Starting phenix.real_space_refine on Mon Jul 28 09:45:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6g1s_4340/07_2025/6g1s_4340.cif Found real_map, /net/cci-nas-00/data/ceres_data/6g1s_4340/07_2025/6g1s_4340.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6g1s_4340/07_2025/6g1s_4340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6g1s_4340/07_2025/6g1s_4340.map" model { file = "/net/cci-nas-00/data/ceres_data/6g1s_4340/07_2025/6g1s_4340.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6g1s_4340/07_2025/6g1s_4340.cif" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 30 5.49 5 S 34 5.16 5 C 3564 2.51 5 N 1007 2.21 5 O 1159 1.98 5 H 4096 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9891 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 9251 Classifications: {'peptide': 645} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 624} Chain breaks: 11 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "X" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 318 Classifications: {'RNA': 15} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 8} Link IDs: {'rna3p': 14} Chain: "Y" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 321 Classifications: {'RNA': 15} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 7} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7868 SG CYS A 910 15.398 66.809 34.431 1.00133.64 S ATOM 8477 SG CYS A 962 17.403 66.721 30.958 1.00137.66 S ATOM 8492 SG CYS A 964 16.208 70.018 33.329 1.00146.40 S Time building chain proxies: 5.27, per 1000 atoms: 0.53 Number of scatterers: 9891 At special positions: 0 Unit cell: (86.67, 96.3, 73.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 34 16.00 P 30 15.00 O 1159 8.00 N 1007 7.00 C 3564 6.00 H 4096 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 611.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 910 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 962 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 964 " 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1236 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 6 sheets defined 55.0% alpha, 6.2% beta 15 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 3.99 Creating SS restraints... Processing helix chain 'A' and resid 310 through 318 removed outlier: 3.791A pdb=" N GLU A 315 " --> pdb=" O PRO A 311 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 322 Processing helix chain 'A' and resid 335 through 355 Processing helix chain 'A' and resid 366 through 377 removed outlier: 3.782A pdb=" N ALA A 370 " --> pdb=" O LYS A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 400 through 407 removed outlier: 3.957A pdb=" N VAL A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 427 removed outlier: 3.999A pdb=" N LEU A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 438 Processing helix chain 'A' and resid 445 through 449 removed outlier: 3.522A pdb=" N HIS A 448 " --> pdb=" O GLU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 473 Processing helix chain 'A' and resid 499 through 515 Processing helix chain 'A' and resid 525 through 533 removed outlier: 3.576A pdb=" N LEU A 529 " --> pdb=" O ASN A 525 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN A 532 " --> pdb=" O GLN A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 566 removed outlier: 3.565A pdb=" N LEU A 555 " --> pdb=" O PHE A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 594 Processing helix chain 'A' and resid 598 through 616 Processing helix chain 'A' and resid 619 through 643 removed outlier: 3.992A pdb=" N ALA A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 692 removed outlier: 4.195A pdb=" N ASN A 683 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LYS A 685 " --> pdb=" O PHE A 681 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N MET A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU A 692 " --> pdb=" O LYS A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 715 Processing helix chain 'A' and resid 727 through 741 removed outlier: 3.662A pdb=" N THR A 731 " --> pdb=" O THR A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 780 Processing helix chain 'A' and resid 812 through 823 removed outlier: 3.658A pdb=" N ARG A 822 " --> pdb=" O GLN A 818 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 863 removed outlier: 3.639A pdb=" N GLU A 844 " --> pdb=" O VAL A 840 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR A 855 " --> pdb=" O GLU A 851 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG A 860 " --> pdb=" O LYS A 856 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN A 863 " --> pdb=" O ASN A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 895 removed outlier: 3.745A pdb=" N GLN A 895 " --> pdb=" O SER A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 938 Processing helix chain 'A' and resid 984 through 987 Processing helix chain 'A' and resid 1002 through 1006 Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 361 removed outlier: 6.231A pdb=" N VAL A 360 " --> pdb=" O ILE A 411 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 440 through 441 Processing sheet with id=AA3, first strand: chain 'A' and resid 751 through 753 removed outlier: 6.781A pdb=" N GLY A 721 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE A 722 " --> pdb=" O ILE A 805 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 913 through 916 removed outlier: 6.664A pdb=" N LEU A 905 " --> pdb=" O VAL A 914 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 921 through 923 Processing sheet with id=AA6, first strand: chain 'A' and resid 940 through 942 removed outlier: 3.996A pdb=" N GLY A 969 " --> pdb=" O ILE A 960 " (cutoff:3.500A) 257 hydrogen bonds defined for protein. 723 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 3.47 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 4085 1.03 - 1.23: 25 1.23 - 1.43: 2471 1.43 - 1.62: 3404 1.62 - 1.82: 54 Bond restraints: 10039 Sorted by residual: bond pdb=" N ARG A 310 " pdb=" H1 ARG A 310 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" CG ASN A 897 " pdb=" ND2 ASN A 897 " ideal model delta sigma weight residual 1.328 1.247 0.081 2.10e-02 2.27e+03 1.48e+01 bond pdb=" CG1 ILE A 458 " pdb=" CD1 ILE A 458 " ideal model delta sigma weight residual 1.513 1.448 0.065 3.90e-02 6.57e+02 2.80e+00 bond pdb=" CB ILE A 708 " pdb=" CG2 ILE A 708 " ideal model delta sigma weight residual 1.521 1.574 -0.053 3.30e-02 9.18e+02 2.58e+00 bond pdb=" CB THR A 521 " pdb=" CG2 THR A 521 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.57e+00 ... (remaining 10034 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.73: 17481 9.73 - 19.47: 0 19.47 - 29.20: 1 29.20 - 38.93: 0 38.93 - 48.66: 2 Bond angle restraints: 17484 Sorted by residual: angle pdb=" C ALA A 497 " pdb=" N LYS A 498 " pdb=" H LYS A 498 " ideal model delta sigma weight residual 124.58 75.91 48.66 3.00e+00 1.11e-01 2.63e+02 angle pdb=" CA LYS A 498 " pdb=" N LYS A 498 " pdb=" H LYS A 498 " ideal model delta sigma weight residual 114.28 68.85 45.43 3.00e+00 1.11e-01 2.29e+02 angle pdb=" C ALA A 497 " pdb=" N LYS A 498 " pdb=" CA LYS A 498 " ideal model delta sigma weight residual 121.15 144.74 -23.59 1.85e+00 2.92e-01 1.63e+02 angle pdb=" N SER A 761 " pdb=" CA SER A 761 " pdb=" C SER A 761 " ideal model delta sigma weight residual 110.80 118.80 -8.00 2.13e+00 2.20e-01 1.41e+01 angle pdb=" C SER A 760 " pdb=" N SER A 761 " pdb=" CA SER A 761 " ideal model delta sigma weight residual 121.54 128.49 -6.95 1.91e+00 2.74e-01 1.32e+01 ... (remaining 17479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.81: 4624 14.81 - 29.61: 295 29.61 - 44.42: 74 44.42 - 59.22: 47 59.22 - 74.03: 31 Dihedral angle restraints: 5071 sinusoidal: 2931 harmonic: 2140 Sorted by residual: dihedral pdb=" CA VAL A 454 " pdb=" C VAL A 454 " pdb=" N TYR A 455 " pdb=" CA TYR A 455 " ideal model delta harmonic sigma weight residual 180.00 115.98 64.02 0 5.00e+00 4.00e-02 1.64e+02 dihedral pdb=" CA GLY A 428 " pdb=" C GLY A 428 " pdb=" N ASP A 429 " pdb=" CA ASP A 429 " ideal model delta harmonic sigma weight residual -180.00 -141.77 -38.23 0 5.00e+00 4.00e-02 5.85e+01 dihedral pdb=" CA GLU A 762 " pdb=" C GLU A 762 " pdb=" N VAL A 763 " pdb=" CA VAL A 763 " ideal model delta harmonic sigma weight residual 180.00 -148.26 -31.74 0 5.00e+00 4.00e-02 4.03e+01 ... (remaining 5068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 739 0.051 - 0.103: 173 0.103 - 0.154: 38 0.154 - 0.206: 2 0.206 - 0.257: 1 Chirality restraints: 953 Sorted by residual: chirality pdb=" CB ILE A 361 " pdb=" CA ILE A 361 " pdb=" CG1 ILE A 361 " pdb=" CG2 ILE A 361 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB THR A 344 " pdb=" CA THR A 344 " pdb=" OG1 THR A 344 " pdb=" CG2 THR A 344 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.40e-01 chirality pdb=" CA TYR A 455 " pdb=" N TYR A 455 " pdb=" C TYR A 455 " pdb=" CB TYR A 455 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.74e-01 ... (remaining 950 not shown) Planarity restraints: 1444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 490 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.74e+00 pdb=" C ALA A 490 " -0.041 2.00e-02 2.50e+03 pdb=" O ALA A 490 " 0.015 2.00e-02 2.50e+03 pdb=" N SER A 491 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 829 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.04e+00 pdb=" C THR A 829 " 0.035 2.00e-02 2.50e+03 pdb=" O THR A 829 " -0.013 2.00e-02 2.50e+03 pdb=" N TYR A 830 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 330 " 0.033 5.00e-02 4.00e+02 4.92e-02 3.88e+00 pdb=" N PRO A 331 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 331 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 331 " 0.027 5.00e-02 4.00e+02 ... (remaining 1441 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 276 2.17 - 2.78: 17013 2.78 - 3.38: 23981 3.38 - 3.99: 31392 3.99 - 4.60: 48766 Nonbonded interactions: 121428 Sorted by model distance: nonbonded pdb=" H LYS A 498 " pdb=" HA LYS A 498 " model vdw 1.562 1.816 nonbonded pdb="HH12 ARG A 720 " pdb=" O PHE A 778 " model vdw 1.673 2.450 nonbonded pdb=" O PHE A 374 " pdb="HD21 ASN A 379 " model vdw 1.673 2.450 nonbonded pdb=" HE2 HIS A 927 " pdb=" O2' U X 5 " model vdw 1.685 2.450 nonbonded pdb=" OE1 GLU A 813 " pdb=" H GLU A 813 " model vdw 1.717 2.450 ... (remaining 121423 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 30.330 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.528 5946 Z= 0.431 Angle : 0.887 23.592 8130 Z= 0.490 Chirality : 0.046 0.257 953 Planarity : 0.005 0.049 913 Dihedral : 13.697 74.027 2474 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.72 % Favored : 87.28 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % Rama-Z (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: -4.00 (0.26), residues: 621 helix: -1.66 (0.23), residues: 306 sheet: -4.23 (0.46), residues: 44 loop : -3.56 (0.31), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 968 HIS 0.004 0.001 HIS A 578 PHE 0.011 0.002 PHE A 987 TYR 0.024 0.003 TYR A 455 ARG 0.014 0.001 ARG A 606 Details of bonding type rmsd hydrogen bonds : bond 0.12703 ( 296) hydrogen bonds : angle 5.92058 ( 801) metal coordination : bond 0.37042 ( 3) covalent geometry : bond 0.00768 ( 5943) covalent geometry : angle 0.88703 ( 8130) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 ASP cc_start: 0.7549 (t70) cc_final: 0.6946 (t0) REVERT: A 454 VAL cc_start: 0.8740 (t) cc_final: 0.8459 (p) REVERT: A 580 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7431 (tm-30) REVERT: A 592 LYS cc_start: 0.9188 (mttp) cc_final: 0.8583 (tptt) REVERT: A 845 ILE cc_start: 0.8896 (mt) cc_final: 0.8489 (tp) REVERT: A 905 LEU cc_start: 0.9280 (mt) cc_final: 0.8975 (tp) REVERT: A 968 TRP cc_start: 0.7309 (m-10) cc_final: 0.6784 (m-10) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.4313 time to fit residues: 103.0050 Evaluate side-chains 103 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 741 ASN A 759 HIS ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 ASN A 974 HIS A 990 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.105567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.083922 restraints weight = 35563.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.088153 restraints weight = 15110.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.090799 restraints weight = 8871.813| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5946 Z= 0.120 Angle : 0.656 20.637 8130 Z= 0.347 Chirality : 0.038 0.144 953 Planarity : 0.004 0.039 913 Dihedral : 15.754 73.950 1149 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer: Outliers : 0.88 % Allowed : 11.03 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -2.33 (0.31), residues: 621 helix: 0.18 (0.27), residues: 310 sheet: -4.08 (0.38), residues: 59 loop : -3.16 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 582 HIS 0.006 0.001 HIS A 626 PHE 0.013 0.001 PHE A 551 TYR 0.021 0.001 TYR A 455 ARG 0.004 0.000 ARG A 606 Details of bonding type rmsd hydrogen bonds : bond 0.03733 ( 296) hydrogen bonds : angle 4.60874 ( 801) metal coordination : bond 0.00788 ( 3) covalent geometry : bond 0.00250 ( 5943) covalent geometry : angle 0.65553 ( 8130) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 ASP cc_start: 0.7424 (t70) cc_final: 0.6728 (t0) REVERT: A 454 VAL cc_start: 0.8779 (t) cc_final: 0.8550 (p) REVERT: A 586 MET cc_start: 0.9195 (tpp) cc_final: 0.8912 (tpp) REVERT: A 587 GLU cc_start: 0.8381 (tp30) cc_final: 0.8160 (tp30) REVERT: A 592 LYS cc_start: 0.9384 (mttp) cc_final: 0.8671 (tptt) REVERT: A 905 LEU cc_start: 0.9405 (mt) cc_final: 0.8988 (tp) REVERT: A 968 TRP cc_start: 0.7436 (m-10) cc_final: 0.6856 (m-10) outliers start: 5 outliers final: 3 residues processed: 112 average time/residue: 0.2673 time to fit residues: 41.2621 Evaluate side-chains 93 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 508 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 50 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 615 ASN A 759 HIS ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.109614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.088478 restraints weight = 37441.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.092856 restraints weight = 15841.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.095512 restraints weight = 9235.368| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5946 Z= 0.106 Angle : 0.619 20.135 8130 Z= 0.325 Chirality : 0.038 0.145 953 Planarity : 0.004 0.041 913 Dihedral : 15.451 73.784 1149 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer: Outliers : 1.05 % Allowed : 12.26 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -1.28 (0.33), residues: 621 helix: 1.30 (0.29), residues: 311 sheet: -3.80 (0.41), residues: 59 loop : -3.00 (0.36), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 737 HIS 0.005 0.001 HIS A 626 PHE 0.013 0.001 PHE A 712 TYR 0.013 0.001 TYR A 455 ARG 0.005 0.000 ARG A 606 Details of bonding type rmsd hydrogen bonds : bond 0.03178 ( 296) hydrogen bonds : angle 4.20448 ( 801) metal coordination : bond 0.00225 ( 3) covalent geometry : bond 0.00229 ( 5943) covalent geometry : angle 0.61903 ( 8130) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.909 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: A 444 ASP cc_start: 0.7437 (t70) cc_final: 0.6840 (t70) REVERT: A 454 VAL cc_start: 0.8612 (t) cc_final: 0.8387 (p) REVERT: A 502 GLU cc_start: 0.8513 (tp30) cc_final: 0.8189 (tp30) REVERT: A 586 MET cc_start: 0.9139 (tpp) cc_final: 0.8836 (tpp) REVERT: A 592 LYS cc_start: 0.9280 (mttp) cc_final: 0.8643 (tptt) REVERT: A 674 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8173 (mm-30) REVERT: A 905 LEU cc_start: 0.9407 (mt) cc_final: 0.9007 (tp) REVERT: A 924 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7348 (mt-10) REVERT: A 968 TRP cc_start: 0.7696 (m-10) cc_final: 0.6865 (m-10) outliers start: 6 outliers final: 6 residues processed: 104 average time/residue: 0.2719 time to fit residues: 38.8444 Evaluate side-chains 95 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 982 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 20.0000 chunk 41 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.102000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.079908 restraints weight = 37523.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.083948 restraints weight = 16507.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.086452 restraints weight = 10008.778| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5946 Z= 0.183 Angle : 0.653 19.590 8130 Z= 0.346 Chirality : 0.038 0.131 953 Planarity : 0.004 0.044 913 Dihedral : 15.314 73.623 1149 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.43 % Favored : 88.57 % Rotamer: Outliers : 2.10 % Allowed : 13.84 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z (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: -1.06 (0.34), residues: 621 helix: 1.57 (0.29), residues: 311 sheet: -3.86 (0.42), residues: 67 loop : -2.89 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 737 HIS 0.003 0.001 HIS A 752 PHE 0.011 0.001 PHE A 712 TYR 0.021 0.001 TYR A 455 ARG 0.006 0.001 ARG A 606 Details of bonding type rmsd hydrogen bonds : bond 0.03367 ( 296) hydrogen bonds : angle 4.22461 ( 801) metal coordination : bond 0.00108 ( 3) covalent geometry : bond 0.00377 ( 5943) covalent geometry : angle 0.65257 ( 8130) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 ASP cc_start: 0.7784 (t70) cc_final: 0.7016 (t0) REVERT: A 586 MET cc_start: 0.9179 (tpp) cc_final: 0.8920 (tpp) REVERT: A 587 GLU cc_start: 0.8678 (tp30) cc_final: 0.8429 (tp30) REVERT: A 592 LYS cc_start: 0.9276 (mttp) cc_final: 0.8754 (tptt) REVERT: A 924 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7575 (mt-10) REVERT: A 968 TRP cc_start: 0.7724 (m-10) cc_final: 0.6937 (m-10) outliers start: 12 outliers final: 10 residues processed: 98 average time/residue: 0.2999 time to fit residues: 39.9785 Evaluate side-chains 89 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 759 HIS Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 982 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 32 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 46 optimal weight: 30.0000 chunk 48 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 GLN A 693 ASN ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.099873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.078354 restraints weight = 37512.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.082264 restraints weight = 16197.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.084730 restraints weight = 9751.652| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5946 Z= 0.201 Angle : 0.670 19.558 8130 Z= 0.354 Chirality : 0.039 0.131 953 Planarity : 0.003 0.028 913 Dihedral : 15.310 73.597 1149 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 21.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 2.10 % Allowed : 14.71 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -0.98 (0.34), residues: 621 helix: 1.67 (0.29), residues: 311 sheet: -3.77 (0.45), residues: 67 loop : -2.94 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 385 HIS 0.004 0.001 HIS A 604 PHE 0.030 0.002 PHE A 712 TYR 0.024 0.001 TYR A 455 ARG 0.004 0.000 ARG A 460 Details of bonding type rmsd hydrogen bonds : bond 0.03412 ( 296) hydrogen bonds : angle 4.30651 ( 801) metal coordination : bond 0.00087 ( 3) covalent geometry : bond 0.00409 ( 5943) covalent geometry : angle 0.67013 ( 8130) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 96 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 ASP cc_start: 0.7935 (t70) cc_final: 0.7250 (t70) REVERT: A 586 MET cc_start: 0.9161 (tpp) cc_final: 0.8879 (tpp) REVERT: A 587 GLU cc_start: 0.8727 (tp30) cc_final: 0.8435 (tp30) REVERT: A 592 LYS cc_start: 0.9312 (mttp) cc_final: 0.8832 (tptt) REVERT: A 855 TYR cc_start: 0.8686 (m-10) cc_final: 0.8436 (m-80) REVERT: A 895 GLN cc_start: 0.7160 (tm-30) cc_final: 0.6666 (tm-30) REVERT: A 968 TRP cc_start: 0.7622 (m-10) cc_final: 0.6893 (m-10) outliers start: 12 outliers final: 11 residues processed: 90 average time/residue: 0.2716 time to fit residues: 33.9699 Evaluate side-chains 90 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 759 HIS Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 982 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.100929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.079117 restraints weight = 37691.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.083114 restraints weight = 16370.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.085593 restraints weight = 9910.830| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5946 Z= 0.131 Angle : 0.611 19.700 8130 Z= 0.320 Chirality : 0.038 0.132 953 Planarity : 0.003 0.030 913 Dihedral : 15.253 73.602 1149 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % Rotamer: Outliers : 2.10 % Allowed : 14.89 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z (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 (0.35), residues: 621 helix: 2.08 (0.29), residues: 313 sheet: -3.51 (0.48), residues: 64 loop : -2.95 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 968 HIS 0.004 0.001 HIS A 604 PHE 0.019 0.001 PHE A 712 TYR 0.019 0.001 TYR A 455 ARG 0.004 0.000 ARG A 606 Details of bonding type rmsd hydrogen bonds : bond 0.03130 ( 296) hydrogen bonds : angle 4.00593 ( 801) metal coordination : bond 0.00050 ( 3) covalent geometry : bond 0.00271 ( 5943) covalent geometry : angle 0.61109 ( 8130) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.820 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: A 444 ASP cc_start: 0.7978 (t70) cc_final: 0.7271 (t70) REVERT: A 586 MET cc_start: 0.9061 (tpp) cc_final: 0.8752 (tpp) REVERT: A 592 LYS cc_start: 0.9297 (mttp) cc_final: 0.8854 (tptt) REVERT: A 764 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7546 (mtmm) REVERT: A 855 TYR cc_start: 0.8642 (m-10) cc_final: 0.8311 (m-80) REVERT: A 894 LYS cc_start: 0.7495 (mttp) cc_final: 0.7223 (tptp) REVERT: A 895 GLN cc_start: 0.7140 (tm-30) cc_final: 0.6793 (tm-30) outliers start: 12 outliers final: 11 residues processed: 94 average time/residue: 0.2463 time to fit residues: 32.7477 Evaluate side-chains 95 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 759 HIS Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 982 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 22 optimal weight: 20.0000 chunk 55 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.099963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.078069 restraints weight = 38228.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.082030 restraints weight = 16721.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.084505 restraints weight = 10154.119| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.5865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5946 Z= 0.170 Angle : 0.638 19.524 8130 Z= 0.334 Chirality : 0.038 0.128 953 Planarity : 0.003 0.027 913 Dihedral : 15.281 73.660 1149 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 2.63 % Allowed : 15.24 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -0.54 (0.35), residues: 621 helix: 2.05 (0.29), residues: 314 sheet: -3.64 (0.46), residues: 67 loop : -2.80 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 968 HIS 0.003 0.001 HIS A 604 PHE 0.020 0.001 PHE A 712 TYR 0.021 0.001 TYR A 455 ARG 0.003 0.000 ARG A 606 Details of bonding type rmsd hydrogen bonds : bond 0.03197 ( 296) hydrogen bonds : angle 4.09098 ( 801) metal coordination : bond 0.00058 ( 3) covalent geometry : bond 0.00349 ( 5943) covalent geometry : angle 0.63837 ( 8130) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.832 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: A 369 LEU cc_start: 0.8911 (mt) cc_final: 0.8475 (tt) REVERT: A 444 ASP cc_start: 0.7930 (t70) cc_final: 0.6799 (t70) REVERT: A 445 GLU cc_start: 0.8324 (mp0) cc_final: 0.7366 (mp0) REVERT: A 586 MET cc_start: 0.9066 (tpp) cc_final: 0.8764 (tpp) REVERT: A 592 LYS cc_start: 0.9313 (mttp) cc_final: 0.8917 (tptt) REVERT: A 620 MET cc_start: 0.8384 (mtt) cc_final: 0.7986 (mtt) REVERT: A 726 LYS cc_start: 0.8807 (mttt) cc_final: 0.8485 (tptp) REVERT: A 759 HIS cc_start: 0.7439 (OUTLIER) cc_final: 0.6612 (m-70) REVERT: A 764 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7785 (mtmm) REVERT: A 855 TYR cc_start: 0.8708 (m-10) cc_final: 0.8370 (m-80) REVERT: A 894 LYS cc_start: 0.7618 (mttp) cc_final: 0.7322 (tptp) REVERT: A 895 GLN cc_start: 0.7365 (tm-30) cc_final: 0.6890 (tm-30) REVERT: A 905 LEU cc_start: 0.9496 (mt) cc_final: 0.9119 (tp) REVERT: A 926 MET cc_start: 0.9143 (mtp) cc_final: 0.8844 (mtp) outliers start: 15 outliers final: 13 residues processed: 96 average time/residue: 0.2688 time to fit residues: 35.6943 Evaluate side-chains 100 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain A residue 759 HIS Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 982 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 26 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 16 optimal weight: 0.0170 chunk 52 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 64 optimal weight: 10.0000 overall best weight: 2.1224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.100709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.078847 restraints weight = 38303.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.082812 restraints weight = 16660.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.085352 restraints weight = 10090.361| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.6054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5946 Z= 0.142 Angle : 0.614 19.494 8130 Z= 0.320 Chirality : 0.038 0.134 953 Planarity : 0.003 0.025 913 Dihedral : 15.330 73.637 1149 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 2.45 % Allowed : 16.11 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -0.34 (0.35), residues: 621 helix: 2.25 (0.29), residues: 315 sheet: -3.61 (0.46), residues: 67 loop : -2.77 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 968 HIS 0.005 0.001 HIS A 752 PHE 0.013 0.001 PHE A 712 TYR 0.017 0.001 TYR A 455 ARG 0.003 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.03063 ( 296) hydrogen bonds : angle 3.99051 ( 801) metal coordination : bond 0.00055 ( 3) covalent geometry : bond 0.00292 ( 5943) covalent geometry : angle 0.61369 ( 8130) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.827 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: A 369 LEU cc_start: 0.8911 (mt) cc_final: 0.8496 (tt) REVERT: A 444 ASP cc_start: 0.7956 (t70) cc_final: 0.6792 (t70) REVERT: A 445 GLU cc_start: 0.8262 (mp0) cc_final: 0.7322 (mp0) REVERT: A 586 MET cc_start: 0.9042 (tpp) cc_final: 0.8704 (tpp) REVERT: A 592 LYS cc_start: 0.9297 (mttp) cc_final: 0.8908 (tptt) REVERT: A 606 ARG cc_start: 0.9098 (ttp80) cc_final: 0.8870 (ttt90) REVERT: A 620 MET cc_start: 0.8405 (mtt) cc_final: 0.7974 (mtt) REVERT: A 726 LYS cc_start: 0.8824 (mttt) cc_final: 0.8509 (tptp) REVERT: A 759 HIS cc_start: 0.7445 (OUTLIER) cc_final: 0.6731 (m-70) REVERT: A 764 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7850 (mtmm) REVERT: A 855 TYR cc_start: 0.8680 (m-10) cc_final: 0.8325 (m-80) REVERT: A 894 LYS cc_start: 0.7616 (mttp) cc_final: 0.7339 (tptp) REVERT: A 895 GLN cc_start: 0.7436 (tm-30) cc_final: 0.6955 (tm-30) REVERT: A 905 LEU cc_start: 0.9495 (mt) cc_final: 0.9102 (tp) REVERT: A 926 MET cc_start: 0.9148 (mtp) cc_final: 0.8833 (mtp) REVERT: A 931 MET cc_start: 0.8265 (mpp) cc_final: 0.7924 (mmm) outliers start: 14 outliers final: 12 residues processed: 98 average time/residue: 0.2641 time to fit residues: 36.0427 Evaluate side-chains 100 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 759 HIS Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 982 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 30.0000 chunk 42 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 chunk 22 optimal weight: 20.0000 chunk 57 optimal weight: 0.0970 chunk 58 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.101445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.079981 restraints weight = 37395.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.083925 restraints weight = 16205.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.086448 restraints weight = 9732.992| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.6167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5946 Z= 0.114 Angle : 0.599 19.480 8130 Z= 0.310 Chirality : 0.037 0.132 953 Planarity : 0.003 0.026 913 Dihedral : 15.335 73.646 1149 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer: Outliers : 2.28 % Allowed : 17.69 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -0.09 (0.36), residues: 621 helix: 2.47 (0.30), residues: 315 sheet: -3.34 (0.49), residues: 64 loop : -2.73 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 968 HIS 0.003 0.001 HIS A 752 PHE 0.011 0.001 PHE A 712 TYR 0.016 0.001 TYR A 455 ARG 0.003 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.02870 ( 296) hydrogen bonds : angle 3.86467 ( 801) metal coordination : bond 0.00042 ( 3) covalent geometry : bond 0.00241 ( 5943) covalent geometry : angle 0.59869 ( 8130) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.789 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: A 369 LEU cc_start: 0.8876 (mt) cc_final: 0.8479 (tt) REVERT: A 444 ASP cc_start: 0.7995 (t70) cc_final: 0.6774 (t70) REVERT: A 445 GLU cc_start: 0.8271 (mp0) cc_final: 0.7313 (mp0) REVERT: A 586 MET cc_start: 0.9016 (tpp) cc_final: 0.8668 (tpp) REVERT: A 592 LYS cc_start: 0.9282 (mttp) cc_final: 0.8931 (tptt) REVERT: A 616 ASP cc_start: 0.9026 (p0) cc_final: 0.8551 (p0) REVERT: A 620 MET cc_start: 0.8368 (mtt) cc_final: 0.7944 (mtt) REVERT: A 726 LYS cc_start: 0.8781 (mttt) cc_final: 0.8469 (tptp) REVERT: A 764 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7765 (mtmm) REVERT: A 855 TYR cc_start: 0.8639 (m-10) cc_final: 0.8280 (m-80) REVERT: A 894 LYS cc_start: 0.7558 (mttp) cc_final: 0.7279 (tptp) REVERT: A 905 LEU cc_start: 0.9523 (mt) cc_final: 0.9064 (tp) REVERT: A 926 MET cc_start: 0.9151 (mtp) cc_final: 0.8852 (mtp) REVERT: A 931 MET cc_start: 0.8327 (mpp) cc_final: 0.7946 (mmm) REVERT: A 971 MET cc_start: 0.8385 (mmm) cc_final: 0.8076 (mmm) outliers start: 13 outliers final: 11 residues processed: 97 average time/residue: 0.3348 time to fit residues: 45.5514 Evaluate side-chains 99 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 982 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 44 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 ASN ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.103391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.081842 restraints weight = 37893.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.085911 restraints weight = 16436.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.088496 restraints weight = 9816.640| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.6348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5946 Z= 0.186 Angle : 0.648 19.295 8130 Z= 0.338 Chirality : 0.039 0.132 953 Planarity : 0.003 0.026 913 Dihedral : 15.294 73.704 1149 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 23.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 2.45 % Allowed : 17.34 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -0.25 (0.35), residues: 621 helix: 2.31 (0.29), residues: 315 sheet: -3.58 (0.48), residues: 67 loop : -2.69 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 968 HIS 0.004 0.001 HIS A 347 PHE 0.009 0.001 PHE A 712 TYR 0.019 0.001 TYR A 455 ARG 0.003 0.000 ARG A 606 Details of bonding type rmsd hydrogen bonds : bond 0.03195 ( 296) hydrogen bonds : angle 4.05832 ( 801) metal coordination : bond 0.00189 ( 3) covalent geometry : bond 0.00381 ( 5943) covalent geometry : angle 0.64772 ( 8130) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue THR 672 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue ILE 798 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.833 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: A 369 LEU cc_start: 0.8922 (mt) cc_final: 0.8569 (tt) REVERT: A 444 ASP cc_start: 0.8040 (t70) cc_final: 0.6797 (t70) REVERT: A 445 GLU cc_start: 0.8220 (mp0) cc_final: 0.7234 (mp0) REVERT: A 586 MET cc_start: 0.9012 (tpp) cc_final: 0.8717 (tpp) REVERT: A 592 LYS cc_start: 0.9303 (mttp) cc_final: 0.8949 (tptt) REVERT: A 616 ASP cc_start: 0.9021 (p0) cc_final: 0.8483 (p0) REVERT: A 620 MET cc_start: 0.8431 (mtt) cc_final: 0.7980 (mtt) REVERT: A 726 LYS cc_start: 0.8815 (mttt) cc_final: 0.8568 (tptp) REVERT: A 764 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7824 (mtmm) REVERT: A 855 TYR cc_start: 0.8612 (m-10) cc_final: 0.8274 (m-80) REVERT: A 894 LYS cc_start: 0.7655 (mttp) cc_final: 0.7379 (tptp) REVERT: A 905 LEU cc_start: 0.9533 (mt) cc_final: 0.9078 (tp) REVERT: A 931 MET cc_start: 0.8309 (mpp) cc_final: 0.7973 (mmm) REVERT: A 971 MET cc_start: 0.8380 (mmm) cc_final: 0.8034 (mmm) outliers start: 14 outliers final: 11 residues processed: 92 average time/residue: 0.3027 time to fit residues: 39.2322 Evaluate side-chains 94 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 982 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 802 ASN ** 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 = 0.3671 r_free = 0.3671 target = 0.105235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.083998 restraints weight = 37514.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.088179 restraints weight = 15870.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.090816 restraints weight = 9328.443| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.6394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5946 Z= 0.113 Angle : 0.601 19.407 8130 Z= 0.310 Chirality : 0.037 0.135 953 Planarity : 0.003 0.026 913 Dihedral : 15.148 73.692 1149 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 21.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 1.58 % Allowed : 18.39 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -0.07 (0.36), residues: 621 helix: 2.35 (0.30), residues: 322 sheet: -3.36 (0.50), residues: 64 loop : -2.65 (0.38), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 968 HIS 0.004 0.001 HIS A 626 PHE 0.012 0.001 PHE A 712 TYR 0.015 0.001 TYR A 455 ARG 0.003 0.000 ARG A 606 Details of bonding type rmsd hydrogen bonds : bond 0.02879 ( 296) hydrogen bonds : angle 3.84338 ( 801) metal coordination : bond 0.00049 ( 3) covalent geometry : bond 0.00239 ( 5943) covalent geometry : angle 0.60102 ( 8130) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3461.21 seconds wall clock time: 60 minutes 37.34 seconds (3637.34 seconds total)