Starting phenix.real_space_refine on Tue Jan 13 10:50:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7unq_26629/01_2026/7unq_26629.cif Found real_map, /net/cci-nas-00/data/ceres_data/7unq_26629/01_2026/7unq_26629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7unq_26629/01_2026/7unq_26629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7unq_26629/01_2026/7unq_26629.map" model { file = "/net/cci-nas-00/data/ceres_data/7unq_26629/01_2026/7unq_26629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7unq_26629/01_2026/7unq_26629.cif" } resolution = 3.4 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= -0.006 sd= 0.026 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 2 5.49 5 S 13 5.16 5 C 2205 2.51 5 N 648 2.21 5 O 660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3528 Number of models: 1 Model: "" Number of chains: 1 Chain: "x" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3528 Unusual residues: {'GDP': 1} Classifications: {'peptide': 486, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 18, 'TRANS': 467, None: 1} Not linked: pdbres="GLU x 835 " pdbres="GDP x 901 " Unresolved chain links: 1 Chain breaks: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 16, 'ASP:plan': 8, 'PHE:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 115 Time building chain proxies: 1.00, per 1000 atoms: 0.28 Number of scatterers: 3528 At special positions: 0 Unit cell: (79.05, 79.9, 85, 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 13 16.00 P 2 15.00 O 660 8.00 N 648 7.00 C 2205 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: 0.32 Conformation dependent library (CDL) restraints added in 149.0 milliseconds 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 868 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 6 sheets defined 28.4% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'x' and resid 354 through 367 removed outlier: 3.593A pdb=" N ILE x 362 " --> pdb=" O LEU x 358 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG x 363 " --> pdb=" O LEU x 359 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL x 367 " --> pdb=" O ARG x 363 " (cutoff:3.500A) Processing helix chain 'x' and resid 400 through 405 Processing helix chain 'x' and resid 429 through 440 removed outlier: 3.959A pdb=" N ALA x 440 " --> pdb=" O HIS x 436 " (cutoff:3.500A) Processing helix chain 'x' and resid 458 through 465 Processing helix chain 'x' and resid 466 through 469 removed outlier: 3.747A pdb=" N ASP x 469 " --> pdb=" O ALA x 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 466 through 469' Processing helix chain 'x' and resid 491 through 506 removed outlier: 3.792A pdb=" N VAL x 505 " --> pdb=" O LEU x 501 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU x 506 " --> pdb=" O GLN x 502 " (cutoff:3.500A) Processing helix chain 'x' and resid 597 through 623 removed outlier: 3.575A pdb=" N LYS x 616 " --> pdb=" O PHE x 612 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU x 617 " --> pdb=" O ARG x 613 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA x 618 " --> pdb=" O GLU x 614 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG x 619 " --> pdb=" O VAL x 615 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA x 620 " --> pdb=" O LYS x 616 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N HIS x 621 " --> pdb=" O LEU x 617 " (cutoff:3.500A) Processing helix chain 'x' and resid 648 through 659 Processing helix chain 'x' and resid 680 through 691 Processing helix chain 'x' and resid 702 through 713 Processing helix chain 'x' and resid 721 through 735 removed outlier: 3.915A pdb=" N ILE x 725 " --> pdb=" O VAL x 721 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE x 726 " --> pdb=" O ILE x 722 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'x' and resid 382 through 385 removed outlier: 6.641A pdb=" N VAL x 416 " --> pdb=" O VAL x 445 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ALA x 447 " --> pdb=" O VAL x 416 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU x 418 " --> pdb=" O ALA x 447 " (cutoff:3.500A) removed outlier: 8.993A pdb=" N VAL x 482 " --> pdb=" O ILE x 444 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL x 446 " --> pdb=" O VAL x 482 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'x' and resid 553 through 556 removed outlier: 4.427A pdb=" N MET x 547 " --> pdb=" O VAL x 595 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG x 517 " --> pdb=" O GLN x 538 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR x 534 " --> pdb=" O VAL x 521 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER x 523 " --> pdb=" O VAL x 532 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL x 532 " --> pdb=" O SER x 523 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU x 525 " --> pdb=" O GLY x 530 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLY x 530 " --> pdb=" O LEU x 525 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA x 533 " --> pdb=" O ILE x 579 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA x 559 " --> pdb=" O LEU x 580 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'x' and resid 670 through 671 removed outlier: 3.863A pdb=" N ILE x 642 " --> pdb=" O ARG x 670 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'x' and resid 670 through 671 removed outlier: 3.863A pdb=" N ILE x 642 " --> pdb=" O ARG x 670 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU x 694 " --> pdb=" O ARG x 717 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N TYR x 719 " --> pdb=" O LEU x 694 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLY x 696 " --> pdb=" O TYR x 719 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'x' and resid 786 through 791 removed outlier: 4.937A pdb=" N VAL x 787 " --> pdb=" O ARG x 783 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ARG x 783 " --> pdb=" O VAL x 787 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL x 781 " --> pdb=" O PHE x 789 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLY x 747 " --> pdb=" O VAL x 830 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N GLU x 832 " --> pdb=" O ILE x 745 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE x 745 " --> pdb=" O GLU x 832 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ALA x 749 " --> pdb=" O THR x 769 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N THR x 769 " --> pdb=" O ALA x 749 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N VAL x 751 " --> pdb=" O MET x 767 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N MET x 767 " --> pdb=" O VAL x 751 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP x 753 " --> pdb=" O GLY x 765 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLY x 815 " --> pdb=" O GLU x 794 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'x' and resid 773 through 774 132 hydrogen bonds defined for protein. 366 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.66 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 800 1.33 - 1.45: 649 1.45 - 1.57: 2095 1.57 - 1.69: 3 1.69 - 1.81: 24 Bond restraints: 3571 Sorted by residual: bond pdb=" N VAL x 426 " pdb=" CA VAL x 426 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.34e+00 bond pdb=" N ASP x 424 " pdb=" CA ASP x 424 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.63e+00 bond pdb=" N SER x 739 " pdb=" CA SER x 739 " ideal model delta sigma weight residual 1.456 1.486 -0.029 1.16e-02 7.43e+03 6.45e+00 bond pdb=" N ASP x 740 " pdb=" CA ASP x 740 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.64e+00 bond pdb=" C PRO x 428 " pdb=" O PRO x 428 " ideal model delta sigma weight residual 1.235 1.208 0.027 1.30e-02 5.92e+03 4.24e+00 ... (remaining 3566 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 4639 1.30 - 2.60: 156 2.60 - 3.89: 41 3.89 - 5.19: 11 5.19 - 6.49: 4 Bond angle restraints: 4851 Sorted by residual: angle pdb=" N ALA x 422 " pdb=" CA ALA x 422 " pdb=" C ALA x 422 " ideal model delta sigma weight residual 111.02 106.72 4.30 1.22e+00 6.72e-01 1.24e+01 angle pdb=" C MET x 427 " pdb=" N PRO x 428 " pdb=" CA PRO x 428 " ideal model delta sigma weight residual 119.84 123.48 -3.64 1.25e+00 6.40e-01 8.47e+00 angle pdb=" CA ASP x 352 " pdb=" C ASP x 352 " pdb=" O ASP x 352 " ideal model delta sigma weight residual 120.81 117.27 3.54 1.24e+00 6.50e-01 8.14e+00 angle pdb=" CA SER x 739 " pdb=" C SER x 739 " pdb=" O SER x 739 " ideal model delta sigma weight residual 121.38 118.36 3.02 1.06e+00 8.90e-01 8.09e+00 angle pdb=" CA ASP x 423 " pdb=" C ASP x 423 " pdb=" O ASP x 423 " ideal model delta sigma weight residual 120.58 117.30 3.28 1.16e+00 7.43e-01 7.99e+00 ... (remaining 4846 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 1960 17.98 - 35.95: 162 35.95 - 53.92: 22 53.92 - 71.90: 7 71.90 - 89.87: 2 Dihedral angle restraints: 2153 sinusoidal: 795 harmonic: 1358 Sorted by residual: dihedral pdb=" C VAL x 426 " pdb=" N VAL x 426 " pdb=" CA VAL x 426 " pdb=" CB VAL x 426 " ideal model delta harmonic sigma weight residual -122.00 -134.34 12.34 0 2.50e+00 1.60e-01 2.44e+01 dihedral pdb=" N VAL x 426 " pdb=" C VAL x 426 " pdb=" CA VAL x 426 " pdb=" CB VAL x 426 " ideal model delta harmonic sigma weight residual 123.40 133.87 -10.47 0 2.50e+00 1.60e-01 1.75e+01 dihedral pdb=" CA ARG x 775 " pdb=" C ARG x 775 " pdb=" N ASN x 776 " pdb=" CA ASN x 776 " ideal model delta harmonic sigma weight residual 180.00 -161.27 -18.73 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 2150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 484 0.063 - 0.126: 93 0.126 - 0.189: 6 0.189 - 0.252: 1 0.252 - 0.315: 1 Chirality restraints: 585 Sorted by residual: chirality pdb=" CA VAL x 426 " pdb=" N VAL x 426 " pdb=" C VAL x 426 " pdb=" CB VAL x 426 " both_signs ideal model delta sigma weight residual False 2.44 2.13 0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CB VAL x 426 " pdb=" CA VAL x 426 " pdb=" CG1 VAL x 426 " pdb=" CG2 VAL x 426 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ALA x 422 " pdb=" N ALA x 422 " pdb=" C ALA x 422 " pdb=" CB ALA x 422 " both_signs ideal model delta sigma weight residual False 2.48 2.63 -0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 582 not shown) Planarity restraints: 633 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA x 342 " -0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO x 343 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO x 343 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO x 343 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL x 442 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.80e+00 pdb=" N PRO x 443 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO x 443 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO x 443 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA x 421 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.75e+00 pdb=" C ALA x 421 " 0.023 2.00e-02 2.50e+03 pdb=" O ALA x 421 " -0.009 2.00e-02 2.50e+03 pdb=" N ALA x 422 " -0.008 2.00e-02 2.50e+03 ... (remaining 630 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 548 2.77 - 3.30: 3381 3.30 - 3.83: 5441 3.83 - 4.37: 5953 4.37 - 4.90: 10958 Nonbonded interactions: 26281 Sorted by model distance: nonbonded pdb=" OG1 THR x 376 " pdb=" N GLN x 377 " model vdw 2.233 3.120 nonbonded pdb=" O MET x 427 " pdb=" N GLN x 429 " model vdw 2.315 3.120 nonbonded pdb=" OG1 THR x 386 " pdb=" O GLY x 389 " model vdw 2.325 3.040 nonbonded pdb=" OH TYR x 719 " pdb=" OD2 ASP x 728 " model vdw 2.351 3.040 nonbonded pdb=" NE2 GLN x 377 " pdb=" O GLU x 563 " model vdw 2.374 3.120 ... (remaining 26276 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.760 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 5.660 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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 : 0.003 0.036 3571 Z= 0.178 Angle : 0.634 6.490 4851 Z= 0.348 Chirality : 0.048 0.315 585 Planarity : 0.004 0.037 633 Dihedral : 13.875 89.872 1285 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 1.04 % Allowed : 8.96 % Favored : 90.00 % Rotamer: Outliers : 1.17 % Allowed : 0.88 % Favored : 97.95 % Cbeta Deviations : 0.23 % 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: -1.44 (0.38), residues: 480 helix: 1.97 (0.49), residues: 113 sheet: -0.94 (0.48), residues: 114 loop : -2.48 (0.34), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG x 752 TYR 0.011 0.001 TYR x 361 PHE 0.006 0.001 PHE x 402 TRP 0.004 0.001 TRP x 475 HIS 0.006 0.001 HIS x 774 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 3571) covalent geometry : angle 0.63443 ( 4851) hydrogen bonds : bond 0.16624 ( 132) hydrogen bonds : angle 7.04947 ( 366) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.137 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 79 average time/residue: 0.0839 time to fit residues: 7.8590 Evaluate side-chains 53 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 352 ASP Chi-restraints excluded: chain x residue 426 VAL Chi-restraints excluded: chain x residue 427 MET Chi-restraints excluded: chain x residue 741 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 435 GLN x 656 GLN x 668 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.078069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.061254 restraints weight = 11259.296| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 4.42 r_work: 0.2727 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 3571 Z= 0.216 Angle : 0.688 9.417 4851 Z= 0.346 Chirality : 0.047 0.133 585 Planarity : 0.005 0.043 633 Dihedral : 6.084 55.388 540 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.62 % Allowed : 9.17 % Favored : 90.21 % Rotamer: Outliers : 2.92 % Allowed : 12.57 % Favored : 84.50 % 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: -1.59 (0.37), residues: 480 helix: 1.55 (0.48), residues: 122 sheet: -1.08 (0.47), residues: 116 loop : -2.54 (0.34), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG x 613 TYR 0.008 0.002 TYR x 361 PHE 0.007 0.001 PHE x 402 TRP 0.004 0.001 TRP x 475 HIS 0.006 0.001 HIS x 774 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 3571) covalent geometry : angle 0.68788 ( 4851) hydrogen bonds : bond 0.03679 ( 132) hydrogen bonds : angle 5.36631 ( 366) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.164 Fit side-chains REVERT: x 716 MET cc_start: 0.8897 (tmm) cc_final: 0.8581 (tmm) REVERT: x 746 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9089 (pp) outliers start: 10 outliers final: 6 residues processed: 57 average time/residue: 0.0531 time to fit residues: 4.0208 Evaluate side-chains 50 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 352 ASP Chi-restraints excluded: chain x residue 525 LEU Chi-restraints excluded: chain x residue 535 VAL Chi-restraints excluded: chain x residue 617 LEU Chi-restraints excluded: chain x residue 714 LEU Chi-restraints excluded: chain x residue 746 LEU Chi-restraints excluded: chain x residue 781 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.080156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.063044 restraints weight = 11125.872| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 4.48 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3571 Z= 0.121 Angle : 0.608 7.134 4851 Z= 0.306 Chirality : 0.045 0.128 585 Planarity : 0.004 0.031 633 Dihedral : 5.230 53.731 534 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.33 % Favored : 91.04 % Rotamer: Outliers : 2.92 % Allowed : 14.91 % Favored : 82.16 % 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: -1.42 (0.37), residues: 480 helix: 1.64 (0.49), residues: 123 sheet: -0.90 (0.48), residues: 116 loop : -2.46 (0.34), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG x 613 TYR 0.011 0.001 TYR x 361 PHE 0.007 0.001 PHE x 607 TRP 0.003 0.001 TRP x 475 HIS 0.006 0.001 HIS x 774 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 3571) covalent geometry : angle 0.60838 ( 4851) hydrogen bonds : bond 0.02938 ( 132) hydrogen bonds : angle 4.95338 ( 366) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.180 Fit side-chains REVERT: x 547 MET cc_start: 0.8091 (tpp) cc_final: 0.7788 (tpp) outliers start: 10 outliers final: 7 residues processed: 57 average time/residue: 0.0780 time to fit residues: 5.4650 Evaluate side-chains 54 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 352 ASP Chi-restraints excluded: chain x residue 525 LEU Chi-restraints excluded: chain x residue 532 VAL Chi-restraints excluded: chain x residue 535 VAL Chi-restraints excluded: chain x residue 617 LEU Chi-restraints excluded: chain x residue 726 ILE Chi-restraints excluded: chain x residue 781 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 12 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 41 optimal weight: 0.0670 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 350 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.081090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.063960 restraints weight = 10959.084| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 4.42 r_work: 0.2785 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3571 Z= 0.117 Angle : 0.625 7.001 4851 Z= 0.310 Chirality : 0.045 0.127 585 Planarity : 0.004 0.038 633 Dihedral : 5.094 51.480 534 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.12 % Favored : 91.25 % Rotamer: Outliers : 3.51 % Allowed : 16.37 % Favored : 80.12 % 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: -1.28 (0.38), residues: 480 helix: 1.78 (0.49), residues: 123 sheet: -0.89 (0.48), residues: 118 loop : -2.34 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG x 742 TYR 0.012 0.001 TYR x 361 PHE 0.006 0.001 PHE x 393 TRP 0.002 0.001 TRP x 475 HIS 0.006 0.001 HIS x 774 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 3571) covalent geometry : angle 0.62463 ( 4851) hydrogen bonds : bond 0.02713 ( 132) hydrogen bonds : angle 4.85754 ( 366) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.119 Fit side-chains REVERT: x 424 ASP cc_start: 0.9157 (t70) cc_final: 0.8933 (t0) REVERT: x 547 MET cc_start: 0.8347 (tpp) cc_final: 0.7882 (tpp) outliers start: 12 outliers final: 5 residues processed: 62 average time/residue: 0.0649 time to fit residues: 5.0213 Evaluate side-chains 51 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 535 VAL Chi-restraints excluded: chain x residue 617 LEU Chi-restraints excluded: chain x residue 640 LEU Chi-restraints excluded: chain x residue 726 ILE Chi-restraints excluded: chain x residue 781 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 0.0670 chunk 17 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.3522 ------------------------------------------------------------------------------- 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 = 0.3240 r_free = 0.3240 target = 0.080036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.062981 restraints weight = 11074.746| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 4.49 r_work: 0.2764 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3571 Z= 0.148 Angle : 0.648 7.611 4851 Z= 0.324 Chirality : 0.045 0.127 585 Planarity : 0.004 0.028 633 Dihedral : 4.665 21.279 532 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.92 % Favored : 91.46 % Rotamer: Outliers : 2.63 % Allowed : 18.13 % Favored : 79.24 % 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: -1.24 (0.38), residues: 480 helix: 1.73 (0.50), residues: 125 sheet: -0.93 (0.50), residues: 111 loop : -2.24 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG x 742 TYR 0.012 0.002 TYR x 361 PHE 0.006 0.001 PHE x 393 TRP 0.003 0.001 TRP x 475 HIS 0.006 0.001 HIS x 774 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 3571) covalent geometry : angle 0.64760 ( 4851) hydrogen bonds : bond 0.02888 ( 132) hydrogen bonds : angle 4.85254 ( 366) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: x 742 ARG cc_start: 0.8618 (mmm-85) cc_final: 0.8135 (mmm-85) REVERT: x 772 MET cc_start: 0.6944 (tmm) cc_final: 0.6597 (tmm) outliers start: 9 outliers final: 8 residues processed: 52 average time/residue: 0.0572 time to fit residues: 3.8379 Evaluate side-chains 52 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 508 LEU Chi-restraints excluded: chain x residue 525 LEU Chi-restraints excluded: chain x residue 535 VAL Chi-restraints excluded: chain x residue 617 LEU Chi-restraints excluded: chain x residue 640 LEU Chi-restraints excluded: chain x residue 726 ILE Chi-restraints excluded: chain x residue 746 LEU Chi-restraints excluded: chain x residue 781 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 41 optimal weight: 0.0050 chunk 0 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.0798 ------------------------------------------------------------------------------- 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 = 0.3253 r_free = 0.3253 target = 0.080707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.063405 restraints weight = 11223.688| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 4.55 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3571 Z= 0.130 Angle : 0.650 7.938 4851 Z= 0.322 Chirality : 0.045 0.136 585 Planarity : 0.004 0.028 633 Dihedral : 4.609 21.502 532 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.71 % Favored : 91.67 % Rotamer: Outliers : 2.92 % Allowed : 21.05 % Favored : 76.02 % 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: -1.24 (0.38), residues: 480 helix: 1.74 (0.49), residues: 124 sheet: -0.94 (0.50), residues: 110 loop : -2.22 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG x 742 TYR 0.015 0.002 TYR x 361 PHE 0.006 0.001 PHE x 393 TRP 0.001 0.001 TRP x 475 HIS 0.005 0.001 HIS x 774 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 3571) covalent geometry : angle 0.65033 ( 4851) hydrogen bonds : bond 0.02775 ( 132) hydrogen bonds : angle 4.73519 ( 366) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.136 Fit side-chains REVERT: x 547 MET cc_start: 0.8107 (tpp) cc_final: 0.7810 (tpp) REVERT: x 772 MET cc_start: 0.6956 (tmm) cc_final: 0.6591 (tmm) outliers start: 10 outliers final: 9 residues processed: 53 average time/residue: 0.0571 time to fit residues: 3.8891 Evaluate side-chains 51 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 525 LEU Chi-restraints excluded: chain x residue 535 VAL Chi-restraints excluded: chain x residue 537 VAL Chi-restraints excluded: chain x residue 617 LEU Chi-restraints excluded: chain x residue 640 LEU Chi-restraints excluded: chain x residue 680 THR Chi-restraints excluded: chain x residue 726 ILE Chi-restraints excluded: chain x residue 746 LEU Chi-restraints excluded: chain x residue 781 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 31 optimal weight: 0.3980 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.3238 r_free = 0.3238 target = 0.079900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.063065 restraints weight = 11300.896| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 4.49 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3571 Z= 0.137 Angle : 0.642 7.701 4851 Z= 0.319 Chirality : 0.046 0.152 585 Planarity : 0.004 0.028 633 Dihedral : 4.608 21.540 532 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.92 % Favored : 91.46 % Rotamer: Outliers : 2.92 % Allowed : 22.22 % Favored : 74.85 % 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: -1.27 (0.38), residues: 480 helix: 1.54 (0.49), residues: 126 sheet: -0.90 (0.50), residues: 108 loop : -2.19 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG x 742 TYR 0.015 0.002 TYR x 361 PHE 0.006 0.001 PHE x 697 TRP 0.002 0.001 TRP x 475 HIS 0.005 0.001 HIS x 774 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 3571) covalent geometry : angle 0.64238 ( 4851) hydrogen bonds : bond 0.02825 ( 132) hydrogen bonds : angle 4.76981 ( 366) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.093 Fit side-chains REVERT: x 547 MET cc_start: 0.8140 (tpp) cc_final: 0.7664 (tpp) REVERT: x 772 MET cc_start: 0.6940 (tmm) cc_final: 0.6587 (tmm) outliers start: 10 outliers final: 9 residues processed: 52 average time/residue: 0.0569 time to fit residues: 3.8568 Evaluate side-chains 51 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 525 LEU Chi-restraints excluded: chain x residue 535 VAL Chi-restraints excluded: chain x residue 537 VAL Chi-restraints excluded: chain x residue 617 LEU Chi-restraints excluded: chain x residue 640 LEU Chi-restraints excluded: chain x residue 680 THR Chi-restraints excluded: chain x residue 726 ILE Chi-restraints excluded: chain x residue 746 LEU Chi-restraints excluded: chain x residue 781 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 39 optimal weight: 10.0000 chunk 34 optimal weight: 0.0050 chunk 9 optimal weight: 0.0170 chunk 32 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 overall best weight: 0.5434 ------------------------------------------------------------------------------- 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 = 0.3278 r_free = 0.3278 target = 0.082363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.064991 restraints weight = 11347.103| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 4.62 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3571 Z= 0.106 Angle : 0.659 8.668 4851 Z= 0.320 Chirality : 0.046 0.157 585 Planarity : 0.003 0.029 633 Dihedral : 4.422 21.110 532 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.12 % Favored : 91.25 % Rotamer: Outliers : 2.92 % Allowed : 21.64 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.17 (0.38), residues: 480 helix: 1.69 (0.49), residues: 125 sheet: -0.85 (0.51), residues: 107 loop : -2.14 (0.35), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG x 742 TYR 0.016 0.001 TYR x 361 PHE 0.006 0.001 PHE x 402 TRP 0.006 0.001 TRP x 475 HIS 0.005 0.001 HIS x 774 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 3571) covalent geometry : angle 0.65876 ( 4851) hydrogen bonds : bond 0.02568 ( 132) hydrogen bonds : angle 4.65299 ( 366) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.112 Fit side-chains REVERT: x 547 MET cc_start: 0.8017 (tpp) cc_final: 0.7758 (tpp) REVERT: x 772 MET cc_start: 0.7152 (tmm) cc_final: 0.6805 (tmm) outliers start: 10 outliers final: 7 residues processed: 55 average time/residue: 0.0554 time to fit residues: 4.0236 Evaluate side-chains 53 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 525 LEU Chi-restraints excluded: chain x residue 535 VAL Chi-restraints excluded: chain x residue 537 VAL Chi-restraints excluded: chain x residue 640 LEU Chi-restraints excluded: chain x residue 680 THR Chi-restraints excluded: chain x residue 726 ILE Chi-restraints excluded: chain x residue 781 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3261 r_free = 0.3261 target = 0.081249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.064182 restraints weight = 11152.147| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 4.52 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3571 Z= 0.127 Angle : 0.662 10.453 4851 Z= 0.320 Chirality : 0.046 0.160 585 Planarity : 0.004 0.035 633 Dihedral : 4.474 21.149 532 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.12 % Favored : 91.25 % Rotamer: Outliers : 2.63 % Allowed : 22.22 % Favored : 75.15 % 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: -1.22 (0.38), residues: 480 helix: 1.56 (0.48), residues: 127 sheet: -0.98 (0.50), residues: 108 loop : -2.10 (0.35), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG x 756 TYR 0.015 0.002 TYR x 361 PHE 0.006 0.001 PHE x 760 TRP 0.002 0.001 TRP x 475 HIS 0.005 0.001 HIS x 774 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 3571) covalent geometry : angle 0.66166 ( 4851) hydrogen bonds : bond 0.02670 ( 132) hydrogen bonds : angle 4.67238 ( 366) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.189 Fit side-chains REVERT: x 547 MET cc_start: 0.8090 (tpp) cc_final: 0.7653 (tpp) REVERT: x 772 MET cc_start: 0.7158 (tmm) cc_final: 0.6827 (tmm) outliers start: 9 outliers final: 8 residues processed: 50 average time/residue: 0.0464 time to fit residues: 3.2302 Evaluate side-chains 53 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 405 MET Chi-restraints excluded: chain x residue 525 LEU Chi-restraints excluded: chain x residue 535 VAL Chi-restraints excluded: chain x residue 537 VAL Chi-restraints excluded: chain x residue 640 LEU Chi-restraints excluded: chain x residue 680 THR Chi-restraints excluded: chain x residue 726 ILE Chi-restraints excluded: chain x residue 781 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 46 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.3239 r_free = 0.3239 target = 0.079834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.062386 restraints weight = 11498.918| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 4.60 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3571 Z= 0.162 Angle : 0.690 10.334 4851 Z= 0.338 Chirality : 0.046 0.160 585 Planarity : 0.004 0.027 633 Dihedral : 4.680 21.777 532 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.12 % Favored : 91.25 % Rotamer: Outliers : 2.63 % Allowed : 22.22 % Favored : 75.15 % 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: -1.26 (0.38), residues: 480 helix: 1.63 (0.49), residues: 126 sheet: -0.89 (0.48), residues: 112 loop : -2.25 (0.35), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG x 742 TYR 0.014 0.002 TYR x 361 PHE 0.008 0.001 PHE x 481 TRP 0.003 0.001 TRP x 475 HIS 0.005 0.001 HIS x 774 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 3571) covalent geometry : angle 0.68988 ( 4851) hydrogen bonds : bond 0.02959 ( 132) hydrogen bonds : angle 4.82305 ( 366) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.137 Fit side-chains REVERT: x 348 MET cc_start: 0.8834 (mtm) cc_final: 0.8530 (mtp) REVERT: x 772 MET cc_start: 0.7239 (tmm) cc_final: 0.6901 (tmm) outliers start: 9 outliers final: 7 residues processed: 48 average time/residue: 0.0382 time to fit residues: 2.7001 Evaluate side-chains 50 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 405 MET Chi-restraints excluded: chain x residue 535 VAL Chi-restraints excluded: chain x residue 537 VAL Chi-restraints excluded: chain x residue 640 LEU Chi-restraints excluded: chain x residue 680 THR Chi-restraints excluded: chain x residue 726 ILE Chi-restraints excluded: chain x residue 781 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 1 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 24 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 = 0.3232 r_free = 0.3232 target = 0.079350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.062001 restraints weight = 11338.230| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 4.57 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 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 : 0.004 0.041 3571 Z= 0.162 Angle : 0.686 10.242 4851 Z= 0.338 Chirality : 0.046 0.158 585 Planarity : 0.004 0.028 633 Dihedral : 4.714 21.817 532 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.50 % Favored : 91.88 % Rotamer: Outliers : 2.63 % Allowed : 22.51 % Favored : 74.85 % 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: -1.26 (0.38), residues: 480 helix: 1.62 (0.49), residues: 126 sheet: -0.85 (0.50), residues: 105 loop : -2.24 (0.35), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG x 742 TYR 0.015 0.002 TYR x 361 PHE 0.007 0.001 PHE x 481 TRP 0.003 0.001 TRP x 475 HIS 0.005 0.001 HIS x 774 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 3571) covalent geometry : angle 0.68564 ( 4851) hydrogen bonds : bond 0.03012 ( 132) hydrogen bonds : angle 4.84047 ( 366) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1045.30 seconds wall clock time: 18 minutes 39.35 seconds (1119.35 seconds total)