Starting phenix.real_space_refine on Fri Sep 11 16:06:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6g1s_4340/09_2026/6g1s_4340.cif Found real_map, /net/cci-nas-00/data/ceres_data/6g1s_4340/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6g1s_4340/09_2026/6g1s_4340.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6g1s_4340/09_2026/6g1s_4340.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6g1s_4340/09_2026/6g1s_4340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6g1s_4340/09_2026/6g1s_4340.map" model { file = "/net/cci-nas-00/data/ceres_data/6g1s_4340/09_2026/6g1s_4340.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6g1s_4340/09_2026/6g1s_4340.cif" } 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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: {'RNAv2': 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: 2.12, per 1000 atoms: 0.21 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: 1.08 Conformation dependent library (CDL) restraints added in 230.2 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: 1.42 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: 2.10 Time building geometry restraints manager: 1.38 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 - 14.40: 4539 14.40 - 28.79: 298 28.79 - 43.19: 89 43.19 - 57.59: 27 57.59 - 71.98: 4 Dihedral angle restraints: 4957 sinusoidal: 2817 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=" O5' G X 15 " pdb=" C5' G X 15 " pdb=" C4' G X 15 " pdb=" C3' G X 15 " ideal model delta sinusoidal sigma weight residual 60.00 110.42 -50.42 3 6.40e+00 2.44e-02 4.89e+01 ... (remaining 4954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 709 0.051 - 0.103: 173 0.103 - 0.154: 38 0.154 - 0.206: 11 0.206 - 0.257: 22 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=" P A Y 15 " pdb=" OP1 A Y 15 " pdb=" OP2 A Y 15 " pdb=" O5' A Y 15 " both_signs ideal model delta sigma weight residual True 2.17 -2.43 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" P A X 13 " pdb=" OP1 A X 13 " pdb=" OP2 A X 13 " pdb=" O5' A X 13 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (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: 0.730 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: 14.560 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 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 : 0.920 23.592 8130 Z= 0.493 Chirality : 0.060 0.257 953 Planarity : 0.005 0.049 913 Dihedral : 10.934 71.984 2360 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 0.00772 / 0.33 ( 5943) covalent geometry : angle 0.92020 / 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 : 0.258 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: 0.1818 time to fit residues: 43.5121 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 : 0.265 ------------------------------------------------------------------------------- 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: 5.9990 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... 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.102625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.080886 restraints weight = 36936.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.084952 restraints weight = 15805.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.087535 restraints weight = 9396.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.089205 restraints weight = 6729.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.090265 restraints weight = 5374.794| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5946 Z= 0.184 Angle : 0.752 20.135 8130 Z= 0.378 Chirality : 0.045 0.191 953 Planarity : 0.004 0.038 913 Dihedral : 9.923 61.288 1035 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 1.40 % Allowed : 10.68 % Favored : 87.92 % 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: -2.50 (0.31), residues: 621 helix: 0.07 (0.27), residues: 313 sheet: -4.33 (0.35), residues: 69 loop : -3.19 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 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 0.00384 / 0.18 ( 5943) covalent geometry : angle 0.75210 / 0.38 ( 8130) hydrogen bonds : bond 0.03860 / 2.62 ( 296) hydrogen bonds : angle 4.74124 / 3.33 ( 801) metal coordination : bond 0.00433 / 0.21 ( 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 108 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.294 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: 0.7649 (t70) cc_final: 0.6906 (t0) REVERT: A 454 VAL cc_start: 0.8779 (t) cc_final: 0.8526 (p) REVERT: A 502 GLU cc_start: 0.8497 (tp30) cc_final: 0.8260 (tp30) REVERT: A 586 MET cc_start: 0.9196 (tpp) cc_final: 0.8962 (tpp) REVERT: A 592 LYS cc_start: 0.9318 (mttp) cc_final: 0.8682 (tptt) REVERT: A 905 LEU cc_start: 0.9409 (mt) cc_final: 0.8996 (tp) REVERT: A 924 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7366 (mt-10) REVERT: A 968 TRP cc_start: 0.7666 (m-10) cc_final: 0.7133 (m-10) outliers start: 8 outliers final: 5 residues processed: 106 average time/residue: 0.1176 time to fit residues: 17.4220 Evaluate side-chains 91 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 982 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 56 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 40 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 58 optimal weight: 0.0470 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3622 r_free = 0.3622 target = 0.103380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.081421 restraints weight = 37459.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.085535 restraints weight = 16173.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.088146 restraints weight = 9684.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.089819 restraints weight = 6946.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.090904 restraints weight = 5558.316| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5946 Z= 0.117 Angle : 0.677 20.156 8130 Z= 0.339 Chirality : 0.043 0.202 953 Planarity : 0.004 0.033 913 Dihedral : 9.449 59.313 1035 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 1.40 % Allowed : 12.08 % Favored : 86.51 % 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: -1.45 (0.33), residues: 621 helix: 1.16 (0.29), residues: 310 sheet: -3.86 (0.41), 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 0.011 0.001 TRP A 737 HIS 0.005 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 5943) covalent geometry : angle 0.67688 / 0.34 ( 8130) hydrogen bonds : bond 0.03352 / 2.28 ( 296) hydrogen bonds : angle 4.27403 / 2.97 ( 801) metal coordination : bond 0.00279 / 0.14 ( 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: 8 poor density : 103 time to evaluate : 0.244 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: A 444 ASP cc_start: 0.7725 (t70) cc_final: 0.6996 (t70) REVERT: A 454 VAL cc_start: 0.8639 (t) cc_final: 0.8421 (p) REVERT: A 502 GLU cc_start: 0.8435 (tp30) cc_final: 0.8224 (tp30) REVERT: A 586 MET cc_start: 0.9166 (tpp) cc_final: 0.8916 (tpp) REVERT: A 592 LYS cc_start: 0.9312 (mttp) cc_final: 0.8731 (tptt) REVERT: A 905 LEU cc_start: 0.9428 (mt) cc_final: 0.9029 (tp) REVERT: A 924 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7452 (mt-10) REVERT: A 968 TRP cc_start: 0.7856 (m-10) cc_final: 0.6972 (m-10) outliers start: 8 outliers final: 8 residues processed: 107 average time/residue: 0.1079 time to fit residues: 16.4917 Evaluate side-chains 95 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 764 LYS Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 902 LEU 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: 0.6980 chunk 43 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 25 optimal weight: 0.0000 chunk 58 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3642 r_free = 0.3642 target = 0.103586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.081935 restraints weight = 36666.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.086003 restraints weight = 15899.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.088532 restraints weight = 9430.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.090072 restraints weight = 6733.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.091161 restraints weight = 5446.622| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5946 Z= 0.111 Angle : 0.654 19.879 8130 Z= 0.329 Chirality : 0.043 0.206 953 Planarity : 0.003 0.035 913 Dihedral : 9.189 57.042 1035 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 1.93 % Allowed : 13.13 % Favored : 84.94 % 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: -0.94 (0.34), residues: 621 helix: 1.68 (0.29), residues: 310 sheet: -3.63 (0.43), residues: 59 loop : -2.96 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 606 TYR 0.014 0.001 TYR A 455 PHE 0.008 0.001 PHE A 574 TRP 0.007 0.001 TRP A 737 HIS 0.004 0.001 HIS A 752 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 5943) covalent geometry : angle 0.65445 / 0.33 ( 8130) hydrogen bonds : bond 0.03192 / 2.16 ( 296) hydrogen bonds : angle 4.07638 / 2.79 ( 801) metal coordination : bond 0.00388 / 0.20 ( 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 113 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.276 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: 0.7695 (t70) cc_final: 0.6921 (t70) REVERT: A 592 LYS cc_start: 0.9249 (mttp) cc_final: 0.8690 (tptt) REVERT: A 968 TRP cc_start: 0.7893 (m-10) cc_final: 0.7159 (m-10) outliers start: 11 outliers final: 9 residues processed: 108 average time/residue: 0.1100 time to fit residues: 16.8696 Evaluate side-chains 89 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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: 4.9990 chunk 38 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 563 GLN ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** 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 = 0.3626 r_free = 0.3626 target = 0.103022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.082356 restraints weight = 37087.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.086458 restraints weight = 15308.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.089035 restraints weight = 8896.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.090646 restraints weight = 6253.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.091666 restraints weight = 4944.900| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5946 Z= 0.113 Angle : 0.658 19.692 8130 Z= 0.325 Chirality : 0.043 0.220 953 Planarity : 0.003 0.038 913 Dihedral : 9.102 53.959 1035 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 1.93 % Allowed : 14.01 % Favored : 84.06 % 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: -0.48 (0.35), residues: 621 helix: 2.10 (0.29), residues: 311 sheet: -3.26 (0.50), residues: 54 loop : -2.90 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 606 TYR 0.018 0.001 TYR A 455 PHE 0.008 0.001 PHE A 374 TRP 0.006 0.001 TRP A 737 HIS 0.003 0.001 HIS A 604 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 5943) covalent geometry : angle 0.65829 / 0.33 ( 8130) hydrogen bonds : bond 0.03071 / 2.07 ( 296) hydrogen bonds : angle 3.97341 / 2.70 ( 801) metal coordination : bond 0.00109 / 0.05 ( 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 102 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.286 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 444 ASP cc_start: 0.7799 (t70) cc_final: 0.7087 (t0) REVERT: A 592 LYS cc_start: 0.9235 (mttp) cc_final: 0.8717 (tptt) REVERT: A 855 TYR cc_start: 0.8691 (m-10) cc_final: 0.8372 (m-80) REVERT: A 894 LYS cc_start: 0.7529 (mttp) cc_final: 0.7218 (tmtt) REVERT: A 895 GLN cc_start: 0.7120 (tm-30) cc_final: 0.6773 (tm-30) REVERT: A 968 TRP cc_start: 0.7849 (m-10) cc_final: 0.7041 (m-10) outliers start: 11 outliers final: 10 residues processed: 97 average time/residue: 0.1042 time to fit residues: 14.7538 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 : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 904 THR 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: 0.9990 chunk 7 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 16 optimal weight: 0.3980 chunk 39 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 416 GLN A 693 ASN ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 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 = 0.3629 r_free = 0.3629 target = 0.102806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.081087 restraints weight = 36889.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.085066 restraints weight = 16195.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.087595 restraints weight = 9713.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.089245 restraints weight = 6956.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.090360 restraints weight = 5544.943| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.5534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5946 Z= 0.123 Angle : 0.662 19.607 8130 Z= 0.326 Chirality : 0.043 0.222 953 Planarity : 0.003 0.048 913 Dihedral : 9.051 53.956 1035 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 1.75 % Allowed : 14.89 % Favored : 83.36 % 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: -0.21 (0.35), residues: 621 helix: 2.38 (0.29), residues: 311 sheet: -3.19 (0.51), residues: 59 loop : -2.81 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 606 TYR 0.019 0.001 TYR A 455 PHE 0.006 0.001 PHE A 401 TRP 0.003 0.001 TRP A 737 HIS 0.003 0.001 HIS A 604 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 5943) covalent geometry : angle 0.66172 / 0.33 ( 8130) hydrogen bonds : bond 0.03025 / 2.05 ( 296) hydrogen bonds : angle 3.92383 / 2.67 ( 801) metal coordination : bond 0.00148 / 0.07 ( 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 100 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.334 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: 0.8950 (tttm) cc_final: 0.8746 (ttpt) REVERT: A 592 LYS cc_start: 0.9241 (mttp) cc_final: 0.8750 (tptt) REVERT: A 764 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7476 (mtmm) REVERT: A 855 TYR cc_start: 0.8617 (m-10) cc_final: 0.8289 (m-80) REVERT: A 894 LYS cc_start: 0.7525 (mttp) cc_final: 0.7289 (tmtt) REVERT: A 895 GLN cc_start: 0.7182 (tm-30) cc_final: 0.6746 (tm-30) REVERT: A 905 LEU cc_start: 0.9471 (mt) cc_final: 0.9123 (tp) outliers start: 10 outliers final: 8 residues processed: 95 average time/residue: 0.1086 time to fit residues: 14.8842 Evaluate side-chains 93 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 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 982 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 36 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 693 ASN ** 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 = 0.3612 r_free = 0.3612 target = 0.102621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.080879 restraints weight = 36680.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.084903 restraints weight = 15676.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.087455 restraints weight = 9330.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.089155 restraints weight = 6653.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.090291 restraints weight = 5272.953| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.5773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5946 Z= 0.122 Angle : 0.663 19.545 8130 Z= 0.324 Chirality : 0.043 0.223 953 Planarity : 0.003 0.026 913 Dihedral : 9.004 54.187 1035 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 1.93 % Allowed : 15.24 % Favored : 82.84 % 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: -0.06 (0.35), residues: 621 helix: 2.46 (0.29), residues: 314 sheet: -2.98 (0.55), residues: 54 loop : -2.80 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 606 TYR 0.020 0.001 TYR A 455 PHE 0.006 0.001 PHE A 401 TRP 0.004 0.001 TRP A 737 HIS 0.003 0.001 HIS A 604 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 5943) covalent geometry : angle 0.66265 / 0.32 ( 8130) hydrogen bonds : bond 0.02968 / 2.02 ( 296) hydrogen bonds : angle 3.90304 / 2.65 ( 801) metal coordination : bond 0.00159 / 0.08 ( 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 104 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.278 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 444 ASP cc_start: 0.7930 (t70) cc_final: 0.7279 (t70) REVERT: A 505 LYS cc_start: 0.8932 (tttm) cc_final: 0.8718 (ttpt) REVERT: A 592 LYS cc_start: 0.9258 (mttp) cc_final: 0.8803 (tptt) REVERT: A 606 ARG cc_start: 0.9038 (ttp80) cc_final: 0.8571 (ttt-90) REVERT: A 764 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7605 (mtmm) REVERT: A 855 TYR cc_start: 0.8740 (m-10) cc_final: 0.8405 (m-80) REVERT: A 894 LYS cc_start: 0.7528 (mttp) cc_final: 0.7268 (tmtt) REVERT: A 895 GLN cc_start: 0.7340 (tm-30) cc_final: 0.6856 (tm-30) REVERT: A 905 LEU cc_start: 0.9474 (mt) cc_final: 0.9089 (tp) outliers start: 11 outliers final: 9 residues processed: 98 average time/residue: 0.1070 time to fit residues: 15.1023 Evaluate side-chains 100 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 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 902 LEU 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: 3.9990 chunk 25 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 61 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 509 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 = 0.3570 r_free = 0.3570 target = 0.100405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.078899 restraints weight = 36884.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.082737 restraints weight = 15826.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.085185 restraints weight = 9452.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.086732 restraints weight = 6778.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.087773 restraints weight = 5450.717| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.6016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5946 Z= 0.212 Angle : 0.751 19.358 8130 Z= 0.368 Chirality : 0.047 0.241 953 Planarity : 0.004 0.025 913 Dihedral : 9.411 55.842 1035 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 22.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % Rotamer: Outliers : 2.10 % Allowed : 16.81 % 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: -0.45 (0.35), residues: 621 helix: 2.15 (0.29), residues: 315 sheet: -3.56 (0.48), residues: 67 loop : -2.84 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 599 TYR 0.024 0.002 TYR A 455 PHE 0.011 0.002 PHE A 401 TRP 0.006 0.001 TRP A 385 HIS 0.005 0.001 HIS A 752 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.21 ( 5943) covalent geometry : angle 0.75096 / 0.37 ( 8130) hydrogen bonds : bond 0.03504 / 2.34 ( 296) hydrogen bonds : angle 4.24321 / 2.90 ( 801) metal coordination : bond 0.00158 / 0.08 ( 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 107 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.248 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: 0.8812 (mt) cc_final: 0.8298 (tt) REVERT: A 444 ASP cc_start: 0.8004 (t70) cc_final: 0.6820 (t70) REVERT: A 445 GLU cc_start: 0.8346 (mp0) cc_final: 0.7338 (mp0) REVERT: A 505 LYS cc_start: 0.9012 (tttm) cc_final: 0.8786 (ttpt) REVERT: A 592 LYS cc_start: 0.9306 (mttp) cc_final: 0.8880 (tptt) REVERT: A 606 ARG cc_start: 0.8964 (ttp80) cc_final: 0.8635 (ttt-90) REVERT: A 616 ASP cc_start: 0.9091 (p0) cc_final: 0.8736 (p0) REVERT: A 726 LYS cc_start: 0.8679 (mttt) cc_final: 0.8348 (tptp) REVERT: A 764 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7935 (mtmm) REVERT: A 855 TYR cc_start: 0.8824 (m-10) cc_final: 0.8493 (m-80) REVERT: A 894 LYS cc_start: 0.7659 (mttp) cc_final: 0.7351 (tptp) REVERT: A 895 GLN cc_start: 0.7370 (tm-30) cc_final: 0.6848 (tm-30) outliers start: 12 outliers final: 11 residues processed: 102 average time/residue: 0.1095 time to fit residues: 15.7783 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 : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 509 ASN 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 902 LEU Chi-restraints excluded: chain A residue 904 THR 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: 10.0000 chunk 62 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 1 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3580 r_free = 0.3580 target = 0.100740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.079140 restraints weight = 37130.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.082993 restraints weight = 16222.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.085473 restraints weight = 9778.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.087095 restraints weight = 7025.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.088089 restraints weight = 5620.491| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.6109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5946 Z= 0.165 Angle : 0.718 19.371 8130 Z= 0.350 Chirality : 0.045 0.232 953 Planarity : 0.003 0.026 913 Dihedral : 9.257 55.817 1035 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 22.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 2.10 % Allowed : 17.51 % Favored : 80.39 % 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: -0.34 (0.35), residues: 621 helix: 2.25 (0.29), residues: 315 sheet: -3.35 (0.50), residues: 64 loop : -2.87 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 599 TYR 0.019 0.001 TYR A 455 PHE 0.016 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 0.00346 / 0.17 ( 5943) covalent geometry : angle 0.71782 / 0.35 ( 8130) hydrogen bonds : bond 0.03330 / 2.27 ( 296) hydrogen bonds : angle 4.11643 / 2.81 ( 801) metal coordination : bond 0.00151 / 0.07 ( 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 102 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.182 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: 0.8832 (mt) cc_final: 0.8352 (tt) REVERT: A 444 ASP cc_start: 0.7993 (t70) cc_final: 0.6736 (t70) REVERT: A 445 GLU cc_start: 0.8351 (mp0) cc_final: 0.7440 (mp0) REVERT: A 505 LYS cc_start: 0.9030 (tttm) cc_final: 0.8814 (ttpt) REVERT: A 592 LYS cc_start: 0.9288 (mttp) cc_final: 0.8863 (tptt) REVERT: A 606 ARG cc_start: 0.8960 (ttp80) cc_final: 0.8644 (ttt-90) REVERT: A 616 ASP cc_start: 0.8993 (p0) cc_final: 0.8651 (p0) REVERT: A 726 LYS cc_start: 0.8749 (mttt) cc_final: 0.8460 (tptp) REVERT: A 764 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7778 (mtmm) REVERT: A 855 TYR cc_start: 0.8637 (m-10) cc_final: 0.8293 (m-80) REVERT: A 894 LYS cc_start: 0.7633 (mttp) cc_final: 0.7346 (tptp) REVERT: A 895 GLN cc_start: 0.7272 (tm-30) cc_final: 0.6672 (tm-30) outliers start: 12 outliers final: 11 residues processed: 96 average time/residue: 0.1139 time to fit residues: 15.2121 Evaluate side-chains 100 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.196 ------------------------------------------------------------------------------- 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 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 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 49 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 46 optimal weight: 20.0000 chunk 1 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3602 r_free = 0.3602 target = 0.102135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.080651 restraints weight = 36689.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.084591 restraints weight = 15945.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.087078 restraints weight = 9524.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.088654 restraints weight = 6838.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.089650 restraints weight = 5489.643| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.6243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5946 Z= 0.127 Angle : 0.689 19.454 8130 Z= 0.335 Chirality : 0.044 0.226 953 Planarity : 0.003 0.026 913 Dihedral : 9.055 55.816 1035 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % Rotamer: Outliers : 2.10 % Allowed : 18.21 % Favored : 79.68 % 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: -0.08 (0.35), residues: 621 helix: 2.37 (0.30), residues: 322 sheet: -2.94 (0.56), residues: 54 loop : -2.89 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 599 TYR 0.017 0.001 TYR A 455 PHE 0.011 0.001 PHE A 712 TRP 0.006 0.001 TRP A 968 HIS 0.003 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 5943) covalent geometry : angle 0.68914 / 0.34 ( 8130) hydrogen bonds : bond 0.03033 / 2.05 ( 296) hydrogen bonds : angle 3.97185 / 2.71 ( 801) metal coordination : bond 0.00112 / 0.05 ( 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 107 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.278 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: 0.8872 (mt) cc_final: 0.8436 (tt) REVERT: A 444 ASP cc_start: 0.8024 (t70) cc_final: 0.7230 (t70) REVERT: A 505 LYS cc_start: 0.8985 (tttm) cc_final: 0.8768 (ttpt) REVERT: A 592 LYS cc_start: 0.9268 (mttp) cc_final: 0.8831 (tptt) REVERT: A 606 ARG cc_start: 0.8956 (ttp80) cc_final: 0.8660 (ttt-90) REVERT: A 616 ASP cc_start: 0.8942 (p0) cc_final: 0.8611 (p0) REVERT: A 726 LYS cc_start: 0.8734 (mttt) cc_final: 0.8443 (tptp) REVERT: A 764 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7740 (mtmm) REVERT: A 855 TYR cc_start: 0.8660 (m-10) cc_final: 0.8311 (m-80) REVERT: A 894 LYS cc_start: 0.7545 (mttp) cc_final: 0.7287 (tptp) REVERT: A 895 GLN cc_start: 0.7265 (tm-30) cc_final: 0.6732 (tm-30) REVERT: A 905 LEU cc_start: 0.9526 (mt) cc_final: 0.9056 (tp) outliers start: 12 outliers final: 11 residues processed: 101 average time/residue: 0.1130 time to fit residues: 16.2895 Evaluate side-chains 100 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 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 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: 10.0000 chunk 52 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 64 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3624 r_free = 0.3624 target = 0.103653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.081980 restraints weight = 37235.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.085988 restraints weight = 16236.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.088535 restraints weight = 9738.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.090187 restraints weight = 6972.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.091083 restraints weight = 5578.467| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.6384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 5946 Z= 0.108 Angle : 0.679 19.468 8130 Z= 0.331 Chirality : 0.044 0.218 953 Planarity : 0.003 0.027 913 Dihedral : 8.902 54.776 1035 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 20.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 1.93 % Allowed : 18.74 % Favored : 79.33 % 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: 0.19 (0.36), residues: 621 helix: 2.54 (0.30), residues: 321 sheet: -2.79 (0.58), residues: 54 loop : -2.67 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 599 TYR 0.018 0.001 TYR A 455 PHE 0.010 0.001 PHE A 712 TRP 0.006 0.001 TRP A 968 HIS 0.002 0.001 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 5943) covalent geometry : angle 0.67942 / 0.33 ( 8130) hydrogen bonds : bond 0.02906 / 1.97 ( 296) hydrogen bonds : angle 3.84855 / 2.64 ( 801) metal coordination : bond 0.00156 / 0.08 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1749.45 seconds wall clock time: 30 minutes 40.44 seconds (1840.44 seconds total)