Starting phenix.real_space_refine on Fri Dec 27 22:45:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ij1_60612/12_2024/9ij1_60612.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ij1_60612/12_2024/9ij1_60612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ij1_60612/12_2024/9ij1_60612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ij1_60612/12_2024/9ij1_60612.map" model { file = "/net/cci-nas-00/data/ceres_data/9ij1_60612/12_2024/9ij1_60612.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ij1_60612/12_2024/9ij1_60612.cif" } resolution = 3.2 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= 0.034 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: 6 Type Number sf(0) Gaussians P 47 5.49 5 Mg 1 5.21 5 S 44 5.16 5 C 4328 2.51 5 N 1221 2.21 5 O 1415 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7056 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 6062 Classifications: {'peptide': 755} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 717} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 550 Classifications: {'RNA': 26} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pyr': 3, 'rna3p_pur': 12, 'rna3p_pyr': 10} Link IDs: {'rna2p': 3, 'rna3p': 22} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "C" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 443 Classifications: {'RNA': 21} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 11} Link IDs: {'rna3p': 20} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.46, per 1000 atoms: 0.63 Number of scatterers: 7056 At special positions: 0 Unit cell: (80.94, 86.64, 103.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 44 16.00 P 47 15.00 Mg 1 11.99 O 1415 8.00 N 1221 7.00 C 4328 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 723.6 milliseconds 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 12 sheets defined 31.1% alpha, 17.4% beta 20 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 2.66 Creating SS restraints... Processing helix chain 'A' and resid 251 through 261 removed outlier: 3.658A pdb=" N ARG A 255 " --> pdb=" O CYS A 251 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 317 through 330 removed outlier: 3.559A pdb=" N PHE A 325 " --> pdb=" O TYR A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 399 Processing helix chain 'A' and resid 403 through 411 Processing helix chain 'A' and resid 450 through 458 Processing helix chain 'A' and resid 502 through 507 removed outlier: 3.861A pdb=" N LYS A 507 " --> pdb=" O GLU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 520 removed outlier: 4.894A pdb=" N GLN A 517 " --> pdb=" O LYS A 513 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLN A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE A 519 " --> pdb=" O LEU A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 539 Processing helix chain 'A' and resid 540 through 549 removed outlier: 3.609A pdb=" N GLU A 546 " --> pdb=" O THR A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 590 removed outlier: 4.109A pdb=" N VAL A 590 " --> pdb=" O VAL A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 624 removed outlier: 3.662A pdb=" N LEU A 619 " --> pdb=" O GLN A 615 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASN A 621 " --> pdb=" O ARG A 617 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N MET A 622 " --> pdb=" O GLU A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 628 Processing helix chain 'A' and resid 649 through 658 removed outlier: 4.213A pdb=" N ILE A 654 " --> pdb=" O TYR A 650 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN A 655 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 664 removed outlier: 4.196A pdb=" N LYS A 663 " --> pdb=" O VAL A 660 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE A 664 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 689 removed outlier: 3.673A pdb=" N TYR A 679 " --> pdb=" O ARG A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 723 Processing helix chain 'A' and resid 785 through 801 Processing helix chain 'A' and resid 819 through 826 Processing helix chain 'A' and resid 827 through 835 removed outlier: 3.924A pdb=" N PHE A 835 " --> pdb=" O LEU A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 838 No H-bonds generated for 'chain 'A' and resid 836 through 838' Processing helix chain 'A' and resid 914 through 927 Processing helix chain 'A' and resid 939 through 955 removed outlier: 3.594A pdb=" N HIS A 946 " --> pdb=" O CYS A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 965 Processing sheet with id=AA1, first strand: chain 'A' and resid 271 through 272 removed outlier: 3.727A pdb=" N ALA A 271 " --> pdb=" O TYR A 278 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N VAL A 238 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE A 309 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLN A 240 " --> pdb=" O THR A 307 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS A 242 " --> pdb=" O GLN A 305 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN A 305 " --> pdb=" O HIS A 242 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 335 through 337 Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 350 removed outlier: 7.766A pdb=" N ASP A 386 " --> pdb=" O MET A 498 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET A 498 " --> pdb=" O ASP A 386 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 499 " --> pdb=" O ILE A 415 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ILE A 415 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 362 through 368 Processing sheet with id=AA5, first strand: chain 'A' and resid 429 through 431 Processing sheet with id=AA6, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AA7, first strand: chain 'A' and resid 577 through 579 Processing sheet with id=AA8, first strand: chain 'A' and resid 605 through 608 removed outlier: 3.783A pdb=" N TYR A 608 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 668 through 671 removed outlier: 6.219A pdb=" N CYS A 669 " --> pdb=" O ILE A 697 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 737 through 740 removed outlier: 7.755A pdb=" N MET A 845 " --> pdb=" O ASN A 909 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASN A 909 " --> pdb=" O MET A 845 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 847 " --> pdb=" O VAL A 907 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL A 885 " --> pdb=" O CYS A 906 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 743 through 745 removed outlier: 4.048A pdb=" N VAL A 756 " --> pdb=" O VAL A 774 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL A 774 " --> pdb=" O VAL A 756 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 860 through 861 208 hydrogen bonds defined for protein. 567 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 3.39 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2077 1.34 - 1.46: 1889 1.46 - 1.59: 3179 1.59 - 1.71: 92 1.71 - 1.83: 69 Bond restraints: 7306 Sorted by residual: bond pdb=" CB VAL A 388 " pdb=" CG2 VAL A 388 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.37e+00 bond pdb=" C ILE A 318 " pdb=" N PRO A 319 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.36e-02 5.41e+03 3.06e+00 bond pdb=" CB GLN A 655 " pdb=" CG GLN A 655 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.45e+00 bond pdb=" CB GLN A 352 " pdb=" CG GLN A 352 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.15e+00 bond pdb=" C ALA A 940 " pdb=" N PRO A 941 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.23e-02 6.61e+03 2.14e+00 ... (remaining 7301 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 9854 2.78 - 5.55: 202 5.55 - 8.33: 34 8.33 - 11.11: 17 11.11 - 13.88: 7 Bond angle restraints: 10114 Sorted by residual: angle pdb=" CA MET A 613 " pdb=" CB MET A 613 " pdb=" CG MET A 613 " ideal model delta sigma weight residual 114.10 125.50 -11.40 2.00e+00 2.50e-01 3.25e+01 angle pdb=" C GLU A 648 " pdb=" N THR A 649 " pdb=" CA THR A 649 " ideal model delta sigma weight residual 121.54 131.47 -9.93 1.91e+00 2.74e-01 2.70e+01 angle pdb=" C ASP A 839 " pdb=" N ASN A 840 " pdb=" CA ASN A 840 " ideal model delta sigma weight residual 122.46 129.51 -7.05 1.41e+00 5.03e-01 2.50e+01 angle pdb=" CB MET A 622 " pdb=" CG MET A 622 " pdb=" SD MET A 622 " ideal model delta sigma weight residual 112.70 126.27 -13.57 3.00e+00 1.11e-01 2.05e+01 angle pdb=" C3' U B 1 " pdb=" O3' U B 1 " pdb=" P U B 2 " ideal model delta sigma weight residual 120.20 126.91 -6.71 1.50e+00 4.44e-01 2.00e+01 ... (remaining 10109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.72: 4052 29.72 - 59.44: 357 59.44 - 89.17: 49 89.17 - 118.89: 2 118.89 - 148.61: 2 Dihedral angle restraints: 4462 sinusoidal: 2252 harmonic: 2210 Sorted by residual: dihedral pdb=" CA MET A 498 " pdb=" C MET A 498 " pdb=" N THR A 499 " pdb=" CA THR A 499 " ideal model delta harmonic sigma weight residual 180.00 144.46 35.54 0 5.00e+00 4.00e-02 5.05e+01 dihedral pdb=" CA LEU A 727 " pdb=" C LEU A 727 " pdb=" N TRP A 728 " pdb=" CA TRP A 728 " ideal model delta harmonic sigma weight residual 180.00 150.53 29.47 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA ILE A 626 " pdb=" C ILE A 626 " pdb=" N ALA A 627 " pdb=" CA ALA A 627 " ideal model delta harmonic sigma weight residual 180.00 156.43 23.57 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 4459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 904 0.060 - 0.120: 224 0.120 - 0.180: 47 0.180 - 0.240: 4 0.240 - 0.300: 3 Chirality restraints: 1182 Sorted by residual: chirality pdb=" C3' G C 12 " pdb=" C4' G C 12 " pdb=" O3' G C 12 " pdb=" C2' G C 12 " both_signs ideal model delta sigma weight residual False -2.48 -2.18 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB ILE A 229 " pdb=" CA ILE A 229 " pdb=" CG1 ILE A 229 " pdb=" CG2 ILE A 229 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" P U B 2 " pdb=" OP1 U B 2 " pdb=" OP2 U B 2 " pdb=" O5' U B 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.66 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 1179 not shown) Planarity restraints: 1110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 435 " -0.056 5.00e-02 4.00e+02 8.50e-02 1.16e+01 pdb=" N PRO A 436 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO A 436 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 436 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 492 " -0.055 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO A 493 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 493 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 493 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 938 " 0.047 5.00e-02 4.00e+02 7.13e-02 8.14e+00 pdb=" N PRO A 939 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 939 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 939 " 0.039 5.00e-02 4.00e+02 ... (remaining 1107 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 154 2.66 - 3.22: 5766 3.22 - 3.78: 12023 3.78 - 4.34: 15296 4.34 - 4.90: 23707 Nonbonded interactions: 56946 Sorted by model distance: nonbonded pdb=" OP1 U C 13 " pdb="MG MG A1001 " model vdw 2.099 2.170 nonbonded pdb=" OD2 ASP A 273 " pdb=" O2' U C 7 " model vdw 2.260 3.040 nonbonded pdb=" OP2 U C 13 " pdb="MG MG A1001 " model vdw 2.330 2.170 nonbonded pdb=" OG SER A 581 " pdb=" OD1 ASP A 583 " model vdw 2.331 3.040 nonbonded pdb=" O HIS A 602 " pdb=" OG SER A 635 " model vdw 2.336 3.040 ... (remaining 56941 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 individual isotropic 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: 0.150 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: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.230 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5916 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 : 0.005 0.067 7306 Z= 0.302 Angle : 1.082 13.884 10114 Z= 0.547 Chirality : 0.057 0.300 1182 Planarity : 0.009 0.085 1110 Dihedral : 20.534 148.611 3032 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 0.88 % Allowed : 36.31 % Favored : 62.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.66 (0.28), residues: 751 helix: -2.19 (0.31), residues: 194 sheet: -0.59 (0.41), residues: 149 loop : -2.01 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 728 HIS 0.011 0.001 HIS A 242 PHE 0.024 0.003 PHE A 578 TYR 0.028 0.003 TYR A 453 ARG 0.006 0.001 ARG A 772 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 548 THR cc_start: 0.5535 (t) cc_final: 0.5107 (t) REVERT: A 947 LYS cc_start: 0.6192 (mmmt) cc_final: 0.5644 (mmtt) outliers start: 6 outliers final: 3 residues processed: 104 average time/residue: 0.1858 time to fit residues: 26.3927 Evaluate side-chains 94 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 91 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 931 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 472 HIS A 518 GLN A 621 ASN ** A 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 7306 Z= 0.357 Angle : 0.817 9.366 10114 Z= 0.421 Chirality : 0.050 0.210 1182 Planarity : 0.007 0.073 1110 Dihedral : 18.054 156.282 1524 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 7.61 % Allowed : 31.92 % Favored : 60.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.65 (0.29), residues: 751 helix: -1.68 (0.34), residues: 201 sheet: -0.97 (0.42), residues: 152 loop : -2.13 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 728 HIS 0.007 0.002 HIS A 893 PHE 0.033 0.003 PHE A 887 TYR 0.030 0.003 TYR A 859 ARG 0.006 0.001 ARG A 709 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 96 time to evaluate : 0.721 Fit side-chains REVERT: A 302 ILE cc_start: 0.5881 (OUTLIER) cc_final: 0.5627 (mp) REVERT: A 320 PHE cc_start: 0.5041 (OUTLIER) cc_final: 0.4086 (p90) REVERT: A 321 TYR cc_start: 0.6614 (m-10) cc_final: 0.5913 (m-10) REVERT: A 526 HIS cc_start: 0.5330 (OUTLIER) cc_final: 0.4521 (m90) REVERT: A 548 THR cc_start: 0.5797 (t) cc_final: 0.5373 (t) REVERT: A 603 PHE cc_start: 0.5717 (OUTLIER) cc_final: 0.5271 (t80) REVERT: A 623 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.5912 (mm) REVERT: A 772 ARG cc_start: 0.6310 (tpp80) cc_final: 0.5995 (ttp80) REVERT: A 799 GLU cc_start: 0.6789 (mt-10) cc_final: 0.6282 (tm-30) REVERT: A 947 LYS cc_start: 0.6639 (mmmt) cc_final: 0.6029 (mmtt) outliers start: 52 outliers final: 23 residues processed: 136 average time/residue: 0.1773 time to fit residues: 33.4864 Evaluate side-chains 119 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 586 TRP Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 859 TYR Chi-restraints excluded: chain A residue 877 HIS Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 931 ASN Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 970 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 GLN ** A 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6169 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7306 Z= 0.195 Angle : 0.681 9.148 10114 Z= 0.344 Chirality : 0.045 0.195 1182 Planarity : 0.006 0.058 1110 Dihedral : 18.054 152.291 1524 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 5.86 % Allowed : 33.67 % Favored : 60.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.30), residues: 751 helix: -1.41 (0.35), residues: 204 sheet: -0.74 (0.43), residues: 154 loop : -1.84 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 728 HIS 0.005 0.001 HIS A 892 PHE 0.018 0.002 PHE A 970 TYR 0.015 0.002 TYR A 944 ARG 0.006 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 91 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: A 320 PHE cc_start: 0.4867 (OUTLIER) cc_final: 0.4360 (p90) REVERT: A 321 TYR cc_start: 0.6521 (m-10) cc_final: 0.5857 (m-10) REVERT: A 369 ASP cc_start: 0.6649 (m-30) cc_final: 0.6438 (m-30) REVERT: A 392 MET cc_start: 0.6612 (tpt) cc_final: 0.6370 (tpt) REVERT: A 450 PHE cc_start: 0.5880 (OUTLIER) cc_final: 0.5456 (t80) REVERT: A 504 LYS cc_start: 0.6162 (mptt) cc_final: 0.5693 (pptt) REVERT: A 526 HIS cc_start: 0.5163 (OUTLIER) cc_final: 0.4392 (m90) REVERT: A 548 THR cc_start: 0.5687 (t) cc_final: 0.5253 (t) REVERT: A 603 PHE cc_start: 0.5587 (OUTLIER) cc_final: 0.5154 (t80) REVERT: A 799 GLU cc_start: 0.6721 (mt-10) cc_final: 0.6250 (tm-30) REVERT: A 927 HIS cc_start: 0.5812 (OUTLIER) cc_final: 0.5520 (m170) REVERT: A 947 LYS cc_start: 0.6458 (mmmt) cc_final: 0.5888 (mmtt) outliers start: 40 outliers final: 22 residues processed: 125 average time/residue: 0.1649 time to fit residues: 28.7718 Evaluate side-chains 117 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 586 TRP Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 859 TYR Chi-restraints excluded: chain A residue 877 HIS Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 927 HIS Chi-restraints excluded: chain A residue 931 ASN Chi-restraints excluded: chain A residue 970 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6204 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7306 Z= 0.214 Angle : 0.676 8.846 10114 Z= 0.343 Chirality : 0.046 0.197 1182 Planarity : 0.006 0.059 1110 Dihedral : 17.961 150.000 1524 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 7.91 % Allowed : 31.77 % Favored : 60.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.30), residues: 751 helix: -1.22 (0.36), residues: 204 sheet: -0.69 (0.44), residues: 153 loop : -1.84 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 728 HIS 0.006 0.001 HIS A 865 PHE 0.020 0.002 PHE A 970 TYR 0.019 0.002 TYR A 859 ARG 0.005 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 96 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 320 PHE cc_start: 0.4813 (OUTLIER) cc_final: 0.4394 (p90) REVERT: A 321 TYR cc_start: 0.6692 (m-10) cc_final: 0.6035 (m-10) REVERT: A 392 MET cc_start: 0.6576 (tpt) cc_final: 0.6352 (tpt) REVERT: A 442 MET cc_start: 0.6562 (ptt) cc_final: 0.6340 (ptt) REVERT: A 450 PHE cc_start: 0.5941 (OUTLIER) cc_final: 0.5481 (t80) REVERT: A 504 LYS cc_start: 0.6124 (mptt) cc_final: 0.5718 (pptt) REVERT: A 526 HIS cc_start: 0.5187 (OUTLIER) cc_final: 0.4784 (m170) REVERT: A 548 THR cc_start: 0.5763 (t) cc_final: 0.5311 (t) REVERT: A 603 PHE cc_start: 0.5655 (OUTLIER) cc_final: 0.5029 (t80) REVERT: A 799 GLU cc_start: 0.6722 (mt-10) cc_final: 0.6292 (tm-30) REVERT: A 947 LYS cc_start: 0.6554 (mmmt) cc_final: 0.5964 (mmtt) outliers start: 54 outliers final: 36 residues processed: 137 average time/residue: 0.1618 time to fit residues: 31.4446 Evaluate side-chains 134 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 94 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 420 TYR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 586 TRP Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 832 GLN Chi-restraints excluded: chain A residue 859 TYR Chi-restraints excluded: chain A residue 877 HIS Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 931 ASN Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 970 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 chunk 38 optimal weight: 7.9990 chunk 68 optimal weight: 0.0970 chunk 19 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN ** A 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6139 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7306 Z= 0.166 Angle : 0.667 9.196 10114 Z= 0.330 Chirality : 0.045 0.195 1182 Planarity : 0.005 0.057 1110 Dihedral : 17.959 150.614 1524 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 7.91 % Allowed : 31.92 % Favored : 60.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.30), residues: 751 helix: -1.06 (0.36), residues: 204 sheet: -0.51 (0.44), residues: 155 loop : -1.76 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 728 HIS 0.006 0.001 HIS A 892 PHE 0.015 0.002 PHE A 970 TYR 0.012 0.001 TYR A 420 ARG 0.007 0.000 ARG A 772 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 95 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 320 PHE cc_start: 0.4757 (OUTLIER) cc_final: 0.4356 (p90) REVERT: A 321 TYR cc_start: 0.6640 (m-10) cc_final: 0.6007 (m-10) REVERT: A 392 MET cc_start: 0.6485 (tpt) cc_final: 0.6284 (tpt) REVERT: A 450 PHE cc_start: 0.5894 (OUTLIER) cc_final: 0.5426 (t80) REVERT: A 504 LYS cc_start: 0.5902 (mptt) cc_final: 0.5634 (pptt) REVERT: A 526 HIS cc_start: 0.5267 (OUTLIER) cc_final: 0.4978 (m170) REVERT: A 548 THR cc_start: 0.5754 (t) cc_final: 0.5313 (t) REVERT: A 603 PHE cc_start: 0.5562 (OUTLIER) cc_final: 0.4938 (t80) REVERT: A 799 GLU cc_start: 0.6730 (mt-10) cc_final: 0.6320 (tm-30) REVERT: A 927 HIS cc_start: 0.5713 (OUTLIER) cc_final: 0.5478 (m170) REVERT: A 947 LYS cc_start: 0.6419 (mmmt) cc_final: 0.5917 (mmtt) outliers start: 54 outliers final: 34 residues processed: 136 average time/residue: 0.1749 time to fit residues: 33.1011 Evaluate side-chains 132 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 93 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 586 TRP Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 832 GLN Chi-restraints excluded: chain A residue 859 TYR Chi-restraints excluded: chain A residue 877 HIS Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 927 HIS Chi-restraints excluded: chain A residue 931 ASN Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 970 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 8 optimal weight: 0.0000 chunk 43 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 overall best weight: 3.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6289 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7306 Z= 0.311 Angle : 0.757 9.529 10114 Z= 0.383 Chirality : 0.049 0.230 1182 Planarity : 0.006 0.060 1110 Dihedral : 17.932 148.255 1524 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 7.03 % Allowed : 32.94 % Favored : 60.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.30), residues: 751 helix: -1.19 (0.36), residues: 204 sheet: -0.77 (0.44), residues: 153 loop : -1.95 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 728 HIS 0.006 0.001 HIS A 893 PHE 0.022 0.002 PHE A 970 TYR 0.024 0.002 TYR A 859 ARG 0.008 0.001 ARG A 772 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 99 time to evaluate : 0.752 Fit side-chains revert: symmetry clash REVERT: A 321 TYR cc_start: 0.6939 (m-10) cc_final: 0.6266 (m-10) REVERT: A 450 PHE cc_start: 0.6144 (OUTLIER) cc_final: 0.5686 (t80) REVERT: A 504 LYS cc_start: 0.6244 (mptt) cc_final: 0.5915 (tmmt) REVERT: A 526 HIS cc_start: 0.5166 (OUTLIER) cc_final: 0.4372 (m90) REVERT: A 548 THR cc_start: 0.5834 (t) cc_final: 0.5398 (t) REVERT: A 603 PHE cc_start: 0.5651 (OUTLIER) cc_final: 0.4834 (t80) REVERT: A 650 TYR cc_start: 0.3527 (OUTLIER) cc_final: 0.2329 (t80) REVERT: A 927 HIS cc_start: 0.6013 (OUTLIER) cc_final: 0.5509 (m170) REVERT: A 947 LYS cc_start: 0.6614 (mmmt) cc_final: 0.6026 (mmtt) outliers start: 48 outliers final: 32 residues processed: 135 average time/residue: 0.1587 time to fit residues: 30.4928 Evaluate side-chains 132 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 95 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 586 TRP Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 859 TYR Chi-restraints excluded: chain A residue 877 HIS Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 927 HIS Chi-restraints excluded: chain A residue 931 ASN Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 970 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6263 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7306 Z= 0.255 Angle : 0.744 9.561 10114 Z= 0.372 Chirality : 0.048 0.203 1182 Planarity : 0.006 0.059 1110 Dihedral : 17.932 149.138 1522 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 6.88 % Allowed : 33.09 % Favored : 60.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.30), residues: 751 helix: -1.13 (0.36), residues: 201 sheet: -0.79 (0.44), residues: 155 loop : -1.98 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 728 HIS 0.007 0.001 HIS A 892 PHE 0.022 0.002 PHE A 970 TYR 0.020 0.002 TYR A 944 ARG 0.008 0.001 ARG A 772 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 97 time to evaluate : 0.723 Fit side-chains revert: symmetry clash REVERT: A 320 PHE cc_start: 0.4672 (OUTLIER) cc_final: 0.4110 (p90) REVERT: A 321 TYR cc_start: 0.6878 (m-10) cc_final: 0.6170 (m-10) REVERT: A 392 MET cc_start: 0.6924 (tpt) cc_final: 0.6656 (tpt) REVERT: A 450 PHE cc_start: 0.6026 (OUTLIER) cc_final: 0.5576 (t80) REVERT: A 504 LYS cc_start: 0.6133 (mptt) cc_final: 0.5916 (tmmt) REVERT: A 526 HIS cc_start: 0.5345 (OUTLIER) cc_final: 0.4593 (m90) REVERT: A 548 THR cc_start: 0.5784 (t) cc_final: 0.5345 (t) REVERT: A 603 PHE cc_start: 0.5612 (OUTLIER) cc_final: 0.4785 (t80) REVERT: A 650 TYR cc_start: 0.3342 (OUTLIER) cc_final: 0.2082 (t80) REVERT: A 927 HIS cc_start: 0.6039 (OUTLIER) cc_final: 0.5568 (m170) REVERT: A 947 LYS cc_start: 0.6625 (mmmt) cc_final: 0.6060 (mmtt) outliers start: 47 outliers final: 34 residues processed: 136 average time/residue: 0.1539 time to fit residues: 29.7282 Evaluate side-chains 131 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 91 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 420 TYR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 586 TRP Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 859 TYR Chi-restraints excluded: chain A residue 877 HIS Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 927 HIS Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 970 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 51 optimal weight: 0.0000 chunk 37 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 66 optimal weight: 0.1980 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6185 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7306 Z= 0.190 Angle : 0.710 9.259 10114 Z= 0.350 Chirality : 0.047 0.196 1182 Planarity : 0.006 0.058 1110 Dihedral : 17.867 149.377 1520 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 6.44 % Allowed : 33.53 % Favored : 60.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.30), residues: 751 helix: -0.93 (0.37), residues: 198 sheet: -0.61 (0.44), residues: 155 loop : -1.90 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 728 HIS 0.008 0.001 HIS A 892 PHE 0.020 0.002 PHE A 970 TYR 0.030 0.002 TYR A 944 ARG 0.004 0.000 ARG A 772 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 94 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 PHE cc_start: 0.4458 (OUTLIER) cc_final: 0.3871 (p90) REVERT: A 321 TYR cc_start: 0.6828 (m-10) cc_final: 0.6131 (m-10) REVERT: A 392 MET cc_start: 0.6818 (tpt) cc_final: 0.6560 (tpt) REVERT: A 450 PHE cc_start: 0.5935 (OUTLIER) cc_final: 0.5440 (t80) REVERT: A 526 HIS cc_start: 0.5421 (OUTLIER) cc_final: 0.4627 (m90) REVERT: A 548 THR cc_start: 0.5772 (t) cc_final: 0.5336 (t) REVERT: A 603 PHE cc_start: 0.5645 (OUTLIER) cc_final: 0.4846 (t80) REVERT: A 927 HIS cc_start: 0.5719 (OUTLIER) cc_final: 0.5424 (m170) REVERT: A 947 LYS cc_start: 0.6464 (mmmt) cc_final: 0.5976 (mmtt) outliers start: 44 outliers final: 32 residues processed: 127 average time/residue: 0.1651 time to fit residues: 29.7988 Evaluate side-chains 128 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 91 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 586 TRP Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 832 GLN Chi-restraints excluded: chain A residue 859 TYR Chi-restraints excluded: chain A residue 877 HIS Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 927 HIS Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 970 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 67 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6260 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7306 Z= 0.259 Angle : 0.756 9.938 10114 Z= 0.374 Chirality : 0.048 0.201 1182 Planarity : 0.006 0.056 1110 Dihedral : 17.813 148.005 1520 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 5.86 % Allowed : 33.97 % Favored : 60.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.30), residues: 751 helix: -0.95 (0.37), residues: 198 sheet: -0.77 (0.44), residues: 153 loop : -1.94 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 728 HIS 0.006 0.001 HIS A 892 PHE 0.023 0.002 PHE A 970 TYR 0.028 0.002 TYR A 944 ARG 0.006 0.001 ARG A 772 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 96 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 254 MET cc_start: 0.7102 (mmm) cc_final: 0.6546 (mmm) REVERT: A 320 PHE cc_start: 0.4545 (OUTLIER) cc_final: 0.3917 (p90) REVERT: A 321 TYR cc_start: 0.6883 (m-10) cc_final: 0.6175 (m-10) REVERT: A 392 MET cc_start: 0.6847 (tpt) cc_final: 0.6544 (tpt) REVERT: A 450 PHE cc_start: 0.6037 (OUTLIER) cc_final: 0.5539 (t80) REVERT: A 526 HIS cc_start: 0.5563 (OUTLIER) cc_final: 0.4754 (m90) REVERT: A 548 THR cc_start: 0.5679 (t) cc_final: 0.5226 (t) REVERT: A 603 PHE cc_start: 0.5668 (OUTLIER) cc_final: 0.4827 (t80) REVERT: A 650 TYR cc_start: 0.3654 (OUTLIER) cc_final: 0.2021 (t80) REVERT: A 799 GLU cc_start: 0.6722 (mt-10) cc_final: 0.6288 (tm-30) REVERT: A 927 HIS cc_start: 0.5884 (OUTLIER) cc_final: 0.5457 (m170) REVERT: A 947 LYS cc_start: 0.6572 (mmmt) cc_final: 0.6067 (mmtt) outliers start: 40 outliers final: 31 residues processed: 127 average time/residue: 0.1557 time to fit residues: 28.2902 Evaluate side-chains 130 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 93 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 586 TRP Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 859 TYR Chi-restraints excluded: chain A residue 877 HIS Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 927 HIS Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 970 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 10.0000 chunk 72 optimal weight: 0.6980 chunk 62 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7306 Z= 0.272 Angle : 0.785 14.117 10114 Z= 0.386 Chirality : 0.049 0.199 1182 Planarity : 0.006 0.056 1110 Dihedral : 17.862 148.215 1520 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 5.86 % Allowed : 33.97 % Favored : 60.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.30), residues: 751 helix: -1.01 (0.37), residues: 198 sheet: -0.77 (0.44), residues: 155 loop : -1.94 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 728 HIS 0.006 0.001 HIS A 893 PHE 0.023 0.002 PHE A 970 TYR 0.028 0.002 TYR A 944 ARG 0.008 0.001 ARG A 772 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 98 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 254 MET cc_start: 0.7018 (mmm) cc_final: 0.6476 (mmm) REVERT: A 320 PHE cc_start: 0.4532 (OUTLIER) cc_final: 0.3909 (p90) REVERT: A 321 TYR cc_start: 0.6837 (m-10) cc_final: 0.6129 (m-10) REVERT: A 392 MET cc_start: 0.6866 (tpt) cc_final: 0.6562 (tpt) REVERT: A 450 PHE cc_start: 0.6051 (OUTLIER) cc_final: 0.5537 (t80) REVERT: A 526 HIS cc_start: 0.5514 (OUTLIER) cc_final: 0.5247 (m-70) REVERT: A 548 THR cc_start: 0.5689 (t) cc_final: 0.5231 (t) REVERT: A 603 PHE cc_start: 0.5785 (OUTLIER) cc_final: 0.4868 (t80) REVERT: A 650 TYR cc_start: 0.3828 (OUTLIER) cc_final: 0.2299 (t80) REVERT: A 799 GLU cc_start: 0.6726 (mt-10) cc_final: 0.6290 (tm-30) REVERT: A 927 HIS cc_start: 0.5842 (OUTLIER) cc_final: 0.5381 (m170) REVERT: A 947 LYS cc_start: 0.6482 (mmmt) cc_final: 0.6023 (mmtt) outliers start: 40 outliers final: 33 residues processed: 129 average time/residue: 0.1550 time to fit residues: 28.5982 Evaluate side-chains 136 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 97 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 586 TRP Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 859 TYR Chi-restraints excluded: chain A residue 877 HIS Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 927 HIS Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 970 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 7 optimal weight: 0.0980 chunk 11 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 45 optimal weight: 20.0000 chunk 71 optimal weight: 0.5980 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 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 896 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 = 0.5132 r_free = 0.5132 target = 0.292187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.5047 r_free = 0.5047 target = 0.252320 restraints weight = 10037.523| |-----------------------------------------------------------------------------| r_work (start): 0.4771 rms_B_bonded: 2.45 r_work: 0.4642 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6129 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7306 Z= 0.206 Angle : 0.744 12.877 10114 Z= 0.363 Chirality : 0.047 0.197 1182 Planarity : 0.006 0.069 1110 Dihedral : 17.872 148.855 1520 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 5.86 % Allowed : 34.55 % Favored : 59.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.31), residues: 751 helix: -0.85 (0.37), residues: 198 sheet: -0.61 (0.45), residues: 155 loop : -1.83 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 728 HIS 0.007 0.001 HIS A 892 PHE 0.020 0.002 PHE A 970 TYR 0.026 0.002 TYR A 944 ARG 0.007 0.001 ARG A 772 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1568.20 seconds wall clock time: 29 minutes 39.81 seconds (1779.81 seconds total)