Starting phenix.real_space_refine on Thu Jun 4 03:18:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6g1s_4340/06_2026/6g1s_4340.cif Found real_map, /net/cci-nas-00/data/ceres_data/6g1s_4340/06_2026/6g1s_4340.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6g1s_4340/06_2026/6g1s_4340.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6g1s_4340/06_2026/6g1s_4340.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6g1s_4340/06_2026/6g1s_4340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6g1s_4340/06_2026/6g1s_4340.map" } resolution = 3.93 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= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 30 5.49 5 S 34 5.16 5 C 3564 2.51 5 N 1007 2.21 5 O 1159 1.98 5 H 4096 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9891 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 9251 Classifications: {'peptide': 645} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 624} Chain breaks: 11 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "X" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 318 Classifications: {'RNA': 15} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 8} Link IDs: {'rna3p': 14} Chain: "Y" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 321 Classifications: {'RNA': 15} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 7} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7868 SG CYS A 910 15.398 66.809 34.431 1.00133.64 S ATOM 8477 SG CYS A 962 17.403 66.721 30.958 1.00137.66 S ATOM 8492 SG CYS A 964 16.208 70.018 33.329 1.00146.40 S Time building chain proxies: 2.18, per 1000 atoms: 0.22 Number of scatterers: 9891 At special positions: 0 Unit cell: (86.67, 96.3, 73.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 34 16.00 P 30 15.00 O 1159 8.00 N 1007 7.00 C 3564 6.00 H 4096 1.00 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: 1.06 Conformation dependent library (CDL) restraints added in 257.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 910 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 962 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 964 " 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1236 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 6 sheets defined 55.0% alpha, 6.2% beta 15 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 310 through 318 removed outlier: 3.791A pdb=" N GLU A 315 " --> pdb=" O PRO A 311 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 322 Processing helix chain 'A' and resid 335 through 355 Processing helix chain 'A' and resid 366 through 377 removed outlier: 3.782A pdb=" N ALA A 370 " --> pdb=" O LYS A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 400 through 407 removed outlier: 3.957A pdb=" N VAL A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 427 removed outlier: 3.999A pdb=" N LEU A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 438 Processing helix chain 'A' and resid 445 through 449 removed outlier: 3.522A pdb=" N HIS A 448 " --> pdb=" O GLU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 473 Processing helix chain 'A' and resid 499 through 515 Processing helix chain 'A' and resid 525 through 533 removed outlier: 3.576A pdb=" N LEU A 529 " --> pdb=" O ASN A 525 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN A 532 " --> pdb=" O GLN A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 566 removed outlier: 3.565A pdb=" N LEU A 555 " --> pdb=" O PHE A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 594 Processing helix chain 'A' and resid 598 through 616 Processing helix chain 'A' and resid 619 through 643 removed outlier: 3.992A pdb=" N ALA A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 692 removed outlier: 4.195A pdb=" N ASN A 683 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LYS A 685 " --> pdb=" O PHE A 681 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N MET A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU A 692 " --> pdb=" O LYS A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 715 Processing helix chain 'A' and resid 727 through 741 removed outlier: 3.662A pdb=" N THR A 731 " --> pdb=" O THR A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 780 Processing helix chain 'A' and resid 812 through 823 removed outlier: 3.658A pdb=" N ARG A 822 " --> pdb=" O GLN A 818 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 863 removed outlier: 3.639A pdb=" N GLU A 844 " --> pdb=" O VAL A 840 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR A 855 " --> pdb=" O GLU A 851 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG A 860 " --> pdb=" O LYS A 856 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN A 863 " --> pdb=" O ASN A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 895 removed outlier: 3.745A pdb=" N GLN A 895 " --> pdb=" O SER A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 938 Processing helix chain 'A' and resid 984 through 987 Processing helix chain 'A' and resid 1002 through 1006 Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 361 removed outlier: 6.231A pdb=" N VAL A 360 " --> pdb=" O ILE A 411 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 440 through 441 Processing sheet with id=AA3, first strand: chain 'A' and resid 751 through 753 removed outlier: 6.781A pdb=" N GLY A 721 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE A 722 " --> pdb=" O ILE A 805 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 913 through 916 removed outlier: 6.664A pdb=" N LEU A 905 " --> pdb=" O VAL A 914 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 921 through 923 Processing sheet with id=AA6, first strand: chain 'A' and resid 940 through 942 removed outlier: 3.996A pdb=" N GLY A 969 " --> pdb=" O ILE A 960 " (cutoff:3.500A) 257 hydrogen bonds defined for protein. 723 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 2.12 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 4085 1.03 - 1.23: 25 1.23 - 1.43: 2471 1.43 - 1.62: 3404 1.62 - 1.82: 54 Bond restraints: 10039 Sorted by residual: bond pdb=" N ARG A 310 " pdb=" H1 ARG A 310 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" CG ASN A 897 " pdb=" ND2 ASN A 897 " ideal model delta sigma weight residual 1.328 1.247 0.081 2.10e-02 2.27e+03 1.48e+01 bond pdb=" CG1 ILE A 458 " pdb=" CD1 ILE A 458 " ideal model delta sigma weight residual 1.513 1.448 0.065 3.90e-02 6.57e+02 2.80e+00 bond pdb=" CB ILE A 708 " pdb=" CG2 ILE A 708 " ideal model delta sigma weight residual 1.521 1.574 -0.053 3.30e-02 9.18e+02 2.58e+00 bond pdb=" CB THR A 521 " pdb=" CG2 THR A 521 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.57e+00 ... (remaining 10034 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.73: 17481 9.73 - 19.47: 0 19.47 - 29.20: 1 29.20 - 38.93: 0 38.93 - 48.66: 2 Bond angle restraints: 17484 Sorted by residual: angle pdb=" C ALA A 497 " pdb=" N LYS A 498 " pdb=" H LYS A 498 " ideal model delta sigma weight residual 124.58 75.91 48.66 3.00e+00 1.11e-01 2.63e+02 angle pdb=" CA LYS A 498 " pdb=" N LYS A 498 " pdb=" H LYS A 498 " ideal model delta sigma weight residual 114.28 68.85 45.43 3.00e+00 1.11e-01 2.29e+02 angle pdb=" C ALA A 497 " pdb=" N LYS A 498 " pdb=" CA LYS A 498 " ideal model delta sigma weight residual 121.15 144.74 -23.59 1.85e+00 2.92e-01 1.63e+02 angle pdb=" N SER A 761 " pdb=" CA SER A 761 " pdb=" C SER A 761 " ideal model delta sigma weight residual 110.80 118.80 -8.00 2.13e+00 2.20e-01 1.41e+01 angle pdb=" C SER A 760 " pdb=" N SER A 761 " pdb=" CA SER A 761 " ideal model delta sigma weight residual 121.54 128.49 -6.95 1.91e+00 2.74e-01 1.32e+01 ... (remaining 17479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.81: 4624 14.81 - 29.61: 295 29.61 - 44.42: 74 44.42 - 59.22: 47 59.22 - 74.03: 31 Dihedral angle restraints: 5071 sinusoidal: 2931 harmonic: 2140 Sorted by residual: dihedral pdb=" CA VAL A 454 " pdb=" C VAL A 454 " pdb=" N TYR A 455 " pdb=" CA TYR A 455 " ideal model delta harmonic sigma weight residual 180.00 115.98 64.02 0 5.00e+00 4.00e-02 1.64e+02 dihedral pdb=" CA GLY A 428 " pdb=" C GLY A 428 " pdb=" N ASP A 429 " pdb=" CA ASP A 429 " ideal model delta harmonic sigma weight residual -180.00 -141.77 -38.23 0 5.00e+00 4.00e-02 5.85e+01 dihedral pdb=" CA GLU A 762 " pdb=" C GLU A 762 " pdb=" N VAL A 763 " pdb=" CA VAL A 763 " ideal model delta harmonic sigma weight residual 180.00 -148.26 -31.74 0 5.00e+00 4.00e-02 4.03e+01 ... (remaining 5068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 739 0.051 - 0.103: 173 0.103 - 0.154: 38 0.154 - 0.206: 2 0.206 - 0.257: 1 Chirality restraints: 953 Sorted by residual: chirality pdb=" CB ILE A 361 " pdb=" CA ILE A 361 " pdb=" CG1 ILE A 361 " pdb=" CG2 ILE A 361 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB THR A 344 " pdb=" CA THR A 344 " pdb=" OG1 THR A 344 " pdb=" CG2 THR A 344 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.40e-01 chirality pdb=" CA TYR A 455 " pdb=" N TYR A 455 " pdb=" C TYR A 455 " pdb=" CB TYR A 455 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.74e-01 ... (remaining 950 not shown) Planarity restraints: 1444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 490 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.74e+00 pdb=" C ALA A 490 " -0.041 2.00e-02 2.50e+03 pdb=" O ALA A 490 " 0.015 2.00e-02 2.50e+03 pdb=" N SER A 491 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 829 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.04e+00 pdb=" C THR A 829 " 0.035 2.00e-02 2.50e+03 pdb=" O THR A 829 " -0.013 2.00e-02 2.50e+03 pdb=" N TYR A 830 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 330 " 0.033 5.00e-02 4.00e+02 4.92e-02 3.88e+00 pdb=" N PRO A 331 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 331 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 331 " 0.027 5.00e-02 4.00e+02 ... (remaining 1441 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 276 2.17 - 2.78: 17013 2.78 - 3.38: 23981 3.38 - 3.99: 31392 3.99 - 4.60: 48766 Nonbonded interactions: 121428 Sorted by model distance: nonbonded pdb=" H LYS A 498 " pdb=" HA LYS A 498 " model vdw 1.562 1.816 nonbonded pdb="HH12 ARG A 720 " pdb=" O PHE A 778 " model vdw 1.673 2.450 nonbonded pdb=" O PHE A 374 " pdb="HD21 ASN A 379 " model vdw 1.673 2.450 nonbonded pdb=" HE2 HIS A 927 " pdb=" O2' U X 5 " model vdw 1.685 2.450 nonbonded pdb=" OE1 GLU A 813 " pdb=" H GLU A 813 " model vdw 1.717 2.450 ... (remaining 121423 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 group one per residue 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: 0.740 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: 0.060 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.450 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 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 : 0.011 0.528 5946 Z= 0.431 Angle : 0.887 23.592 8130 Z= 0.490 Chirality : 0.046 0.257 953 Planarity : 0.005 0.049 913 Dihedral : 13.697 74.027 2474 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.72 % Favored : 87.28 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -4.00 (0.26), residues: 621 helix: -1.66 (0.23), residues: 306 sheet: -4.23 (0.46), residues: 44 loop : -3.56 (0.31), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 606 TYR 0.024 0.003 TYR A 455 PHE 0.011 0.002 PHE A 987 TRP 0.014 0.002 TRP A 968 HIS 0.004 0.001 HIS A 578 Details of bonding type rmsd/Z covalent geometry : bond 0.00768 / 0.33 ( 5943) covalent geometry : angle 0.88703 / 0.49 ( 8130) hydrogen bonds : bond 0.12703 / 8.43 ( 296) hydrogen bonds : angle 5.92058 / 4.07 ( 801) metal coordination : bond 0.37042 / 18.32 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 ASP cc_start: 0.7549 (t70) cc_final: 0.6958 (t0) REVERT: A 454 VAL cc_start: 0.8740 (t) cc_final: 0.8461 (p) REVERT: A 580 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7432 (tm-30) REVERT: A 592 LYS cc_start: 0.9188 (mttp) cc_final: 0.8582 (tptt) REVERT: A 845 ILE cc_start: 0.8896 (mt) cc_final: 0.8488 (tp) REVERT: A 905 LEU cc_start: 0.9280 (mt) cc_final: 0.8976 (tp) REVERT: A 968 TRP cc_start: 0.7309 (m-10) cc_final: 0.6782 (m-10) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.1884 time to fit residues: 44.5661 Evaluate side-chains 101 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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: 0.8980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 615 ASN A 683 ASN A 741 ASN A 759 HIS ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 ASN ** A 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.102779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.080851 restraints weight = 36886.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.084968 restraints weight = 15540.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.087570 restraints weight = 9172.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.089249 restraints weight = 6548.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.090207 restraints weight = 5232.034| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5946 Z= 0.181 Angle : 0.687 20.080 8130 Z= 0.366 Chirality : 0.039 0.136 953 Planarity : 0.004 0.038 913 Dihedral : 15.582 73.857 1149 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 21.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 1.58 % Allowed : 10.68 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -2.48 (0.31), residues: 621 helix: 0.10 (0.27), residues: 313 sheet: -4.32 (0.35), residues: 69 loop : -3.19 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 720 TYR 0.027 0.002 TYR A 455 PHE 0.013 0.001 PHE A 551 TRP 0.007 0.001 TRP A 582 HIS 0.007 0.002 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 ( 5943) covalent geometry : angle 0.68708 / 0.37 ( 8130) hydrogen bonds : bond 0.03830 / 2.59 ( 296) hydrogen bonds : angle 4.71479 / 3.31 ( 801) metal coordination : bond 0.00216 / 0.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 ASP cc_start: 0.7653 (t70) cc_final: 0.6905 (t0) REVERT: A 454 VAL cc_start: 0.8783 (t) cc_final: 0.8533 (p) REVERT: A 502 GLU cc_start: 0.8520 (tp30) cc_final: 0.8278 (tp30) REVERT: A 586 MET cc_start: 0.9198 (tpp) cc_final: 0.8964 (tpp) REVERT: A 592 LYS cc_start: 0.9328 (mttp) cc_final: 0.8691 (tptt) REVERT: A 905 LEU cc_start: 0.9420 (mt) cc_final: 0.9007 (tp) REVERT: A 924 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7365 (mt-10) REVERT: A 968 TRP cc_start: 0.7662 (m-10) cc_final: 0.7121 (m-10) outliers start: 9 outliers final: 7 residues processed: 110 average time/residue: 0.1167 time to fit residues: 17.8763 Evaluate side-chains 95 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 982 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 41 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 40 optimal weight: 0.0980 chunk 49 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 615 ASN A 759 HIS ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.103935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.081992 restraints weight = 37007.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.086088 restraints weight = 15735.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.088800 restraints weight = 9398.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.090477 restraints weight = 6676.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.091565 restraints weight = 5329.843| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5946 Z= 0.106 Angle : 0.622 20.118 8130 Z= 0.326 Chirality : 0.038 0.148 953 Planarity : 0.004 0.033 913 Dihedral : 15.407 73.692 1149 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 1.05 % Allowed : 12.08 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -1.40 (0.33), residues: 621 helix: 1.22 (0.29), residues: 310 sheet: -3.80 (0.42), residues: 59 loop : -3.07 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 606 TYR 0.014 0.001 TYR A 455 PHE 0.008 0.001 PHE A 680 TRP 0.012 0.001 TRP A 737 HIS 0.005 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 ( 5943) covalent geometry : angle 0.62183 / 0.33 ( 8130) hydrogen bonds : bond 0.03303 / 2.25 ( 296) hydrogen bonds : angle 4.23128 / 2.94 ( 801) metal coordination : bond 0.00203 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 ASP cc_start: 0.7667 (t70) cc_final: 0.6935 (t70) REVERT: A 454 VAL cc_start: 0.8637 (t) cc_final: 0.8424 (p) REVERT: A 502 GLU cc_start: 0.8467 (tp30) cc_final: 0.8248 (tp30) REVERT: A 579 TYR cc_start: 0.8104 (t80) cc_final: 0.7567 (t80) REVERT: A 586 MET cc_start: 0.9172 (tpp) cc_final: 0.8918 (tpp) REVERT: A 592 LYS cc_start: 0.9324 (mttp) cc_final: 0.8748 (tptt) REVERT: A 905 LEU cc_start: 0.9427 (mt) cc_final: 0.9026 (tp) REVERT: A 924 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7416 (mt-10) REVERT: A 968 TRP cc_start: 0.7831 (m-10) cc_final: 0.7059 (m-10) outliers start: 6 outliers final: 6 residues processed: 108 average time/residue: 0.1105 time to fit residues: 16.9926 Evaluate side-chains 93 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 982 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 5 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 ASN A 693 ASN ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.102145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.080275 restraints weight = 37850.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.084395 restraints weight = 16321.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.086968 restraints weight = 9737.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.088638 restraints weight = 6944.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.089612 restraints weight = 5541.051| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5946 Z= 0.145 Angle : 0.631 19.740 8130 Z= 0.332 Chirality : 0.038 0.132 953 Planarity : 0.003 0.032 913 Dihedral : 15.308 73.647 1149 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.63 % Favored : 89.37 % Rotamer: Outliers : 1.93 % Allowed : 13.49 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -1.08 (0.34), residues: 621 helix: 1.59 (0.29), residues: 311 sheet: -3.74 (0.43), residues: 64 loop : -3.05 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 606 TYR 0.018 0.001 TYR A 455 PHE 0.008 0.001 PHE A 401 TRP 0.005 0.001 TRP A 737 HIS 0.004 0.001 HIS A 752 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 ( 5943) covalent geometry : angle 0.63054 / 0.33 ( 8130) hydrogen bonds : bond 0.03344 / 2.25 ( 296) hydrogen bonds : angle 4.24011 / 2.90 ( 801) metal coordination : bond 0.00054 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 ASP cc_start: 0.7773 (t70) cc_final: 0.6954 (t0) REVERT: A 505 LYS cc_start: 0.8950 (tttm) cc_final: 0.8750 (ttpt) REVERT: A 592 LYS cc_start: 0.9251 (mttp) cc_final: 0.8732 (tptt) REVERT: A 620 MET cc_start: 0.7638 (pmm) cc_final: 0.7090 (pmm) REVERT: A 968 TRP cc_start: 0.7902 (m-10) cc_final: 0.7136 (m-10) outliers start: 11 outliers final: 9 residues processed: 100 average time/residue: 0.1119 time to fit residues: 15.4491 Evaluate side-chains 90 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 759 HIS Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 982 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 30 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 693 ASN ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.102089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.080112 restraints weight = 37871.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.084189 restraints weight = 16583.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.086741 restraints weight = 10049.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.088380 restraints weight = 7264.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.089403 restraints weight = 5842.409| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5946 Z= 0.131 Angle : 0.622 19.696 8130 Z= 0.325 Chirality : 0.038 0.134 953 Planarity : 0.004 0.043 913 Dihedral : 15.260 73.600 1149 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 2.10 % Allowed : 13.31 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -0.69 (0.35), residues: 621 helix: 1.92 (0.29), residues: 311 sheet: -3.49 (0.46), residues: 64 loop : -2.91 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 606 TYR 0.019 0.001 TYR A 455 PHE 0.007 0.001 PHE A 374 TRP 0.005 0.001 TRP A 737 HIS 0.003 0.001 HIS A 752 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 5943) covalent geometry : angle 0.62203 / 0.33 ( 8130) hydrogen bonds : bond 0.03236 / 2.18 ( 296) hydrogen bonds : angle 4.13264 / 2.81 ( 801) metal coordination : bond 0.00663 / 0.34 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 LYS cc_start: 0.8965 (tttm) cc_final: 0.8750 (ttpt) REVERT: A 592 LYS cc_start: 0.9290 (mttp) cc_final: 0.8789 (tptt) REVERT: A 855 TYR cc_start: 0.8609 (m-10) cc_final: 0.8306 (m-80) REVERT: A 894 LYS cc_start: 0.7584 (mttp) cc_final: 0.7289 (tmtt) REVERT: A 895 GLN cc_start: 0.7154 (tm-30) cc_final: 0.6760 (tm-30) REVERT: A 968 TRP cc_start: 0.7710 (m-10) cc_final: 0.7050 (m-10) outliers start: 12 outliers final: 12 residues processed: 94 average time/residue: 0.1056 time to fit residues: 14.1227 Evaluate side-chains 93 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 693 ASN Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 759 HIS Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 982 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 29 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 16 optimal weight: 0.0770 chunk 39 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 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 = 0.3644 r_free = 0.3644 target = 0.103841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.082021 restraints weight = 36633.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.086083 restraints weight = 16002.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.088634 restraints weight = 9552.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.090265 restraints weight = 6846.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.091335 restraints weight = 5492.724| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5946 Z= 0.103 Angle : 0.607 19.754 8130 Z= 0.316 Chirality : 0.037 0.137 953 Planarity : 0.003 0.045 913 Dihedral : 15.217 73.610 1149 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 1.75 % Allowed : 15.24 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -0.36 (0.35), residues: 621 helix: 2.24 (0.29), residues: 311 sheet: -3.44 (0.45), residues: 69 loop : -2.74 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 606 TYR 0.016 0.001 TYR A 455 PHE 0.007 0.001 PHE A 680 TRP 0.004 0.000 TRP A 737 HIS 0.004 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 5943) covalent geometry : angle 0.60679 / 0.32 ( 8130) hydrogen bonds : bond 0.02988 / 2.01 ( 296) hydrogen bonds : angle 3.97817 / 2.69 ( 801) metal coordination : bond 0.00243 / 0.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 96 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 592 LYS cc_start: 0.9254 (mttp) cc_final: 0.8761 (tptt) REVERT: A 620 MET cc_start: 0.8058 (mtt) cc_final: 0.7666 (mtt) REVERT: A 764 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7283 (mtmm) REVERT: A 855 TYR cc_start: 0.8579 (m-10) cc_final: 0.8242 (m-80) REVERT: A 894 LYS cc_start: 0.7515 (mttp) cc_final: 0.7274 (tmtt) REVERT: A 895 GLN cc_start: 0.7166 (tm-30) cc_final: 0.6723 (tm-30) REVERT: A 912 MET cc_start: 0.8634 (ptt) cc_final: 0.8349 (ptt) REVERT: A 968 TRP cc_start: 0.7663 (m-10) cc_final: 0.6989 (m-10) outliers start: 10 outliers final: 9 residues processed: 90 average time/residue: 0.1140 time to fit residues: 14.6372 Evaluate side-chains 90 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 759 HIS Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 982 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 60 optimal weight: 0.0010 overall best weight: 1.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 GLN ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.102103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.080127 restraints weight = 38001.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.084163 restraints weight = 16577.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.086665 restraints weight = 10044.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.088304 restraints weight = 7296.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.089343 restraints weight = 5873.110| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.5753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5946 Z= 0.131 Angle : 0.626 19.582 8130 Z= 0.322 Chirality : 0.038 0.131 953 Planarity : 0.004 0.047 913 Dihedral : 15.180 73.631 1149 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer: Outliers : 2.28 % Allowed : 15.24 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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 (0.35), residues: 621 helix: 2.33 (0.29), residues: 313 sheet: -3.32 (0.50), residues: 64 loop : -2.79 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 606 TYR 0.021 0.001 TYR A 455 PHE 0.007 0.001 PHE A 401 TRP 0.004 0.001 TRP A 968 HIS 0.005 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 5943) covalent geometry : angle 0.62564 / 0.32 ( 8130) hydrogen bonds : bond 0.03020 / 2.03 ( 296) hydrogen bonds : angle 4.02141 / 2.72 ( 801) metal coordination : bond 0.00025 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 ASP cc_start: 0.7916 (t70) cc_final: 0.7256 (t70) REVERT: A 505 LYS cc_start: 0.8984 (tttm) cc_final: 0.8764 (ttpt) REVERT: A 592 LYS cc_start: 0.9260 (mttp) cc_final: 0.8810 (tptt) REVERT: A 620 MET cc_start: 0.8119 (mtt) cc_final: 0.7763 (mtt) REVERT: A 764 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7453 (mtmm) REVERT: A 855 TYR cc_start: 0.8656 (m-10) cc_final: 0.8329 (m-80) REVERT: A 894 LYS cc_start: 0.7555 (mttp) cc_final: 0.7279 (tptp) REVERT: A 895 GLN cc_start: 0.7144 (tm-30) cc_final: 0.6593 (tm-30) REVERT: A 968 TRP cc_start: 0.7688 (m-10) cc_final: 0.6983 (m-10) outliers start: 13 outliers final: 12 residues processed: 91 average time/residue: 0.1181 time to fit residues: 15.0174 Evaluate side-chains 94 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain A residue 759 HIS Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 982 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 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 = 0.3580 r_free = 0.3580 target = 0.100804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.079121 restraints weight = 36968.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.082985 restraints weight = 15797.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.085444 restraints weight = 9461.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.087071 restraints weight = 6808.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.088121 restraints weight = 5458.262| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.6005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5946 Z= 0.179 Angle : 0.658 19.515 8130 Z= 0.342 Chirality : 0.039 0.133 953 Planarity : 0.004 0.051 913 Dihedral : 15.275 73.694 1149 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 22.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % Rotamer: Outliers : 2.45 % Allowed : 15.24 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -0.44 (0.35), residues: 621 helix: 2.12 (0.29), residues: 315 sheet: -3.31 (0.50), residues: 63 loop : -2.87 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 606 TYR 0.024 0.001 TYR A 455 PHE 0.026 0.002 PHE A 712 TRP 0.005 0.001 TRP A 385 HIS 0.005 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.18 ( 5943) covalent geometry : angle 0.65816 / 0.34 ( 8130) hydrogen bonds : bond 0.03339 / 2.22 ( 296) hydrogen bonds : angle 4.21927 / 2.86 ( 801) metal coordination : bond 0.00103 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 LEU cc_start: 0.8833 (mt) cc_final: 0.8322 (tt) REVERT: A 444 ASP cc_start: 0.8020 (t70) cc_final: 0.6799 (t70) REVERT: A 445 GLU cc_start: 0.8356 (mp0) cc_final: 0.7453 (mp0) REVERT: A 505 LYS cc_start: 0.9045 (tttm) cc_final: 0.8807 (ttpt) REVERT: A 592 LYS cc_start: 0.9297 (mttp) cc_final: 0.8858 (tptt) REVERT: A 726 LYS cc_start: 0.8720 (mttt) cc_final: 0.8412 (tptp) REVERT: A 759 HIS cc_start: 0.7433 (OUTLIER) cc_final: 0.6629 (m-70) REVERT: A 764 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7766 (mtmm) REVERT: A 855 TYR cc_start: 0.8711 (m-10) cc_final: 0.8368 (m-80) REVERT: A 894 LYS cc_start: 0.7654 (mttp) cc_final: 0.7345 (tptp) REVERT: A 895 GLN cc_start: 0.7297 (tm-30) cc_final: 0.6758 (tm-30) REVERT: A 968 TRP cc_start: 0.8007 (m-10) cc_final: 0.7260 (m-10) outliers start: 14 outliers final: 12 residues processed: 94 average time/residue: 0.1162 time to fit residues: 15.2478 Evaluate side-chains 99 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain A residue 759 HIS Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 982 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 4 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 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 = 0.3596 r_free = 0.3596 target = 0.101665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.080260 restraints weight = 36907.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.084110 restraints weight = 15949.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.086543 restraints weight = 9555.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.088111 restraints weight = 6884.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.089023 restraints weight = 5540.111| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.6159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5946 Z= 0.139 Angle : 0.636 19.531 8130 Z= 0.327 Chirality : 0.038 0.135 953 Planarity : 0.004 0.056 913 Dihedral : 15.255 73.641 1149 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.63 % Favored : 89.37 % Rotamer: Outliers : 2.28 % Allowed : 16.64 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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 (0.35), residues: 621 helix: 2.37 (0.29), residues: 315 sheet: -3.23 (0.51), residues: 63 loop : -2.84 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 606 TYR 0.020 0.001 TYR A 455 PHE 0.018 0.001 PHE A 712 TRP 0.004 0.001 TRP A 968 HIS 0.004 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 ( 5943) covalent geometry : angle 0.63558 / 0.33 ( 8130) hydrogen bonds : bond 0.03076 / 2.06 ( 296) hydrogen bonds : angle 4.06515 / 2.75 ( 801) metal coordination : bond 0.00078 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 LEU cc_start: 0.8865 (mt) cc_final: 0.8427 (tt) REVERT: A 444 ASP cc_start: 0.8031 (t70) cc_final: 0.6795 (t70) REVERT: A 445 GLU cc_start: 0.8269 (mp0) cc_final: 0.7339 (mp0) REVERT: A 505 LYS cc_start: 0.9006 (tttm) cc_final: 0.8762 (ttpt) REVERT: A 592 LYS cc_start: 0.9286 (mttp) cc_final: 0.8871 (tptt) REVERT: A 620 MET cc_start: 0.8353 (mtt) cc_final: 0.7928 (mtt) REVERT: A 726 LYS cc_start: 0.8764 (mttt) cc_final: 0.8469 (tptp) REVERT: A 764 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7745 (mtmm) REVERT: A 855 TYR cc_start: 0.8628 (m-10) cc_final: 0.8275 (m-80) REVERT: A 894 LYS cc_start: 0.7607 (mttp) cc_final: 0.7334 (tptp) REVERT: A 895 GLN cc_start: 0.7258 (tm-30) cc_final: 0.6703 (tm-30) REVERT: A 905 LEU cc_start: 0.9482 (mt) cc_final: 0.9102 (tp) outliers start: 13 outliers final: 11 residues processed: 96 average time/residue: 0.1143 time to fit residues: 15.4194 Evaluate side-chains 98 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 982 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 46 optimal weight: 30.0000 chunk 1 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 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 = 0.3604 r_free = 0.3604 target = 0.102162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.080480 restraints weight = 36760.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.084382 restraints weight = 15779.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.086848 restraints weight = 9453.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.088460 restraints weight = 6826.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.089391 restraints weight = 5485.464| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.6304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5946 Z= 0.124 Angle : 0.626 19.555 8130 Z= 0.321 Chirality : 0.038 0.136 953 Planarity : 0.004 0.060 913 Dihedral : 15.250 73.633 1149 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 20.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer: Outliers : 2.10 % Allowed : 17.69 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -0.13 (0.35), residues: 621 helix: 2.30 (0.29), residues: 322 sheet: -3.13 (0.52), residues: 63 loop : -2.77 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 606 TYR 0.017 0.001 TYR A 455 PHE 0.018 0.001 PHE A 712 TRP 0.003 0.001 TRP A 968 HIS 0.003 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 5943) covalent geometry : angle 0.62596 / 0.32 ( 8130) hydrogen bonds : bond 0.03018 / 1.99 ( 296) hydrogen bonds : angle 4.01778 / 2.73 ( 801) metal coordination : bond 0.00114 / 0.06 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 LEU cc_start: 0.8830 (mt) cc_final: 0.8401 (tt) REVERT: A 444 ASP cc_start: 0.8065 (t70) cc_final: 0.6810 (t70) REVERT: A 445 GLU cc_start: 0.8309 (mp0) cc_final: 0.7376 (mp0) REVERT: A 592 LYS cc_start: 0.9262 (mttp) cc_final: 0.8870 (tptt) REVERT: A 620 MET cc_start: 0.8406 (mtt) cc_final: 0.7971 (mtt) REVERT: A 726 LYS cc_start: 0.8753 (mttt) cc_final: 0.8404 (tptp) REVERT: A 855 TYR cc_start: 0.8737 (m-10) cc_final: 0.8379 (m-80) REVERT: A 894 LYS cc_start: 0.7568 (mttp) cc_final: 0.7307 (tptp) REVERT: A 895 GLN cc_start: 0.7353 (tm-30) cc_final: 0.6823 (tm-30) REVERT: A 905 LEU cc_start: 0.9495 (mt) cc_final: 0.9057 (tp) outliers start: 12 outliers final: 12 residues processed: 95 average time/residue: 0.1006 time to fit residues: 13.7857 Evaluate side-chains 97 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 982 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 9.9990 chunk 52 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 39 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 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 = 0.3631 r_free = 0.3631 target = 0.103906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.082209 restraints weight = 36950.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.086151 restraints weight = 16148.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.088695 restraints weight = 9748.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.090270 restraints weight = 7024.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.091352 restraints weight = 5683.959| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.6446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 5946 Z= 0.100 Angle : 0.614 19.503 8130 Z= 0.312 Chirality : 0.038 0.136 953 Planarity : 0.004 0.057 913 Dihedral : 15.224 73.631 1149 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 1.58 % Allowed : 18.21 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: 0.17 (0.36), residues: 621 helix: 2.49 (0.30), residues: 321 sheet: -2.95 (0.53), residues: 63 loop : -2.55 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 606 TYR 0.015 0.001 TYR A 455 PHE 0.019 0.001 PHE A 712 TRP 0.004 0.001 TRP A 582 HIS 0.002 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 5943) covalent geometry : angle 0.61386 / 0.31 ( 8130) hydrogen bonds : bond 0.02799 / 1.85 ( 296) hydrogen bonds : angle 3.86630 / 2.63 ( 801) metal coordination : bond 0.00234 / 0.12 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1753.90 seconds wall clock time: 30 minutes 51.78 seconds (1851.78 seconds total)