Starting phenix.real_space_refine (version: dev) on Fri May 13 06:40:01 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gkm_0024/05_2022/6gkm_0024_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gkm_0024/05_2022/6gkm_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_0024/05_2022/6gkm_0024.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gkm_0024/05_2022/6gkm_0024.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gkm_0024/05_2022/6gkm_0024_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gkm_0024/05_2022/6gkm_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 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 806": "NH1" <-> "NH2" Residue "A TYR 939": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 942": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: 6.15, per 1000 atoms: 0.58 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 Amino 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: 8.74 Conformation dependent library (CDL) restraints added in 976.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 962 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 910 " 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, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. 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 14 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 5.07 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: 37 hydrogen bonds 74 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 3.99 Time building geometry restraints manager: 9.06 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: 18993 2.80 - 3.40: 24847 3.40 - 4.00: 33528 4.00 - 4.60: 52539 Nonbonded interactions: 130398 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 130393 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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 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: 0.410 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: 0.170 Extract box with map and model: 3.510 Check model and map are aligned: 0.160 Convert atoms to be neutral: 0.080 Process input model: 45.000 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 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 : 0.007 0.074 6316 Z= 0.471 Angle : 0.982 20.849 8634 Z= 0.616 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 : 11.46 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, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 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 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 fitting. rotamer outliers: 1 poor density : 180 time to evaluate : 0.931 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 outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.4200 time to fit residues: 94.6663 Evaluate side-chains 83 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.017 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2252 ------------------------------------------------------------------------------- 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: 2.9990 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 ASN A 595 ASN ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 986 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 6316 Z= 0.174 Angle : 0.694 21.170 8634 Z= 0.386 Chirality : 0.038 0.160 995 Planarity : 0.004 0.037 991 Dihedral : 7.264 78.503 1068 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.52 % Favored : 91.34 % Rotamer Outliers : 0.65 % 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: -2.20 (0.31), residues: 681 helix: 0.40 (0.28), residues: 332 sheet: -2.67 (0.49), residues: 86 loop : -3.57 (0.32), residues: 263 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 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 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 95 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 91 time to evaluate : 0.950 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 outliers start: 4 outliers final: 4 residues processed: 94 average time/residue: 0.3485 time to fit residues: 43.1781 Evaluate side-chains 82 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.935 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.2968 time to fit residues: 2.7262 ------------------------------------------------------------------------------- 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: 8.9990 chunk 19 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 63 optimal weight: 8.9990 chunk 68 optimal weight: 9.9990 chunk 56 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 6316 Z= 0.198 Angle : 0.671 20.933 8634 Z= 0.373 Chirality : 0.037 0.161 995 Planarity : 0.003 0.034 991 Dihedral : 7.279 74.161 1068 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.66 % Favored : 91.19 % Rotamer Outliers : 1.62 % 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: -1.38 (0.32), residues: 681 helix: 1.15 (0.29), residues: 338 sheet: -2.43 (0.50), residues: 86 loop : -3.31 (0.33), residues: 257 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 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 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 90 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 0.943 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 outliers start: 10 outliers final: 7 residues processed: 87 average time/residue: 0.3088 time to fit residues: 36.7910 Evaluate side-chains 81 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 0.922 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.1261 time to fit residues: 2.7848 ------------------------------------------------------------------------------- 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: 1.9990 chunk 33 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 18 optimal weight: 0.3980 chunk 56 optimal weight: 0.0020 chunk 38 optimal weight: 1.9990 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 6316 Z= 0.124 Angle : 0.644 21.133 8634 Z= 0.357 Chirality : 0.037 0.157 995 Planarity : 0.002 0.033 991 Dihedral : 6.918 73.152 1068 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.49 % Favored : 92.36 % Rotamer Outliers : 0.65 % 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: -0.89 (0.33), residues: 681 helix: 1.61 (0.30), residues: 338 sheet: -2.20 (0.57), residues: 73 loop : -3.16 (0.32), residues: 270 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 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 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 fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 0.985 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 outliers start: 4 outliers final: 2 residues processed: 84 average time/residue: 0.3012 time to fit residues: 35.2576 Evaluate side-chains 75 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 0.960 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1353 time to fit residues: 1.7126 ------------------------------------------------------------------------------- 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: 6.9990 chunk 27 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 6316 Z= 0.217 Angle : 0.669 20.893 8634 Z= 0.369 Chirality : 0.037 0.146 995 Planarity : 0.003 0.027 991 Dihedral : 7.013 77.077 1068 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 20.94 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.96 % Favored : 90.90 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.77 (0.33), residues: 681 helix: 1.77 (0.29), residues: 333 sheet: -2.14 (0.56), residues: 76 loop : -3.10 (0.32), residues: 272 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 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 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 fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 1.048 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 outliers start: 6 outliers final: 4 residues processed: 82 average time/residue: 0.2990 time to fit residues: 33.9580 Evaluate side-chains 80 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.949 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1682 time to fit residues: 2.2568 ------------------------------------------------------------------------------- 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: 1.9990 chunk 67 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 ASN ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 6316 Z= 0.183 Angle : 0.651 21.030 8634 Z= 0.361 Chirality : 0.037 0.147 995 Planarity : 0.002 0.021 991 Dihedral : 6.768 83.479 1068 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % 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: -0.57 (0.33), residues: 681 helix: 1.96 (0.29), residues: 331 sheet: -1.82 (0.58), residues: 75 loop : -3.10 (0.32), residues: 275 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 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 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 fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.953 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 outliers start: 1 outliers final: 1 residues processed: 79 average time/residue: 0.3200 time to fit residues: 34.4591 Evaluate side-chains 68 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.953 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1166 time to fit residues: 1.3975 ------------------------------------------------------------------------------- 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: 5.9990 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 678 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: 0.8242 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 6316 Z= 0.216 Angle : 0.677 20.952 8634 Z= 0.372 Chirality : 0.038 0.268 995 Planarity : 0.003 0.021 991 Dihedral : 6.806 84.317 1068 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 21.18 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.66 % Favored : 91.19 % Rotamer Outliers : 0.81 % 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: -0.49 (0.33), residues: 681 helix: 1.90 (0.29), residues: 333 sheet: -1.92 (0.53), residues: 88 loop : -2.85 (0.34), residues: 260 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 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 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 73 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.903 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 outliers start: 5 outliers final: 2 residues processed: 70 average time/residue: 0.3130 time to fit residues: 30.9559 Evaluate side-chains 68 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 0.932 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1407 time to fit residues: 1.6629 ------------------------------------------------------------------------------- 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: 5.9990 chunk 45 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 6316 Z= 0.245 Angle : 0.682 20.966 8634 Z= 0.377 Chirality : 0.038 0.148 995 Planarity : 0.003 0.025 991 Dihedral : 6.759 68.106 1068 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 22.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer Outliers : 0.49 % 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: 338 sheet: -1.67 (0.56), residues: 84 loop : -3.05 (0.33), residues: 259 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 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 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 71 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.982 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 outliers start: 3 outliers final: 2 residues processed: 70 average time/residue: 0.2885 time to fit residues: 28.4226 Evaluate side-chains 65 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 0.979 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1384 time to fit residues: 1.6997 ------------------------------------------------------------------------------- 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: 0.9990 chunk 49 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 41 optimal weight: 0.3980 chunk 66 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.5643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 6316 Z= 0.178 Angle : 0.659 21.023 8634 Z= 0.363 Chirality : 0.036 0.150 995 Planarity : 0.002 0.021 991 Dihedral : 5.919 53.554 1068 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.08 % Favored : 91.78 % Rotamer Outliers : 0.81 % 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: -0.37 (0.33), residues: 681 helix: 2.06 (0.29), residues: 332 sheet: -1.70 (0.53), residues: 88 loop : -2.94 (0.33), residues: 261 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 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 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 72 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 1.061 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 outliers start: 5 outliers final: 3 residues processed: 68 average time/residue: 0.3261 time to fit residues: 30.3602 Evaluate side-chains 67 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.959 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1374 time to fit residues: 1.9457 ------------------------------------------------------------------------------- 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: 3.9990 chunk 55 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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: 0.8238 moved from start: 0.5848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 6316 Z= 0.200 Angle : 0.673 20.964 8634 Z= 0.368 Chirality : 0.037 0.149 995 Planarity : 0.003 0.022 991 Dihedral : 5.778 37.974 1068 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 22.09 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: -0.38 (0.33), residues: 681 helix: 1.90 (0.29), residues: 344 sheet: -1.66 (0.52), residues: 88 loop : -2.97 (0.34), residues: 249 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 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 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 61 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.2803 time to fit residues: 24.4478 Evaluate side-chains 60 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.886 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1780 ------------------------------------------------------------------------------- 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: 3.9990 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.089472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.070592 restraints weight = 35646.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.074449 restraints weight = 14893.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.076949 restraints weight = 8742.597| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.5919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 6316 Z= 0.179 Angle : 0.662 21.046 8634 Z= 0.365 Chirality : 0.036 0.150 995 Planarity : 0.002 0.021 991 Dihedral : 5.595 32.212 1068 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer Outliers : 0.32 % 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: -0.37 (0.33), residues: 681 helix: 1.90 (0.29), residues: 344 sheet: -1.70 (0.55), residues: 78 loop : -2.90 (0.34), residues: 259 =============================================================================== Job complete usr+sys time: 2355.44 seconds wall clock time: 42 minutes 37.81 seconds (2557.81 seconds total)