0.8539 (m-80) cc_final: 0.7660 (m-80) outliers start: 4 outliers final: 2 residues processed: 17 average time/residue: 0.0921 time to fit residues: 2.2772 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 : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 564 GLU 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: 20.0000 chunk 50 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 HIS A 574 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.063670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.045329 restraints weight = 48842.031| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.34 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 9374 Z= 0.310 Angle : 0.688 7.426 13832 Z= 0.353 Chirality : 0.039 0.265 1724 Planarity : 0.005 0.035 870 Dihedral : 26.252 178.399 4135 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.81 % Allowed : 7.77 % Favored : 90.41 % 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: 0.20 (0.41), residues: 429 helix: 1.60 (0.33), residues: 229 sheet: -1.88 (0.52), residues: 86 loop : -1.10 (0.63), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 421 TYR 0.011 0.002 TYR A 374 PHE 0.009 0.002 PHE A 285 TRP 0.015 0.002 TRP A 94 HIS 0.005 0.001 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00623 ( 9374) covalent geometry : angle 0.68776 (13832) hydrogen bonds : bond 0.05511 ( 426) hydrogen bonds : angle 3.92735 ( 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 18 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 11 time to evaluate : 0.213 Fit side-chains REVERT: A 281 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7961 (m-80) outliers start: 7 outliers final: 3 residues processed: 17 average time/residue: 0.1289 time to fit residues: 3.0189 Evaluate side-chains 13 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 9 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 281 PHE 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: 5.9990 chunk 30 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 4 optimal weight: 0.0980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.064386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.046139 restraints weight = 49252.552| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.24 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3137 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= 0.203 Angle : 0.609 7.175 13832 Z= 0.312 Chirality : 0.035 0.276 1724 Planarity : 0.004 0.042 870 Dihedral : 26.001 179.267 4135 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.55 % Allowed : 9.84 % Favored : 88.60 % 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: 0.58 (0.42), residues: 429 helix: 1.95 (0.33), residues: 229 sheet: -1.57 (0.53), residues: 85 loop : -1.17 (0.62), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 17 TYR 0.010 0.001 TYR A 474 PHE 0.012 0.002 PHE A 285 TRP 0.012 0.001 TRP A 94 HIS 0.002 0.001 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 9374) covalent geometry : angle 0.60926 (13832) hydrogen bonds : bond 0.04708 ( 426) hydrogen bonds : angle 3.56322 ( 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 15 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 9 time to evaluate : 0.191 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 14 average time/residue: 0.1139 time to fit residues: 2.3419 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 : 0.194 ------------------------------------------------------------------------------- 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 376 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 64 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 47 optimal weight: 10.9990 chunk 17 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.064473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.046222 restraints weight = 49239.363| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.25 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9374 Z= 0.200 Angle : 0.603 7.221 13832 Z= 0.308 Chirality : 0.034 0.249 1724 Planarity : 0.004 0.032 870 Dihedral : 25.785 178.495 4135 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.11 % Allowed : 9.84 % Favored : 87.05 % 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: 0.78 (0.42), residues: 429 helix: 2.03 (0.34), residues: 230 sheet: -1.30 (0.55), residues: 82 loop : -1.11 (0.60), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 17 TYR 0.009 0.001 TYR A 474 PHE 0.011 0.001 PHE A 285 TRP 0.009 0.001 TRP A 94 HIS 0.002 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 9374) covalent geometry : angle 0.60336 (13832) hydrogen bonds : bond 0.04792 ( 426) hydrogen bonds : angle 3.44911 ( 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 23 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 11 time to evaluate : 0.215 Fit side-chains REVERT: A 281 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.8006 (m-80) REVERT: A 405 MET cc_start: 0.7613 (ppp) cc_final: 0.6709 (ppp) outliers start: 12 outliers final: 7 residues processed: 21 average time/residue: 0.0926 time to fit residues: 2.9513 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 : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 281 PHE 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 527 LEU 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: 20.0000 chunk 57 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 overall best weight: 7.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 GLN A 575 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.064866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.046616 restraints weight = 51846.614| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.47 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 9374 Z= 0.336 Angle : 0.690 7.072 13832 Z= 0.352 Chirality : 0.038 0.235 1724 Planarity : 0.005 0.034 870 Dihedral : 25.835 177.930 4135 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.37 % Allowed : 11.40 % Favored : 85.23 % 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: 0.22 (0.41), residues: 429 helix: 1.60 (0.33), residues: 229 sheet: -1.76 (0.53), residues: 86 loop : -1.16 (0.61), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 300 TYR 0.017 0.002 TYR A 474 PHE 0.010 0.002 PHE A 281 TRP 0.013 0.002 TRP A 94 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00674 ( 9374) covalent geometry : angle 0.69030 (13832) hydrogen bonds : bond 0.05721 ( 426) hydrogen bonds : angle 3.74296 ( 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 : 0.215 Fit side-chains REVERT: A 281 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.7962 (m-80) REVERT: A 405 MET cc_start: 0.7900 (ppp) cc_final: 0.7589 (ppp) REVERT: A 527 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8383 (mp) REVERT: A 570 TYR cc_start: 0.8194 (t80) cc_final: 0.7686 (t80) outliers start: 13 outliers final: 7 residues processed: 21 average time/residue: 0.0921 time to fit residues: 2.8813 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 : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 281 PHE 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 460 THR 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: 2.9990 chunk 55 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 chunk 34 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.064957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.046892 restraints weight = 48956.618| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.21 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9374 Z= 0.168 Angle : 0.586 7.063 13832 Z= 0.298 Chirality : 0.033 0.251 1724 Planarity : 0.004 0.033 870 Dihedral : 25.642 178.858 4135 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.85 % Allowed : 12.18 % 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: 0.65 (0.42), residues: 429 helix: 2.05 (0.34), residues: 228 sheet: -1.45 (0.52), residues: 84 loop : -1.30 (0.60), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 17 TYR 0.013 0.001 TYR A 474 PHE 0.009 0.001 PHE A 285 TRP 0.005 0.001 TRP A 588 HIS 0.002 0.001 HIS A 522 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 9374) covalent geometry : angle 0.58614 (13832) hydrogen bonds : bond 0.04631 ( 426) hydrogen bonds : angle 3.37466 ( 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 20 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 9 time to evaluate : 0.205 Fit side-chains REVERT: A 281 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.7969 (m-80) REVERT: A 321 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8406 (pm20) REVERT: A 405 MET cc_start: 0.7893 (ppp) cc_final: 0.7348 (ppp) outliers start: 11 outliers final: 7 residues processed: 19 average time/residue: 0.0856 time to fit residues: 2.4248 Evaluate side-chains 18 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 9 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 291 MET 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 376 CYS Chi-restraints excluded: chain A residue 460 THR 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: 10.0000 chunk 35 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.064277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.046025 restraints weight = 49283.937| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.31 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9374 Z= 0.228 Angle : 0.612 7.078 13832 Z= 0.312 Chirality : 0.034 0.234 1724 Planarity : 0.004 0.033 870 Dihedral : 25.622 178.851 4135 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.85 % Allowed : 12.18 % 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: 0.56 (0.42), residues: 429 helix: 1.97 (0.34), residues: 227 sheet: -1.49 (0.52), residues: 84 loop : -1.32 (0.59), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 300 TYR 0.014 0.002 TYR A 474 PHE 0.007 0.001 PHE A 325 TRP 0.008 0.002 TRP A 94 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 9374) covalent geometry : angle 0.61229 (13832) hydrogen bonds : bond 0.04992 ( 426) hydrogen bonds : angle 3.46271 ( 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: 11 poor density : 10 time to evaluate : 0.155 Fit side-chains REVERT: A 281 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.8076 (m-80) REVERT: A 405 MET cc_start: 0.7907 (ppp) cc_final: 0.7663 (ppp) outliers start: 11 outliers final: 10 residues processed: 20 average time/residue: 0.0938 time to fit residues: 2.7102 Evaluate side-chains 20 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 9 time to evaluate : 0.172 ------------------------------------------------------------------------------- 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 281 PHE Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 291 MET 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 376 CYS Chi-restraints excluded: chain A residue 460 THR 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: 10.0000 chunk 36 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 4 optimal weight: 30.0000 chunk 48 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 19 optimal weight: 30.0000 chunk 44 optimal weight: 10.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.063302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.044965 restraints weight = 49862.761| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 3.37 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 9374 Z= 0.332 Angle : 0.698 12.711 13832 Z= 0.353 Chirality : 0.039 0.371 1724 Planarity : 0.004 0.033 870 Dihedral : 25.726 179.103 4135 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % 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: 0.20 (0.41), residues: 429 helix: 1.68 (0.34), residues: 227 sheet: -1.70 (0.52), residues: 86 loop : -1.42 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 300 TYR 0.015 0.002 TYR A 474 PHE 0.009 0.001 PHE A 281 TRP 0.009 0.002 TRP A 94 HIS 0.004 0.001 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00668 ( 9374) covalent geometry : angle 0.69750 (13832) hydrogen bonds : bond 0.05754 ( 426) hydrogen bonds : angle 3.75177 ( 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 : 0.182 Fit side-chains REVERT: A 281 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.8000 (m-80) REVERT: A 405 MET cc_start: 0.7886 (ppp) cc_final: 0.7654 (ppp) outliers start: 13 outliers final: 10 residues processed: 22 average time/residue: 0.1201 time to fit residues: 3.6928 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 : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 291 MET 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 376 CYS Chi-restraints excluded: chain A residue 460 THR 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: 7.9990 chunk 54 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.065099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.047065 restraints weight = 49422.596| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 3.27 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9374 Z= 0.147 Angle : 0.599 16.688 13832 Z= 0.297 Chirality : 0.034 0.393 1724 Planarity : 0.004 0.034 870 Dihedral : 25.547 179.655 4135 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.33 % Allowed : 12.44 % Favored : 85.23 % 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: 0.72 (0.42), residues: 429 helix: 2.21 (0.34), residues: 228 sheet: -1.56 (0.49), residues: 86 loop : -1.38 (0.60), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 17 TYR 0.012 0.001 TYR A 474 PHE 0.007 0.001 PHE A 285 TRP 0.006 0.001 TRP A 588 HIS 0.002 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9374) covalent geometry : angle 0.59906 (13832) hydrogen bonds : bond 0.04572 ( 426) hydrogen bonds : angle 3.36601 ( 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 21 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 12 time to evaluate : 0.233 Fit side-chains REVERT: A 281 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.8055 (m-80) REVERT: A 405 MET cc_start: 0.7840 (ppp) cc_final: 0.7607 (ppp) outliers start: 9 outliers final: 7 residues processed: 19 average time/residue: 0.1199 time to fit residues: 3.1661 Evaluate side-chains 19 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 11 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 281 PHE 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 460 THR 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: 10.0000 chunk 36 optimal weight: 6.9990 chunk 45 optimal weight: 20.0000 chunk 13 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 overall best weight: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.063348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.044994 restraints weight = 49781.692| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 3.43 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 9374 Z= 0.348 Angle : 0.714 16.193 13832 Z= 0.360 Chirality : 0.039 0.347 1724 Planarity : 0.005 0.052 870 Dihedral : 25.667 179.108 4135 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.59 % Allowed : 12.18 % Favored : 85.23 % 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: 1.74 (0.33), residues: 227 sheet: -1.77 (0.51), residues: 88 loop : -1.52 (0.59), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 17 TYR 0.014 0.002 TYR A 474 PHE 0.010 0.002 PHE A 281 TRP 0.014 0.002 TRP A 21 HIS 0.004 0.001 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00699 ( 9374) covalent geometry : angle 0.71447 (13832) hydrogen bonds : bond 0.05886 ( 426) hydrogen bonds : angle 3.77489 ( 1009) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1906.17 seconds wall clock time: 33 minutes 23.75 seconds (2003.75 seconds total)