Starting phenix.real_space_refine (version: 1.19rc7) on Tue Jan 5 16:28:26 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gkm_0024/01_2021/6gkm_0024_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gkm_0024/01_2021/6gkm_0024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gkm_0024/01_2021/6gkm_0024.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gkm_0024/01_2021/6gkm_0024.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gkm_0024/01_2021/6gkm_0024_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gkm_0024/01_2021/6gkm_0024_updated.pdb" } resolution = 3.87 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 ------------------------------------------------------------------------------- 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= 0.013 Set model interpretation parameters Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.19rc7-4070/modules/chem_data/mon_lib" Total number of atoms: 10562 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 9933 Classifications: {'peptide': 689} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 667} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "X" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 308 Classifications: {'RNA': 14} Modifications used: {'rna3p_pyr': 3, 'rna3p_pur': 11} Link IDs: {'rna3p': 13} Chain: "Y" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 289 Classifications: {'RNA': 14} Modifications used: {'rna3p_pyr': 11, 'rna3p_pur': 3} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8383 SG CYS A 907 77.644 31.514 37.882 1.00129.19 S ATOM 8430 SG CYS A 910 80.696 31.296 37.972 1.00129.60 S ATOM 9100 SG CYS A 962 79.571 31.817 41.539 1.00129.10 S ATOM 9119 SG CYS A 964 79.466 34.419 39.261 1.00130.93 S Time building chain proxies: 5.50, per 1000 atoms: 0.52 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Number of scatterers: 10562 At special positions: 0 Unit cell: (101.65, 85.6, 68.48, 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 35 16.00 P 31 15.00 O 1243 8.00 N 1072 7.00 C 3778 6.00 H 4402 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 - 3.50 Amimo acid : False - 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: 8.68 Conformation dependent library (CDL) restraints added in 903.9 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 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 907 " Number of angles added : 6 1362 Ramachandran restraints generated. 681 Oldfield and 0 Emsley and 681 emsley8k. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1318 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 5 sheets defined 45.1% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 311 through 321 removed outlier: 3.573A pdb=" N GLU A 315 " --> pdb=" O PRO A 311 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Proline residue: A 319 - end of helix Processing helix chain 'A' and resid 336 through 353 Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 379 through 382 No H-bonds generated for 'chain 'A' and resid 379 through 382' Processing helix chain 'A' and resid 401 through 406 removed outlier: 3.533A pdb=" N VAL A 405 " --> pdb=" O PHE A 401 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS A 406 " --> pdb=" O PRO A 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 401 through 406' Processing helix chain 'A' and resid 416 through 427 Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 446 through 448 No H-bonds generated for 'chain 'A' and resid 446 through 448' Processing helix chain 'A' and resid 456 through 475 removed outlier: 4.108A pdb=" N LYS A 474 " --> pdb=" O ASN A 470 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN A 475 " --> pdb=" O ASP A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 513 Processing helix chain 'A' and resid 526 through 532 Processing helix chain 'A' and resid 549 through 566 removed outlier: 3.963A pdb=" N ILE A 558 " --> pdb=" O LYS A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 593 Processing helix chain 'A' and resid 599 through 616 removed outlier: 3.688A pdb=" N LYS A 607 " --> pdb=" O GLU A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 642 Processing helix chain 'A' and resid 671 through 691 removed outlier: 3.926A pdb=" N ASP A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASN A 683 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LYS A 685 " --> pdb=" O PHE A 681 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N MET A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 696 No H-bonds generated for 'chain 'A' and resid 694 through 696' Processing helix chain 'A' and resid 700 through 714 removed outlier: 3.567A pdb=" N GLN A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 740 Processing helix chain 'A' and resid 742 through 746 Processing helix chain 'A' and resid 768 through 780 Processing helix chain 'A' and resid 813 through 821 Processing helix chain 'A' and resid 841 through 862 removed outlier: 3.797A pdb=" N TYR A 855 " --> pdb=" O GLU A 851 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS A 856 " --> pdb=" O LYS A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 882 Processing helix chain 'A' and resid 886 through 892 removed outlier: 3.669A pdb=" N ARG A 890 " --> pdb=" O MET A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 937 Processing sheet with id= A, first strand: chain 'A' and resid 326 through 329 Processing sheet with id= B, first strand: chain 'A' and resid 537 through 542 removed outlier: 3.672A pdb=" N THR A 834 " --> pdb=" O VAL A 541 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 721 through 724 Processing sheet with id= D, first strand: chain 'A' and resid 987 through 991 removed outlier: 5.247A pdb=" N CYS A 907 " --> pdb=" O LEU A 913 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU A 913 " --> pdb=" O CYS A 907 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 920 through 923 231 hydrogen bonds defined for protein. 687 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.86 Time building geometry restraints manager: 8.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4391 1.03 - 1.23: 18 1.23 - 1.42: 2607 1.42 - 1.62: 3646 1.62 - 1.81: 56 Bond restraints: 10718 Sorted by residual: bond pdb=" C4 ATP A1102 " pdb=" C5 ATP A1102 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.52e+01 bond pdb=" C5 ATP A1102 " pdb=" C6 ATP A1102 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.49e+01 bond pdb=" C8 ATP A1102 " pdb=" N7 ATP A1102 " ideal model delta sigma weight residual 1.310 1.358 -0.048 1.00e-02 1.00e+04 2.32e+01 bond pdb=" C4 ATP A1102 " pdb=" N9 ATP A1102 " ideal model delta sigma weight residual 1.374 1.327 0.047 1.00e-02 1.00e+04 2.17e+01 bond pdb=" C5 ATP A1102 " pdb=" N7 ATP A1102 " ideal model delta sigma weight residual 1.387 1.345 0.042 1.00e-02 1.00e+04 1.76e+01 ... (remaining 10713 not shown) Histogram of bond angle deviations from ideal: 60.44 - 76.99: 14 76.99 - 93.53: 0 93.53 - 110.07: 8301 110.07 - 126.62: 10247 126.62 - 143.16: 141 Bond angle restraints: 18703 Sorted by residual: angle pdb=" PB ATP A1102 " pdb=" O3B ATP A1102 " pdb=" PG ATP A1102 " ideal model delta sigma weight residual 139.87 120.71 19.16 1.00e+00 1.00e+00 3.67e+02 angle pdb=" C LYS A 884 " pdb=" N LYS A 885 " pdb=" H LYS A 885 " ideal model delta sigma weight residual 124.88 70.66 54.22 3.00e+00 1.11e-01 3.27e+02 angle pdb=" CA VAL A 888 " pdb=" N VAL A 888 " pdb=" H VAL A 888 " ideal model delta sigma weight residual 114.62 60.44 54.18 3.00e+00 1.11e-01 3.26e+02 angle pdb=" C LYS A 887 " pdb=" N VAL A 888 " pdb=" H VAL A 888 " ideal model delta sigma weight residual 124.92 70.76 54.16 3.00e+00 1.11e-01 3.26e+02 angle pdb=" C MET A 886 " pdb=" N LYS A 887 " pdb=" H LYS A 887 " ideal model delta sigma weight residual 125.01 71.07 53.94 3.00e+00 1.11e-01 3.23e+02 ... (remaining 18698 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.35: 4258 16.35 - 32.69: 339 32.69 - 49.04: 38 49.04 - 65.39: 8 65.39 - 81.74: 6 Dihedral angle restraints: 4649 sinusoidal: 2362 harmonic: 2287 Sorted by residual: dihedral pdb=" CA SER A 413 " pdb=" C SER A 413 " pdb=" N THR A 414 " pdb=" CA THR A 414 " ideal model delta harmonic sigma weight residual 180.00 150.05 29.95 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA ASN A 802 " pdb=" C ASN A 802 " pdb=" N ILE A 803 " pdb=" CA ILE A 803 " ideal model delta harmonic sigma weight residual 180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA SER A 995 " pdb=" C SER A 995 " pdb=" N PRO A 996 " pdb=" CA PRO A 996 " ideal model delta harmonic sigma weight residual 180.00 155.90 24.10 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 4646 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 664 0.038 - 0.075: 225 0.075 - 0.113: 79 0.113 - 0.150: 24 0.150 - 0.188: 3 Chirality restraints: 995 Sorted by residual: chirality pdb=" CB ILE A 803 " pdb=" CA ILE A 803 " pdb=" CG1 ILE A 803 " pdb=" CG2 ILE A 803 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.80e-01 chirality pdb=" CB ILE A 458 " pdb=" CA ILE A 458 " pdb=" CG1 ILE A 458 " pdb=" CG2 ILE A 458 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" CA ILE A 480 " pdb=" N ILE A 480 " pdb=" C ILE A 480 " pdb=" CB ILE A 480 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.42e-01 ... (remaining 992 not shown) Planarity restraints: 1576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 995 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO A 996 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 996 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 996 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 724 " -0.017 2.00e-02 2.50e+03 8.17e-03 2.00e+00 pdb=" CG PHE A 724 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE A 724 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 724 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 724 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 724 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 724 " -0.006 2.00e-02 2.50e+03 pdb=" HD1 PHE A 724 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 724 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 PHE A 724 " -0.005 2.00e-02 2.50e+03 pdb=" HE2 PHE A 724 " -0.003 2.00e-02 2.50e+03 pdb=" HZ PHE A 724 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 330 " -0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO A 331 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 331 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 331 " -0.020 5.00e-02 4.00e+02 ... (remaining 1573 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 491 2.19 - 2.80: 19000 2.80 - 3.40: 24877 3.40 - 4.00: 33630 4.00 - 4.60: 52539 Nonbonded interactions: 130537 Sorted by model distance: nonbonded pdb=" H LYS A 498 " pdb=" HA LYS A 498 " model vdw 1.594 1.816 nonbonded pdb=" H VAL A 888 " pdb=" HA VAL A 888 " model vdw 1.611 1.816 nonbonded pdb=" H LYS A 887 " pdb=" HA LYS A 887 " model vdw 1.623 1.816 nonbonded pdb=" H GLU A 794 " pdb=" HA GLU A 794 " model vdw 1.644 1.816 nonbonded pdb="HH21 ARG A 728 " pdb=" OP2 U Y 7 " model vdw 1.653 1.850 ... (remaining 130532 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Set up NCS constraints 0 10562 True True No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 31 5.49 5 S 35 5.16 5 C 3778 2.51 5 N 1072 2.21 5 O 1243 1.98 5 H 4402 0.53 5 sf(0) = scattering factor at diffraction angle 0. 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 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: 0.600 Set model interpretation parameters: 0.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.400 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.050 Process input model: 41.730 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.430 Internal consistency checks: 0.000 Total: 48.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.007 0.074 6316 Angle : 0.982 20.849 8634 Chirality : 0.046 0.188 995 Planarity : 0.004 0.036 991 Dihedral : 10.314 81.736 2513 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.69 % Favored : 90.16 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.27), residues: 681 helix: -1.11 (0.25), residues: 335 sheet: -3.19 (0.46), residues: 87 loop : -3.90 (0.31), residues: 259 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield and 0 Emsley and 681 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield and 0 Emsley and 681 emsley8k. ------------------------------------------------------------------------------- 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 474 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 LEU 669 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 743 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 LYS 799 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 SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 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 181 residues out of total 619 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 180 time to evaluate : 1.049 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.4393 time to fit residues: 81.1005 Evaluate side-chains 80 residues out of total 619 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.875 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN A 457 ASN A 581 GLN ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 ASN A 986 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.022 6316 Angle : 0.633 21.103 8634 Chirality : 0.036 0.158 995 Planarity : 0.003 0.037 991 Dihedral : 6.494 72.434 1068 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.31), residues: 681 helix: 0.58 (0.28), residues: 335 sheet: -2.57 (0.49), residues: 83 loop : -3.55 (0.32), residues: 263 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield and 0 Emsley and 681 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield and 0 Emsley and 681 emsley8k. ------------------------------------------------------------------------------- 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 474 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 LEU 669 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 743 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 LYS 799 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 SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 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 123 residues out of total 619 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.903 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 123 average time/residue: 0.3484 time to fit residues: 44.4023 Evaluate side-chains 83 residues out of total 619 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.978 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 63 optimal weight: 0.5980 chunk 68 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 615 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.031 6316 Angle : 0.668 21.300 8634 Chirality : 0.037 0.148 995 Planarity : 0.003 0.034 991 Dihedral : 7.136 64.320 1068 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.54 % Favored : 90.31 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.33), residues: 681 helix: 1.38 (0.30), residues: 339 sheet: -2.46 (0.53), residues: 76 loop : -3.30 (0.32), residues: 266 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield and 0 Emsley and 681 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield and 0 Emsley and 681 emsley8k. ------------------------------------------------------------------------------- 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 474 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 LEU 669 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 743 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 LYS 799 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 SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 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 619 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.969 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.3211 time to fit residues: 34.9311 Evaluate side-chains 78 residues out of total 619 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.970 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 HIS ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 ASN ** A 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.5298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.037 6316 Angle : 0.675 20.950 8634 Chirality : 0.038 0.148 995 Planarity : 0.003 0.032 991 Dihedral : 7.206 82.134 1068 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.33), residues: 681 helix: 1.44 (0.29), residues: 345 sheet: -2.21 (0.54), residues: 74 loop : -3.24 (0.31), residues: 262 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield and 0 Emsley and 681 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield and 0 Emsley and 681 emsley8k. ------------------------------------------------------------------------------- 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 474 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 LEU 669 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 743 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 LYS 799 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 SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 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 91 residues out of total 619 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.968 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.3307 time to fit residues: 31.6878 Evaluate side-chains 72 residues out of total 619 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 72 time to evaluate : 1.022 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.5595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.026 6316 Angle : 0.634 21.058 8634 Chirality : 0.036 0.162 995 Planarity : 0.003 0.035 991 Dihedral : 6.425 66.822 1068 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.08 % Favored : 91.78 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.33), residues: 681 helix: 1.79 (0.29), residues: 344 sheet: -1.88 (0.52), residues: 82 loop : -3.07 (0.32), residues: 255 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield and 0 Emsley and 681 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield and 0 Emsley and 681 emsley8k. ------------------------------------------------------------------------------- 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 474 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 LEU 669 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 743 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 LYS 799 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 SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 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 87 residues out of total 619 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 87 time to evaluate : 1.045 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.3459 time to fit residues: 31.8006 Evaluate side-chains 69 residues out of total 619 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 69 time to evaluate : 1.053 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 5.9990 chunk 67 optimal weight: 0.0670 chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 overall best weight: 2.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 HIS ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.5910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.025 6316 Angle : 0.638 20.959 8634 Chirality : 0.036 0.148 995 Planarity : 0.003 0.033 991 Dihedral : 6.221 50.480 1068 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.96 % Favored : 90.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.33), residues: 681 helix: 2.01 (0.29), residues: 344 sheet: -1.75 (0.54), residues: 82 loop : -2.99 (0.34), residues: 255 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield and 0 Emsley and 681 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield and 0 Emsley and 681 emsley8k. ------------------------------------------------------------------------------- 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 474 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 LEU 669 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 743 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 LYS 799 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 SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 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 85 residues out of total 619 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.932 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.3042 time to fit residues: 27.2868 Evaluate side-chains 63 residues out of total 619 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.925 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 41 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.6038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.025 6316 Angle : 0.614 21.051 8634 Chirality : 0.036 0.149 995 Planarity : 0.002 0.037 991 Dihedral : 5.347 46.071 1068 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.05 % Favored : 92.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.34), residues: 681 helix: 2.31 (0.29), residues: 343 sheet: -1.36 (0.55), residues: 85 loop : -2.95 (0.34), residues: 253 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield and 0 Emsley and 681 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield and 0 Emsley and 681 emsley8k. ------------------------------------------------------------------------------- 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 474 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 LEU 669 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 743 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 LYS 799 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 SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 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 86 residues out of total 619 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 86 time to evaluate : 1.028 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.3172 time to fit residues: 28.8845 Evaluate side-chains 69 residues out of total 619 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 69 time to evaluate : 1.030 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 HIS ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.6274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.026 6316 Angle : 0.668 21.198 8634 Chirality : 0.038 0.169 995 Planarity : 0.003 0.036 991 Dihedral : 6.632 51.800 1068 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.10 % Favored : 90.75 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.33), residues: 681 helix: 1.82 (0.29), residues: 349 sheet: -1.89 (0.51), residues: 90 loop : -2.96 (0.35), residues: 242 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield and 0 Emsley and 681 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield and 0 Emsley and 681 emsley8k. ------------------------------------------------------------------------------- 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 474 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 LEU 669 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 743 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 LYS 799 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 SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 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 81 residues out of total 619 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 81 time to evaluate : 1.026 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2809 time to fit residues: 24.4076 Evaluate side-chains 64 residues out of total 619 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.973 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 56 optimal weight: 0.1980 chunk 59 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.6332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.031 6316 Angle : 0.619 21.045 8634 Chirality : 0.036 0.150 995 Planarity : 0.002 0.039 991 Dihedral : 5.436 46.752 1068 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.05 % Favored : 92.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.34), residues: 681 helix: 2.27 (0.29), residues: 342 sheet: -1.59 (0.52), residues: 93 loop : -2.85 (0.35), residues: 246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield and 0 Emsley and 681 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield and 0 Emsley and 681 emsley8k. ------------------------------------------------------------------------------- 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 474 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 LEU 669 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 743 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 LYS 799 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 SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 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 86 residues out of total 619 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 86 time to evaluate : 1.083 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2868 time to fit residues: 26.2843 Evaluate side-chains 72 residues out of total 619 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 72 time to evaluate : 1.007 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 17 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 HIS ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.6510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.039 6316 Angle : 0.640 20.883 8634 Chirality : 0.036 0.142 995 Planarity : 0.003 0.035 991 Dihedral : 6.117 48.970 1068 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.81 % Favored : 91.04 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.34), residues: 681 helix: 2.11 (0.29), residues: 343 sheet: -1.65 (0.53), residues: 88 loop : -2.76 (0.35), residues: 250 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield and 0 Emsley and 681 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield and 0 Emsley and 681 emsley8k. ------------------------------------------------------------------------------- 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 474 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 LEU 669 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 743 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 LYS 799 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 SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 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 79 residues out of total 619 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.996 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.2891 time to fit residues: 24.4788 Evaluate side-chains 68 residues out of total 619 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.034 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 7 optimal weight: 0.0870 chunk 10 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Group ADP refinement ******************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.117694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.098763 restraints weight = 37274.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.102624 restraints weight = 15616.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.105142 restraints weight = 9164.909| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.002 0.034 6316 ANGLE : 0.623 21.133 8634 CHIRALITY : 0.036 0.155 995 PLANARITY : 0.002 0.037 991 DIHEDRAL : 5.365 45.069 1068 MIN NONBONDED DISTANCE : 2.100 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 16.90 RAMACHANDRAN PLOT: OUTLIERS : 0.15 % ALLOWED : 7.34 % FAVORED : 92.51 % ROTAMER OUTLIERS : 0.00 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 0.00 % CIS-GENERAL : 0.00 % TWISTED PROLINE : 0.00 % TWISTED GENERAL : 0.00 % RAMA-Z (RAMACHANDRAN PLOT Z-SCORE): INTERPRETATION: BAD |RAMA-Z| > 3; SUSPICIOUS 2 < |RAMA-Z| < 3; GOOD |RAMA-Z| < 2. SCORES FOR WHOLE/HELIX/SHEET/LOOP ARE SCALED INDEPENDENTLY; THEREFORE, THE VALUES ARE NOT RELATED IN A SIMPLE MANNER. WHOLE: 0.18 (0.34), RESIDUES: 681 HELIX: 2.42 (0.29), RESIDUES: 337 SHEET: -1.50 (0.54), RESIDUES: 88 LOOP : -2.60 (0.36), RESIDUES: 256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.6557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.034 6316 Angle : 0.623 21.133 8634 Chirality : 0.036 0.155 995 Planarity : 0.002 0.037 991 Dihedral : 5.365 45.069 1068 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.34 % Favored : 92.51 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.34), residues: 681 helix: 2.42 (0.29), residues: 337 sheet: -1.50 (0.54), residues: 88 loop : -2.60 (0.36), residues: 256 =============================================================================== Job complete usr+sys time: 2771.58 seconds wall clock time: 50 minutes 3.93 seconds (3003.93 seconds total)