Starting phenix.real_space_refine on Fri Dec 27 19:31:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n8x_24248/12_2024/7n8x_24248.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n8x_24248/12_2024/7n8x_24248.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n8x_24248/12_2024/7n8x_24248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n8x_24248/12_2024/7n8x_24248.map" model { file = "/net/cci-nas-00/data/ceres_data/7n8x_24248/12_2024/7n8x_24248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n8x_24248/12_2024/7n8x_24248.cif" } resolution = 3.4 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= 0.023 sd= 0.773 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: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 4202 2.51 5 N 1073 2.21 5 O 1319 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6617 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1093 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 13, 'TRANS': 126} Chain: "A" Number of atoms: 5524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5524 Classifications: {'peptide': 691} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 669} Chain breaks: 1 Time building chain proxies: 4.31, per 1000 atoms: 0.65 Number of scatterers: 6617 At special positions: 0 Unit cell: (109.61, 84.75, 91.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 1319 8.00 N 1073 7.00 C 4202 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 6 " - pdb=" SG CYS B 124 " distance=2.03 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: 1.72 Conformation dependent library (CDL) restraints added in 1.0 seconds 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1580 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 8 sheets defined 29.0% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'B' and resid 13 through 17 Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 87 through 92 Processing helix chain 'B' and resid 123 through 127 Processing helix chain 'A' and resid 398 through 415 Processing helix chain 'A' and resid 416 through 420 removed outlier: 3.708A pdb=" N GLU A 420 " --> pdb=" O ALA A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 438 removed outlier: 3.657A pdb=" N GLU A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 450 removed outlier: 4.326A pdb=" N GLU A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A 450 " --> pdb=" O PHE A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 456 removed outlier: 4.616A pdb=" N LEU A 454 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 456 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 470 removed outlier: 3.513A pdb=" N ASN A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 removed outlier: 4.334A pdb=" N ALA A 476 " --> pdb=" O GLU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 511 through 516 Processing helix chain 'A' and resid 523 through 539 removed outlier: 4.483A pdb=" N ALA A 529 " --> pdb=" O ALA A 525 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLU A 532 " --> pdb=" O LYS A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 569 Processing helix chain 'A' and resid 588 through 601 removed outlier: 4.026A pdb=" N THR A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 682 Processing helix chain 'A' and resid 710 through 727 removed outlier: 4.533A pdb=" N ASP A 721 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS A 722 " --> pdb=" O LYS A 718 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU A 725 " --> pdb=" O ASP A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 775 removed outlier: 3.741A pdb=" N ILE A 768 " --> pdb=" O LYS A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 809 Processing helix chain 'A' and resid 814 through 836 Processing helix chain 'A' and resid 1773 through 1778 removed outlier: 3.690A pdb=" N ASN A1778 " --> pdb=" O LYS A1774 " (cutoff:3.500A) Processing helix chain 'A' and resid 1792 through 1796 Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.870A pdb=" N VAL B 30 " --> pdb=" O ASN B 138 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 135 " --> pdb=" O ASP B 107 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 110 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG B 65 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.870A pdb=" N VAL B 30 " --> pdb=" O ASN B 138 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 135 " --> pdb=" O ASP B 107 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 110 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG B 65 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 36 through 37 Processing sheet with id=AA4, first strand: chain 'A' and resid 628 through 629 removed outlier: 4.517A pdb=" N TYR A 621 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N SER A 605 " --> pdb=" O TYR A 621 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 649 " --> pdb=" O TYR A 580 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE A 646 " --> pdb=" O GLU A 692 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ASN A 694 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU A 648 " --> pdb=" O ASN A 694 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LEU A 696 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N PHE A 650 " --> pdb=" O LEU A 696 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 744 through 746 Processing sheet with id=AA6, first strand: chain 'A' and resid 1654 through 1657 removed outlier: 5.879A pdb=" N MET A1655 " --> pdb=" O VAL A1692 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL A1691 " --> pdb=" O ILE A1718 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A1765 " --> pdb=" O LEU A1751 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1701 through 1704 removed outlier: 6.043A pdb=" N ILE A1702 " --> pdb=" O ASN A1732 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL A1731 " --> pdb=" O ASN A1783 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1844 through 1845 removed outlier: 4.631A pdb=" N TYR A1844 " --> pdb=" O ILE A1853 " (cutoff:3.500A) 190 hydrogen bonds defined for protein. 504 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.97 Time building geometry restraints manager: 1.93 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: 2171 1.34 - 1.46: 927 1.46 - 1.57: 3604 1.57 - 1.69: 0 1.69 - 1.81: 39 Bond restraints: 6741 Sorted by residual: bond pdb=" C VAL B 43 " pdb=" O VAL B 43 " ideal model delta sigma weight residual 1.236 1.220 0.016 1.19e-02 7.06e+03 1.84e+00 bond pdb=" N ASP A 614 " pdb=" CA ASP A 614 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.70e+00 bond pdb=" CB PRO A 644 " pdb=" CG PRO A 644 " ideal model delta sigma weight residual 1.492 1.552 -0.060 5.00e-02 4.00e+02 1.45e+00 bond pdb=" C PRO A1847 " pdb=" N PRO A1848 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.33e+00 bond pdb=" CG1 ILE A 578 " pdb=" CD1 ILE A 578 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.09e+00 ... (remaining 6736 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 9026 2.74 - 5.47: 100 5.47 - 8.21: 9 8.21 - 10.94: 1 10.94 - 13.68: 2 Bond angle restraints: 9138 Sorted by residual: angle pdb=" C LEU A 519 " pdb=" CA LEU A 519 " pdb=" CB LEU A 519 " ideal model delta sigma weight residual 116.63 111.22 5.41 1.16e+00 7.43e-01 2.18e+01 angle pdb=" CA LEU B 72 " pdb=" CB LEU B 72 " pdb=" CG LEU B 72 " ideal model delta sigma weight residual 116.30 129.98 -13.68 3.50e+00 8.16e-02 1.53e+01 angle pdb=" CG1 ILE A 640 " pdb=" CB ILE A 640 " pdb=" CG2 ILE A 640 " ideal model delta sigma weight residual 110.70 99.57 11.13 3.00e+00 1.11e-01 1.38e+01 angle pdb=" CA PRO A 644 " pdb=" N PRO A 644 " pdb=" CD PRO A 644 " ideal model delta sigma weight residual 112.00 107.10 4.90 1.40e+00 5.10e-01 1.23e+01 angle pdb=" C GLU A 613 " pdb=" N ASP A 614 " pdb=" CA ASP A 614 " ideal model delta sigma weight residual 121.54 127.62 -6.08 1.91e+00 2.74e-01 1.01e+01 ... (remaining 9133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 3728 17.27 - 34.54: 316 34.54 - 51.80: 47 51.80 - 69.07: 6 69.07 - 86.34: 8 Dihedral angle restraints: 4105 sinusoidal: 1658 harmonic: 2447 Sorted by residual: dihedral pdb=" CA ARG A 643 " pdb=" C ARG A 643 " pdb=" N PRO A 644 " pdb=" CA PRO A 644 " ideal model delta harmonic sigma weight residual 180.00 -147.82 -32.18 0 5.00e+00 4.00e-02 4.14e+01 dihedral pdb=" CA LYS A1764 " pdb=" C LYS A1764 " pdb=" N ILE A1765 " pdb=" CA ILE A1765 " ideal model delta harmonic sigma weight residual -180.00 -152.92 -27.08 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA ASP B 104 " pdb=" C ASP B 104 " pdb=" N THR B 105 " pdb=" CA THR B 105 " ideal model delta harmonic sigma weight residual 180.00 154.24 25.76 0 5.00e+00 4.00e-02 2.65e+01 ... (remaining 4102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 734 0.047 - 0.095: 220 0.095 - 0.142: 72 0.142 - 0.189: 2 0.189 - 0.237: 3 Chirality restraints: 1031 Sorted by residual: chirality pdb=" CB ILE A 640 " pdb=" CA ILE A 640 " pdb=" CG1 ILE A 640 " pdb=" CG2 ILE A 640 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB THR A 430 " pdb=" CA THR A 430 " pdb=" OG1 THR A 430 " pdb=" CG2 THR A 430 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA PRO A 644 " pdb=" N PRO A 644 " pdb=" C PRO A 644 " pdb=" CB PRO A 644 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.88e-01 ... (remaining 1028 not shown) Planarity restraints: 1193 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 643 " -0.092 5.00e-02 4.00e+02 1.39e-01 3.08e+01 pdb=" N PRO A 644 " 0.240 5.00e-02 4.00e+02 pdb=" CA PRO A 644 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO A 644 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 699 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.55e+00 pdb=" C ASN A 699 " 0.033 2.00e-02 2.50e+03 pdb=" O ASN A 699 " -0.012 2.00e-02 2.50e+03 pdb=" N MET A 700 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 462 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C VAL A 462 " -0.032 2.00e-02 2.50e+03 pdb=" O VAL A 462 " 0.012 2.00e-02 2.50e+03 pdb=" N LYS A 463 " 0.011 2.00e-02 2.50e+03 ... (remaining 1190 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 188 2.70 - 3.25: 6969 3.25 - 3.80: 9773 3.80 - 4.35: 12870 4.35 - 4.90: 21155 Nonbonded interactions: 50955 Sorted by model distance: nonbonded pdb=" O ARG A1739 " pdb=" NZ LYS A1764 " model vdw 2.153 3.120 nonbonded pdb=" N GLY A1814 " pdb=" O TYR A1824 " model vdw 2.227 3.120 nonbonded pdb=" OD2 ASP B 89 " pdb=" OH TYR A1819 " model vdw 2.237 3.040 nonbonded pdb=" OD1 ASP A 423 " pdb=" OG1 THR A 426 " model vdw 2.243 3.040 nonbonded pdb=" O ASN A 699 " pdb=" ND2 ASN A 699 " model vdw 2.269 3.120 ... (remaining 50950 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: 0.250 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.940 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 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 : 0.003 0.060 6741 Z= 0.226 Angle : 0.735 13.681 9138 Z= 0.390 Chirality : 0.049 0.237 1031 Planarity : 0.006 0.139 1193 Dihedral : 13.271 86.339 2522 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.61 % Allowed : 10.06 % Favored : 89.33 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.42 (0.30), residues: 825 helix: 0.74 (0.38), residues: 209 sheet: -1.64 (0.44), residues: 141 loop : -1.52 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 40 HIS 0.009 0.002 HIS B 69 PHE 0.030 0.002 PHE A1676 TYR 0.014 0.001 TYR A1661 ARG 0.002 0.000 ARG A 643 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.747 Fit side-chains REVERT: B 108 GLN cc_start: 0.7970 (pm20) cc_final: 0.7311 (pp30) REVERT: A 375 ILE cc_start: 0.6364 (tp) cc_final: 0.5961 (tp) REVERT: A 384 ASN cc_start: 0.5695 (t0) cc_final: 0.5350 (t0) REVERT: A 466 ILE cc_start: 0.8196 (tp) cc_final: 0.7912 (tp) REVERT: A 705 ILE cc_start: 0.7805 (tp) cc_final: 0.7566 (tp) REVERT: A 742 TYR cc_start: 0.7319 (m-80) cc_final: 0.7054 (m-10) REVERT: A 1705 THR cc_start: 0.7932 (m) cc_final: 0.7684 (m) REVERT: A 1727 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6572 (pt0) REVERT: A 1752 MET cc_start: 0.5166 (ttp) cc_final: 0.4879 (ttp) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1977 time to fit residues: 37.8977 Evaluate side-chains 128 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 8.9990 chunk 62 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6741 Z= 0.214 Angle : 0.691 12.679 9138 Z= 0.350 Chirality : 0.049 0.216 1031 Planarity : 0.005 0.134 1193 Dihedral : 6.168 34.514 894 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.12 % Favored : 91.39 % Rotamer: Outliers : 0.66 % Allowed : 7.70 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.50 (0.30), residues: 825 helix: 0.74 (0.37), residues: 213 sheet: -1.88 (0.43), residues: 140 loop : -1.56 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 520 HIS 0.003 0.001 HIS B 69 PHE 0.021 0.002 PHE A 780 TYR 0.021 0.002 TYR A1819 ARG 0.002 0.000 ARG B 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 144 time to evaluate : 0.774 Fit side-chains REVERT: A 375 ILE cc_start: 0.6601 (tp) cc_final: 0.6173 (tp) REVERT: A 384 ASN cc_start: 0.5774 (t0) cc_final: 0.5220 (t0) REVERT: A 394 TYR cc_start: 0.5642 (m-80) cc_final: 0.4197 (m-10) REVERT: A 410 LEU cc_start: 0.7956 (tp) cc_final: 0.7329 (mp) REVERT: A 466 ILE cc_start: 0.7859 (tp) cc_final: 0.7576 (tp) REVERT: A 569 LEU cc_start: 0.6257 (tp) cc_final: 0.5956 (pp) REVERT: A 705 ILE cc_start: 0.8009 (tp) cc_final: 0.7694 (tp) REVERT: A 766 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7158 (tt0) REVERT: A 818 LYS cc_start: 0.8107 (tptt) cc_final: 0.7549 (tptt) REVERT: A 1705 THR cc_start: 0.7660 (m) cc_final: 0.7443 (m) REVERT: A 1727 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6082 (tp30) REVERT: A 1734 ASN cc_start: 0.7633 (m110) cc_final: 0.7165 (p0) REVERT: A 1735 ASP cc_start: 0.6682 (m-30) cc_final: 0.6479 (m-30) REVERT: A 1752 MET cc_start: 0.4988 (ttp) cc_final: 0.4729 (ttp) outliers start: 5 outliers final: 3 residues processed: 146 average time/residue: 0.1949 time to fit residues: 37.9652 Evaluate side-chains 133 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 130 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain A residue 1679 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6741 Z= 0.185 Angle : 0.660 11.609 9138 Z= 0.330 Chirality : 0.048 0.201 1031 Planarity : 0.005 0.132 1193 Dihedral : 5.877 35.049 894 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.36 % Favored : 91.15 % Rotamer: Outliers : 1.20 % Allowed : 11.42 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.40 (0.30), residues: 825 helix: 0.78 (0.37), residues: 214 sheet: -1.98 (0.43), residues: 141 loop : -1.42 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 520 HIS 0.003 0.001 HIS B 69 PHE 0.009 0.001 PHE A 459 TYR 0.015 0.001 TYR A1819 ARG 0.001 0.000 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 54 LEU cc_start: 0.7862 (mt) cc_final: 0.7424 (tp) REVERT: A 375 ILE cc_start: 0.6677 (tp) cc_final: 0.6254 (mm) REVERT: A 384 ASN cc_start: 0.5716 (t0) cc_final: 0.5073 (t0) REVERT: A 394 TYR cc_start: 0.5546 (m-80) cc_final: 0.3736 (m-10) REVERT: A 401 LYS cc_start: 0.6607 (mtmt) cc_final: 0.5463 (mtmt) REVERT: A 410 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7376 (mp) REVERT: A 436 MET cc_start: 0.5345 (ptp) cc_final: 0.5137 (ptm) REVERT: A 466 ILE cc_start: 0.7814 (tp) cc_final: 0.7555 (tp) REVERT: A 569 LEU cc_start: 0.6229 (tp) cc_final: 0.5798 (pp) REVERT: A 705 ILE cc_start: 0.8022 (tp) cc_final: 0.7754 (tp) REVERT: A 766 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7093 (tt0) REVERT: A 781 ASN cc_start: 0.7665 (t0) cc_final: 0.7438 (t0) REVERT: A 1727 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6064 (tp30) REVERT: A 1752 MET cc_start: 0.5079 (ttp) cc_final: 0.4854 (ttp) outliers start: 9 outliers final: 6 residues processed: 147 average time/residue: 0.2202 time to fit residues: 43.3569 Evaluate side-chains 141 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 1849 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 50 optimal weight: 0.0070 chunk 75 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6741 Z= 0.186 Angle : 0.652 11.045 9138 Z= 0.329 Chirality : 0.048 0.193 1031 Planarity : 0.005 0.130 1193 Dihedral : 5.802 34.799 894 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.76 % Favored : 91.76 % Rotamer: Outliers : 2.39 % Allowed : 13.55 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.30 (0.30), residues: 825 helix: 0.94 (0.38), residues: 208 sheet: -1.99 (0.43), residues: 139 loop : -1.35 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 37 HIS 0.002 0.001 HIS B 69 PHE 0.022 0.001 PHE A 780 TYR 0.015 0.001 TYR A1819 ARG 0.002 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.740 Fit side-chains REVERT: B 54 LEU cc_start: 0.7976 (mt) cc_final: 0.7550 (tp) REVERT: A 375 ILE cc_start: 0.6617 (tp) cc_final: 0.6216 (tp) REVERT: A 384 ASN cc_start: 0.5717 (t0) cc_final: 0.5154 (t0) REVERT: A 394 TYR cc_start: 0.5582 (m-80) cc_final: 0.3526 (m-80) REVERT: A 404 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.6053 (mp0) REVERT: A 410 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7340 (mp) REVERT: A 448 MET cc_start: 0.6366 (mtm) cc_final: 0.5692 (mpp) REVERT: A 466 ILE cc_start: 0.7779 (tp) cc_final: 0.7536 (tp) REVERT: A 569 LEU cc_start: 0.6342 (tp) cc_final: 0.5975 (pp) REVERT: A 705 ILE cc_start: 0.8123 (tp) cc_final: 0.7695 (tp) REVERT: A 709 GLU cc_start: 0.6173 (tt0) cc_final: 0.5724 (tm-30) REVERT: A 766 GLU cc_start: 0.7337 (mt-10) cc_final: 0.7118 (tt0) REVERT: A 818 LYS cc_start: 0.8049 (tptt) cc_final: 0.7423 (tptt) REVERT: A 1727 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6257 (tp30) REVERT: A 1752 MET cc_start: 0.5032 (ttp) cc_final: 0.4781 (ttp) outliers start: 18 outliers final: 13 residues processed: 150 average time/residue: 0.1900 time to fit residues: 38.1350 Evaluate side-chains 149 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 1676 PHE Chi-restraints excluded: chain A residue 1763 VAL Chi-restraints excluded: chain A residue 1849 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 0.0060 chunk 1 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 827 ASN A1744 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6741 Z= 0.169 Angle : 0.636 10.523 9138 Z= 0.322 Chirality : 0.047 0.194 1031 Planarity : 0.005 0.129 1193 Dihedral : 5.624 34.192 894 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.00 % Favored : 91.52 % Rotamer: Outliers : 2.66 % Allowed : 13.94 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.30 (0.30), residues: 825 helix: 0.78 (0.38), residues: 214 sheet: -1.93 (0.43), residues: 139 loop : -1.32 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 37 HIS 0.002 0.001 HIS B 69 PHE 0.007 0.001 PHE A 459 TYR 0.013 0.001 TYR A1819 ARG 0.001 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.915 Fit side-chains REVERT: B 54 LEU cc_start: 0.8045 (mt) cc_final: 0.7618 (tp) REVERT: B 56 LYS cc_start: 0.8278 (tttt) cc_final: 0.8016 (mttt) REVERT: A 375 ILE cc_start: 0.6598 (tp) cc_final: 0.6072 (mm) REVERT: A 384 ASN cc_start: 0.5713 (t0) cc_final: 0.5279 (t0) REVERT: A 394 TYR cc_start: 0.5465 (m-80) cc_final: 0.3372 (m-80) REVERT: A 404 GLU cc_start: 0.6370 (OUTLIER) cc_final: 0.5931 (mp0) REVERT: A 410 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7313 (mp) REVERT: A 466 ILE cc_start: 0.7758 (tp) cc_final: 0.7515 (tp) REVERT: A 516 MET cc_start: 0.6039 (ptm) cc_final: 0.5748 (ptt) REVERT: A 569 LEU cc_start: 0.6309 (tp) cc_final: 0.5924 (pp) REVERT: A 583 GLN cc_start: 0.7895 (tt0) cc_final: 0.7649 (tt0) REVERT: A 709 GLU cc_start: 0.5968 (tt0) cc_final: 0.5603 (tm-30) REVERT: A 766 GLU cc_start: 0.7337 (mt-10) cc_final: 0.7079 (tt0) REVERT: A 776 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6490 (tt0) REVERT: A 818 LYS cc_start: 0.8187 (tptt) cc_final: 0.7579 (tptt) REVERT: A 1727 GLU cc_start: 0.6896 (mt-10) cc_final: 0.6249 (tp30) REVERT: A 1735 ASP cc_start: 0.7038 (m-30) cc_final: 0.6779 (m-30) REVERT: A 1752 MET cc_start: 0.4772 (ttp) cc_final: 0.4529 (ttp) REVERT: A 1850 ASN cc_start: 0.7389 (m110) cc_final: 0.7164 (m110) outliers start: 20 outliers final: 13 residues processed: 149 average time/residue: 0.2007 time to fit residues: 40.7364 Evaluate side-chains 151 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 1676 PHE Chi-restraints excluded: chain A residue 1744 ASN Chi-restraints excluded: chain A residue 1763 VAL Chi-restraints excluded: chain A residue 1811 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 0.9980 chunk 15 optimal weight: 0.0060 chunk 47 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1744 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6741 Z= 0.211 Angle : 0.661 10.671 9138 Z= 0.336 Chirality : 0.048 0.207 1031 Planarity : 0.005 0.128 1193 Dihedral : 5.831 34.105 894 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.73 % Favored : 90.79 % Rotamer: Outliers : 3.32 % Allowed : 15.14 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.43 (0.30), residues: 825 helix: 0.68 (0.38), residues: 214 sheet: -2.17 (0.40), residues: 142 loop : -1.33 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1742 HIS 0.002 0.001 HIS B 69 PHE 0.021 0.001 PHE A 780 TYR 0.013 0.002 TYR A1819 ARG 0.001 0.000 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 1.009 Fit side-chains REVERT: B 54 LEU cc_start: 0.8141 (mt) cc_final: 0.7694 (tp) REVERT: B 62 SER cc_start: 0.8554 (OUTLIER) cc_final: 0.8208 (p) REVERT: B 130 THR cc_start: 0.8304 (m) cc_final: 0.8099 (p) REVERT: A 375 ILE cc_start: 0.6786 (tp) cc_final: 0.6403 (tp) REVERT: A 384 ASN cc_start: 0.5848 (t0) cc_final: 0.5479 (t0) REVERT: A 394 TYR cc_start: 0.5713 (OUTLIER) cc_final: 0.3266 (m-80) REVERT: A 404 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.6154 (mp0) REVERT: A 410 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7359 (mp) REVERT: A 448 MET cc_start: 0.6383 (mtm) cc_final: 0.5952 (ttp) REVERT: A 466 ILE cc_start: 0.7778 (tp) cc_final: 0.7547 (tp) REVERT: A 516 MET cc_start: 0.6073 (ptm) cc_final: 0.5809 (ptt) REVERT: A 709 GLU cc_start: 0.6098 (tt0) cc_final: 0.5668 (tm-30) REVERT: A 766 GLU cc_start: 0.7364 (mt-10) cc_final: 0.7151 (tt0) REVERT: A 776 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6562 (tt0) REVERT: A 818 LYS cc_start: 0.8130 (tptt) cc_final: 0.7535 (tptt) REVERT: A 1727 GLU cc_start: 0.6930 (mt-10) cc_final: 0.6291 (tp30) REVERT: A 1735 ASP cc_start: 0.6944 (m-30) cc_final: 0.6687 (m-30) outliers start: 25 outliers final: 15 residues processed: 152 average time/residue: 0.1887 time to fit residues: 38.0211 Evaluate side-chains 157 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain A residue 394 TYR Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 1676 PHE Chi-restraints excluded: chain A residue 1738 ILE Chi-restraints excluded: chain A residue 1744 ASN Chi-restraints excluded: chain A residue 1763 VAL Chi-restraints excluded: chain A residue 1811 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 79 optimal weight: 0.0570 chunk 50 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1744 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6741 Z= 0.175 Angle : 0.646 10.580 9138 Z= 0.326 Chirality : 0.047 0.214 1031 Planarity : 0.005 0.127 1193 Dihedral : 5.659 33.554 894 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.36 % Favored : 91.15 % Rotamer: Outliers : 2.79 % Allowed : 16.47 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.35 (0.30), residues: 825 helix: 0.74 (0.38), residues: 214 sheet: -2.13 (0.41), residues: 142 loop : -1.27 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 520 HIS 0.002 0.001 HIS B 69 PHE 0.007 0.001 PHE A 459 TYR 0.011 0.001 TYR A1819 ARG 0.001 0.000 ARG A 643 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: B 54 LEU cc_start: 0.8096 (mt) cc_final: 0.7608 (tp) REVERT: B 62 SER cc_start: 0.8399 (p) cc_final: 0.7950 (p) REVERT: B 112 GLU cc_start: 0.7862 (mp0) cc_final: 0.7615 (mp0) REVERT: A 375 ILE cc_start: 0.6709 (tp) cc_final: 0.6151 (mm) REVERT: A 384 ASN cc_start: 0.5873 (t0) cc_final: 0.5465 (t0) REVERT: A 394 TYR cc_start: 0.5589 (m-80) cc_final: 0.3313 (m-80) REVERT: A 410 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7312 (mp) REVERT: A 448 MET cc_start: 0.6361 (mtm) cc_final: 0.5910 (ttp) REVERT: A 466 ILE cc_start: 0.7730 (tp) cc_final: 0.7495 (tp) REVERT: A 516 MET cc_start: 0.6091 (ptm) cc_final: 0.5790 (ptt) REVERT: A 709 GLU cc_start: 0.6137 (tt0) cc_final: 0.5669 (tm-30) REVERT: A 766 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7100 (tt0) REVERT: A 776 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6421 (tt0) REVERT: A 818 LYS cc_start: 0.8227 (tptt) cc_final: 0.7606 (tptt) REVERT: A 1727 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6267 (tp30) REVERT: A 1735 ASP cc_start: 0.6980 (m-30) cc_final: 0.6723 (m-30) REVERT: A 1752 MET cc_start: 0.5133 (ttp) cc_final: 0.4705 (mmm) REVERT: A 1850 ASN cc_start: 0.7455 (m110) cc_final: 0.7225 (m110) outliers start: 21 outliers final: 13 residues processed: 148 average time/residue: 0.1793 time to fit residues: 36.1937 Evaluate side-chains 149 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 1676 PHE Chi-restraints excluded: chain A residue 1744 ASN Chi-restraints excluded: chain A residue 1763 VAL Chi-restraints excluded: chain A residue 1770 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.0070 chunk 50 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 GLN A1744 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6741 Z= 0.173 Angle : 0.636 10.577 9138 Z= 0.322 Chirality : 0.047 0.218 1031 Planarity : 0.005 0.126 1193 Dihedral : 5.590 33.343 894 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.61 % Favored : 90.91 % Rotamer: Outliers : 2.79 % Allowed : 16.73 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.32 (0.30), residues: 825 helix: 0.76 (0.38), residues: 214 sheet: -2.07 (0.41), residues: 142 loop : -1.25 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 520 HIS 0.002 0.001 HIS B 69 PHE 0.023 0.001 PHE A 780 TYR 0.010 0.001 TYR A1819 ARG 0.001 0.000 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: B 54 LEU cc_start: 0.7681 (mt) cc_final: 0.7182 (tp) REVERT: B 56 LYS cc_start: 0.8315 (tttt) cc_final: 0.8037 (mtpp) REVERT: B 108 GLN cc_start: 0.7965 (pm20) cc_final: 0.7429 (pp30) REVERT: B 130 THR cc_start: 0.8174 (m) cc_final: 0.7886 (p) REVERT: A 375 ILE cc_start: 0.6687 (tp) cc_final: 0.6058 (mm) REVERT: A 384 ASN cc_start: 0.5868 (t0) cc_final: 0.5451 (t0) REVERT: A 394 TYR cc_start: 0.5472 (OUTLIER) cc_final: 0.3088 (m-80) REVERT: A 410 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7314 (mp) REVERT: A 448 MET cc_start: 0.6370 (mtm) cc_final: 0.5872 (ttp) REVERT: A 466 ILE cc_start: 0.7710 (tp) cc_final: 0.7478 (tp) REVERT: A 516 MET cc_start: 0.6098 (ptm) cc_final: 0.5790 (ptt) REVERT: A 709 GLU cc_start: 0.6113 (tt0) cc_final: 0.5639 (tm-30) REVERT: A 766 GLU cc_start: 0.7322 (mt-10) cc_final: 0.7118 (tt0) REVERT: A 776 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.6328 (tt0) REVERT: A 818 LYS cc_start: 0.8234 (tptt) cc_final: 0.7602 (tptt) REVERT: A 1676 PHE cc_start: 0.0667 (OUTLIER) cc_final: -0.0623 (t80) REVERT: A 1727 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6275 (tp30) REVERT: A 1735 ASP cc_start: 0.6983 (m-30) cc_final: 0.6726 (m-30) REVERT: A 1752 MET cc_start: 0.5314 (ttp) cc_final: 0.4662 (mmm) REVERT: A 1850 ASN cc_start: 0.7448 (m110) cc_final: 0.7208 (m110) outliers start: 21 outliers final: 12 residues processed: 149 average time/residue: 0.1878 time to fit residues: 37.8810 Evaluate side-chains 148 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain A residue 394 TYR Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 1676 PHE Chi-restraints excluded: chain A residue 1738 ILE Chi-restraints excluded: chain A residue 1744 ASN Chi-restraints excluded: chain A residue 1763 VAL Chi-restraints excluded: chain A residue 1770 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1744 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6741 Z= 0.234 Angle : 0.680 10.735 9138 Z= 0.348 Chirality : 0.048 0.216 1031 Planarity : 0.006 0.126 1193 Dihedral : 5.898 33.402 894 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.70 % Favored : 89.82 % Rotamer: Outliers : 3.19 % Allowed : 16.60 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.44 (0.30), residues: 825 helix: 0.62 (0.38), residues: 214 sheet: -2.20 (0.41), residues: 142 loop : -1.29 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1742 HIS 0.002 0.001 HIS B 69 PHE 0.014 0.001 PHE A 531 TYR 0.014 0.002 TYR A1682 ARG 0.002 0.000 ARG A 643 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: B 54 LEU cc_start: 0.8145 (mt) cc_final: 0.7649 (tp) REVERT: B 62 SER cc_start: 0.8549 (OUTLIER) cc_final: 0.8120 (p) REVERT: B 112 GLU cc_start: 0.7910 (mp0) cc_final: 0.7698 (mp0) REVERT: A 375 ILE cc_start: 0.6851 (tp) cc_final: 0.6492 (tp) REVERT: A 384 ASN cc_start: 0.5902 (t0) cc_final: 0.5518 (t0) REVERT: A 394 TYR cc_start: 0.5559 (OUTLIER) cc_final: 0.2878 (m-80) REVERT: A 401 LYS cc_start: 0.6024 (mtmt) cc_final: 0.5492 (mtmm) REVERT: A 404 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.6051 (mp0) REVERT: A 410 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7356 (mp) REVERT: A 448 MET cc_start: 0.6499 (mtm) cc_final: 0.6105 (ttp) REVERT: A 466 ILE cc_start: 0.7771 (tp) cc_final: 0.7547 (tp) REVERT: A 516 MET cc_start: 0.6183 (ptm) cc_final: 0.5982 (ptt) REVERT: A 601 THR cc_start: 0.8211 (p) cc_final: 0.7882 (p) REVERT: A 766 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7165 (tt0) REVERT: A 776 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6619 (tt0) REVERT: A 818 LYS cc_start: 0.8300 (tptt) cc_final: 0.7958 (tptt) REVERT: A 1727 GLU cc_start: 0.6930 (mt-10) cc_final: 0.6444 (mt-10) REVERT: A 1735 ASP cc_start: 0.7051 (m-30) cc_final: 0.6787 (m-30) REVERT: A 1752 MET cc_start: 0.5242 (ttp) cc_final: 0.5033 (mtp) outliers start: 24 outliers final: 15 residues processed: 150 average time/residue: 0.1987 time to fit residues: 39.3766 Evaluate side-chains 153 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain A residue 394 TYR Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 1676 PHE Chi-restraints excluded: chain A residue 1738 ILE Chi-restraints excluded: chain A residue 1744 ASN Chi-restraints excluded: chain A residue 1763 VAL Chi-restraints excluded: chain A residue 1770 VAL Chi-restraints excluded: chain A residue 1811 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1744 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6741 Z= 0.280 Angle : 0.718 10.779 9138 Z= 0.369 Chirality : 0.050 0.216 1031 Planarity : 0.006 0.126 1193 Dihedral : 6.239 33.327 894 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.70 % Favored : 89.82 % Rotamer: Outliers : 2.79 % Allowed : 18.06 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.57 (0.30), residues: 825 helix: 0.57 (0.38), residues: 208 sheet: -2.38 (0.40), residues: 142 loop : -1.35 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1742 HIS 0.002 0.001 HIS B 69 PHE 0.022 0.002 PHE A 780 TYR 0.018 0.002 TYR A 742 ARG 0.002 0.000 ARG B 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 54 LEU cc_start: 0.8290 (mt) cc_final: 0.7824 (tp) REVERT: B 62 SER cc_start: 0.8600 (OUTLIER) cc_final: 0.8168 (p) REVERT: B 112 GLU cc_start: 0.8021 (mp0) cc_final: 0.7665 (mp0) REVERT: A 375 ILE cc_start: 0.6903 (tp) cc_final: 0.6543 (tp) REVERT: A 384 ASN cc_start: 0.5671 (t0) cc_final: 0.5270 (t0) REVERT: A 410 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7480 (mp) REVERT: A 448 MET cc_start: 0.6545 (mtm) cc_final: 0.6143 (ttp) REVERT: A 466 ILE cc_start: 0.7816 (tp) cc_final: 0.7572 (tp) REVERT: A 569 LEU cc_start: 0.6983 (tp) cc_final: 0.6373 (pp) REVERT: A 601 THR cc_start: 0.8259 (p) cc_final: 0.7950 (p) REVERT: A 766 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7210 (tt0) REVERT: A 776 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6709 (tt0) REVERT: A 818 LYS cc_start: 0.8309 (tptt) cc_final: 0.7986 (tptt) REVERT: A 1727 GLU cc_start: 0.7040 (mt-10) cc_final: 0.6731 (pt0) REVERT: A 1735 ASP cc_start: 0.7032 (m-30) cc_final: 0.6761 (m-30) REVERT: A 1752 MET cc_start: 0.5145 (ttp) cc_final: 0.4288 (mmm) outliers start: 21 outliers final: 17 residues processed: 148 average time/residue: 0.1960 time to fit residues: 38.3372 Evaluate side-chains 159 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain A residue 394 TYR Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 1676 PHE Chi-restraints excluded: chain A residue 1684 ILE Chi-restraints excluded: chain A residue 1738 ILE Chi-restraints excluded: chain A residue 1744 ASN Chi-restraints excluded: chain A residue 1763 VAL Chi-restraints excluded: chain A residue 1770 VAL Chi-restraints excluded: chain A residue 1795 ILE Chi-restraints excluded: chain A residue 1811 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 57 optimal weight: 0.1980 chunk 3 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 0.0000 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1744 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.206957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.193634 restraints weight = 8728.750| |-----------------------------------------------------------------------------| r_work (start): 0.4329 rms_B_bonded: 2.00 r_work: 0.4245 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.4115 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6741 Z= 0.171 Angle : 0.651 10.648 9138 Z= 0.331 Chirality : 0.047 0.215 1031 Planarity : 0.005 0.124 1193 Dihedral : 5.749 32.500 894 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.12 % Favored : 91.39 % Rotamer: Outliers : 2.12 % Allowed : 18.33 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.31 (0.31), residues: 825 helix: 0.79 (0.38), residues: 208 sheet: -2.20 (0.42), residues: 142 loop : -1.19 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1742 HIS 0.002 0.001 HIS A 579 PHE 0.020 0.001 PHE A 431 TYR 0.010 0.001 TYR A1819 ARG 0.002 0.000 ARG B 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1848.48 seconds wall clock time: 34 minutes 30.35 seconds (2070.35 seconds total)