Starting phenix.real_space_refine on Tue Mar 3 15:14:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n8x_24248/03_2026/7n8x_24248.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n8x_24248/03_2026/7n8x_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_24248/03_2026/7n8x_24248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n8x_24248/03_2026/7n8x_24248.map" model { file = "/net/cci-nas-00/data/ceres_data/7n8x_24248/03_2026/7n8x_24248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n8x_24248/03_2026/7n8x_24248.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.43, per 1000 atoms: 0.22 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: 0.56 Conformation dependent library (CDL) restraints added in 240.9 milliseconds 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: 0.21 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: 0.91 Time building geometry restraints manager: 0.74 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: 0.330 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.820 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.810 ------------------------------------------------------------------------------- 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 6742 Z= 0.160 Angle : 0.734 13.681 9140 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG A 643 TYR 0.014 0.001 TYR A1661 PHE 0.030 0.002 PHE A1676 TRP 0.010 0.001 TRP B 40 HIS 0.009 0.002 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 6741) covalent geometry : angle 0.73451 ( 9138) SS BOND : bond 0.00042 ( 1) SS BOND : angle 0.33749 ( 2) hydrogen bonds : bond 0.16882 ( 185) hydrogen bonds : angle 7.66333 ( 504) *********************** 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 : 0.245 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: 0.5696 (t0) cc_final: 0.5351 (t0) REVERT: A 466 ILE cc_start: 0.8195 (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: 0.7931 (m) cc_final: 0.7684 (m) REVERT: A 1727 GLU cc_start: 0.6977 (mt-10) cc_final: 0.6571 (pt0) REVERT: A 1752 MET cc_start: 0.5166 (ttp) cc_final: 0.4880 (ttp) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.0838 time to fit residues: 16.2218 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 : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.0980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN A1870 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.209390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.196375 restraints weight = 8822.990| |-----------------------------------------------------------------------------| r_work (start): 0.4351 rms_B_bonded: 1.83 r_work: 0.4272 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.4146 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6742 Z= 0.126 Angle : 0.672 12.283 9140 Z= 0.340 Chirality : 0.048 0.217 1031 Planarity : 0.005 0.133 1193 Dihedral : 5.985 34.221 894 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.76 % Favored : 91.76 % Rotamer: Outliers : 0.80 % Allowed : 7.17 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.30), residues: 825 helix: 0.80 (0.37), residues: 213 sheet: -1.82 (0.43), residues: 140 loop : -1.48 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 93 TYR 0.021 0.002 TYR A1819 PHE 0.021 0.001 PHE A 780 TRP 0.008 0.001 TRP B 37 HIS 0.003 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 6741) covalent geometry : angle 0.67183 ( 9138) SS BOND : bond 0.00041 ( 1) SS BOND : angle 0.08903 ( 2) hydrogen bonds : bond 0.04199 ( 185) hydrogen bonds : angle 5.22413 ( 504) *********************** 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 153 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 147 time to evaluate : 0.205 Fit side-chains REVERT: A 375 ILE cc_start: 0.6631 (tp) cc_final: 0.6263 (mm) REVERT: A 384 ASN cc_start: 0.6005 (t0) cc_final: 0.5405 (t0) REVERT: A 394 TYR cc_start: 0.5486 (m-80) cc_final: 0.4079 (m-80) REVERT: A 410 LEU cc_start: 0.7976 (tp) cc_final: 0.7380 (mp) REVERT: A 466 ILE cc_start: 0.8083 (tp) cc_final: 0.7840 (tp) REVERT: A 569 LEU cc_start: 0.6315 (tp) cc_final: 0.5980 (pp) REVERT: A 705 ILE cc_start: 0.8032 (tp) cc_final: 0.7685 (tp) REVERT: A 709 GLU cc_start: 0.7435 (mp0) cc_final: 0.7225 (tm-30) REVERT: A 766 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7614 (tt0) REVERT: A 818 LYS cc_start: 0.8379 (tptt) cc_final: 0.7816 (tptt) REVERT: A 1727 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6361 (tp30) REVERT: A 1734 ASN cc_start: 0.7962 (m110) cc_final: 0.7518 (p0) REVERT: A 1735 ASP cc_start: 0.7392 (m-30) cc_final: 0.7121 (m-30) REVERT: A 1752 MET cc_start: 0.5310 (ttp) cc_final: 0.5036 (ttp) outliers start: 6 outliers final: 2 residues processed: 150 average time/residue: 0.0783 time to fit residues: 15.7137 Evaluate side-chains 136 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR 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 36 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 76 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.202578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.189581 restraints weight = 8668.298| |-----------------------------------------------------------------------------| r_work (start): 0.4316 rms_B_bonded: 1.82 r_work: 0.4231 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.4105 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6742 Z= 0.189 Angle : 0.714 12.423 9140 Z= 0.364 Chirality : 0.050 0.199 1031 Planarity : 0.006 0.132 1193 Dihedral : 6.292 35.212 894 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.58 % Favored : 89.94 % Rotamer: Outliers : 1.33 % Allowed : 12.22 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.29), residues: 825 helix: 0.58 (0.37), residues: 214 sheet: -2.10 (0.42), residues: 141 loop : -1.53 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 499 TYR 0.017 0.002 TYR A1819 PHE 0.017 0.002 PHE A 459 TRP 0.011 0.001 TRP A 520 HIS 0.002 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 6741) covalent geometry : angle 0.71438 ( 9138) SS BOND : bond 0.00091 ( 1) SS BOND : angle 0.31705 ( 2) hydrogen bonds : bond 0.04637 ( 185) hydrogen bonds : angle 5.23573 ( 504) *********************** 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 145 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: B 54 LEU cc_start: 0.8437 (mt) cc_final: 0.8055 (tp) REVERT: A 375 ILE cc_start: 0.6895 (tp) cc_final: 0.6487 (tp) REVERT: A 384 ASN cc_start: 0.5990 (t0) cc_final: 0.5422 (t0) REVERT: A 394 TYR cc_start: 0.6237 (m-80) cc_final: 0.3726 (m-80) REVERT: A 401 LYS cc_start: 0.6871 (mtmt) cc_final: 0.6499 (mtmt) REVERT: A 410 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7424 (mp) REVERT: A 436 MET cc_start: 0.5811 (ptp) cc_final: 0.5550 (ptm) REVERT: A 466 ILE cc_start: 0.8128 (tp) cc_final: 0.7870 (tp) REVERT: A 569 LEU cc_start: 0.6553 (tp) cc_final: 0.6165 (pp) REVERT: A 705 ILE cc_start: 0.8119 (tp) cc_final: 0.7798 (tp) REVERT: A 709 GLU cc_start: 0.7547 (mp0) cc_final: 0.7303 (tm-30) REVERT: A 1705 THR cc_start: 0.7754 (m) cc_final: 0.7551 (m) REVERT: A 1727 GLU cc_start: 0.7443 (mt-10) cc_final: 0.6989 (pt0) REVERT: A 1752 MET cc_start: 0.5294 (ttp) cc_final: 0.5072 (ttp) outliers start: 10 outliers final: 7 residues processed: 137 average time/residue: 0.0814 time to fit residues: 14.6454 Evaluate side-chains 135 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 410 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 532 GLU 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 51 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 60 optimal weight: 0.0270 chunk 26 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 overall best weight: 0.7042 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.207899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.194732 restraints weight = 8770.011| |-----------------------------------------------------------------------------| r_work (start): 0.4331 rms_B_bonded: 1.83 r_work: 0.4251 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.4130 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6742 Z= 0.118 Angle : 0.641 11.019 9140 Z= 0.322 Chirality : 0.047 0.194 1031 Planarity : 0.005 0.130 1193 Dihedral : 5.831 34.638 894 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.12 % Favored : 91.39 % Rotamer: Outliers : 1.46 % Allowed : 14.08 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.30), residues: 825 helix: 0.89 (0.38), residues: 208 sheet: -2.04 (0.43), residues: 140 loop : -1.40 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 68 TYR 0.013 0.001 TYR A1819 PHE 0.021 0.001 PHE A 780 TRP 0.009 0.001 TRP B 37 HIS 0.004 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 6741) covalent geometry : angle 0.64151 ( 9138) SS BOND : bond 0.00041 ( 1) SS BOND : angle 0.05152 ( 2) hydrogen bonds : bond 0.03668 ( 185) hydrogen bonds : angle 4.79268 ( 504) *********************** 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 160 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 0.224 Fit side-chains REVERT: B 54 LEU cc_start: 0.8293 (mt) cc_final: 0.7893 (tp) REVERT: B 108 GLN cc_start: 0.8292 (pm20) cc_final: 0.7726 (pp30) REVERT: A 375 ILE cc_start: 0.6774 (tp) cc_final: 0.6276 (mm) REVERT: A 384 ASN cc_start: 0.6009 (t0) cc_final: 0.5445 (t0) REVERT: A 394 TYR cc_start: 0.5899 (m-80) cc_final: 0.3257 (m-80) REVERT: A 401 LYS cc_start: 0.6875 (mtmt) cc_final: 0.6639 (mtmt) REVERT: A 410 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7397 (mp) REVERT: A 436 MET cc_start: 0.5542 (ptp) cc_final: 0.5325 (ptm) REVERT: A 466 ILE cc_start: 0.8010 (tp) cc_final: 0.7758 (tp) REVERT: A 516 MET cc_start: 0.7490 (ptm) cc_final: 0.7216 (ptm) REVERT: A 569 LEU cc_start: 0.6559 (tp) cc_final: 0.6134 (pp) REVERT: A 705 ILE cc_start: 0.8104 (tp) cc_final: 0.7734 (tp) REVERT: A 766 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7638 (tt0) REVERT: A 818 LYS cc_start: 0.8339 (tptt) cc_final: 0.7866 (tptt) REVERT: A 1727 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6587 (tp30) REVERT: A 1735 ASP cc_start: 0.7643 (m-30) cc_final: 0.7377 (m-30) REVERT: A 1752 MET cc_start: 0.5251 (ttp) cc_final: 0.4988 (ttp) outliers start: 11 outliers final: 7 residues processed: 152 average time/residue: 0.0802 time to fit residues: 16.3833 Evaluate side-chains 143 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 115 VAL 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 1763 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 17 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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** ** 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 = 0.4415 r_free = 0.4415 target = 0.201734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.188944 restraints weight = 8908.349| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 1.84 r_work: 0.4225 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4095 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6742 Z= 0.192 Angle : 0.707 11.481 9140 Z= 0.361 Chirality : 0.049 0.185 1031 Planarity : 0.006 0.130 1193 Dihedral : 6.177 34.672 894 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.70 % Favored : 89.82 % Rotamer: Outliers : 2.66 % Allowed : 16.20 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.30), residues: 825 helix: 0.66 (0.38), residues: 208 sheet: -2.16 (0.42), residues: 137 loop : -1.48 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 127 TYR 0.017 0.002 TYR A1819 PHE 0.016 0.002 PHE A 531 TRP 0.010 0.002 TRP A 520 HIS 0.002 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 6741) covalent geometry : angle 0.70725 ( 9138) SS BOND : bond 0.00025 ( 1) SS BOND : angle 0.38856 ( 2) hydrogen bonds : bond 0.04376 ( 185) hydrogen bonds : angle 5.11574 ( 504) *********************** 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 165 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 54 LEU cc_start: 0.8453 (mt) cc_final: 0.8037 (tp) REVERT: A 375 ILE cc_start: 0.6990 (tp) cc_final: 0.6561 (tp) REVERT: A 384 ASN cc_start: 0.5943 (t0) cc_final: 0.5544 (t0) REVERT: A 410 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7460 (mp) REVERT: A 436 MET cc_start: 0.5569 (ptp) cc_final: 0.5315 (ptm) REVERT: A 466 ILE cc_start: 0.8113 (tp) cc_final: 0.7843 (tp) REVERT: A 489 MET cc_start: 0.7121 (ttm) cc_final: 0.6893 (ttm) REVERT: A 569 LEU cc_start: 0.6915 (tp) cc_final: 0.6440 (pp) REVERT: A 703 TYR cc_start: 0.8219 (m-80) cc_final: 0.8002 (m-80) REVERT: A 705 ILE cc_start: 0.8156 (tp) cc_final: 0.7786 (tp) REVERT: A 766 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7613 (tt0) REVERT: A 776 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7052 (tt0) REVERT: A 1727 GLU cc_start: 0.7412 (mt-10) cc_final: 0.6972 (pt0) REVERT: A 1752 MET cc_start: 0.5000 (ttp) cc_final: 0.4758 (ttp) REVERT: A 1794 GLU cc_start: 0.7850 (tt0) cc_final: 0.7262 (tp30) outliers start: 20 outliers final: 12 residues processed: 156 average time/residue: 0.0846 time to fit residues: 17.4835 Evaluate side-chains 153 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain A residue 394 TYR 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 1744 ASN Chi-restraints excluded: chain A residue 1763 VAL Chi-restraints excluded: chain A residue 1867 ASN Chi-restraints excluded: chain A residue 1870 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 18 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 22 optimal weight: 0.0970 chunk 47 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 740 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 = 0.4457 r_free = 0.4457 target = 0.206015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.193373 restraints weight = 8828.007| |-----------------------------------------------------------------------------| r_work (start): 0.4323 rms_B_bonded: 1.83 r_work: 0.4245 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4120 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6742 Z= 0.121 Angle : 0.654 10.661 9140 Z= 0.329 Chirality : 0.047 0.211 1031 Planarity : 0.005 0.128 1193 Dihedral : 5.860 34.229 894 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.00 % Favored : 91.52 % Rotamer: Outliers : 2.92 % Allowed : 16.73 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.30), residues: 825 helix: 0.65 (0.38), residues: 214 sheet: -2.16 (0.42), residues: 142 loop : -1.40 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 68 TYR 0.012 0.001 TYR A1819 PHE 0.023 0.001 PHE A 780 TRP 0.010 0.001 TRP A 520 HIS 0.002 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 6741) covalent geometry : angle 0.65383 ( 9138) SS BOND : bond 0.00004 ( 1) SS BOND : angle 0.01508 ( 2) hydrogen bonds : bond 0.03583 ( 185) hydrogen bonds : angle 4.73623 ( 504) *********************** 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: 22 poor density : 143 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 54 LEU cc_start: 0.8315 (mt) cc_final: 0.7895 (tp) REVERT: A 375 ILE cc_start: 0.6875 (tp) cc_final: 0.6345 (mm) REVERT: A 384 ASN cc_start: 0.6078 (t0) cc_final: 0.5630 (t0) REVERT: A 394 TYR cc_start: 0.6065 (OUTLIER) cc_final: 0.3063 (m-80) REVERT: A 410 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7407 (mp) REVERT: A 436 MET cc_start: 0.5424 (ptp) cc_final: 0.5144 (ptm) REVERT: A 466 ILE cc_start: 0.8046 (tp) cc_final: 0.7788 (tp) REVERT: A 489 MET cc_start: 0.7110 (ttm) cc_final: 0.6856 (ttm) REVERT: A 569 LEU cc_start: 0.6856 (tp) cc_final: 0.6368 (pp) REVERT: A 709 GLU cc_start: 0.7269 (tt0) cc_final: 0.6845 (tm-30) REVERT: A 766 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7620 (tt0) REVERT: A 776 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6875 (tt0) REVERT: A 818 LYS cc_start: 0.8422 (tptt) cc_final: 0.7805 (tptt) REVERT: A 1676 PHE cc_start: 0.1176 (OUTLIER) cc_final: 0.0671 (t80) REVERT: A 1727 GLU cc_start: 0.7349 (mt-10) cc_final: 0.6565 (tp30) REVERT: A 1752 MET cc_start: 0.5230 (ttp) cc_final: 0.4982 (ttp) REVERT: A 1846 LYS cc_start: 0.7338 (mtmt) cc_final: 0.7029 (pttm) outliers start: 22 outliers final: 15 residues processed: 155 average time/residue: 0.0731 time to fit residues: 15.3054 Evaluate side-chains 156 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 115 VAL Chi-restraints excluded: chain A residue 394 TYR 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 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 1736 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 3 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 67 optimal weight: 0.8980 chunk 45 optimal weight: 0.0980 chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 66 optimal weight: 0.4980 chunk 56 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.208219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.195668 restraints weight = 8729.386| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 1.80 r_work: 0.4273 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.4147 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6742 Z= 0.118 Angle : 0.654 10.606 9140 Z= 0.329 Chirality : 0.047 0.220 1031 Planarity : 0.005 0.126 1193 Dihedral : 5.686 33.740 894 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.52 % Favored : 92.00 % Rotamer: Outliers : 3.05 % Allowed : 17.00 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.30), residues: 825 helix: 0.72 (0.38), residues: 214 sheet: -2.11 (0.42), residues: 142 loop : -1.34 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 68 TYR 0.011 0.001 TYR A1819 PHE 0.008 0.001 PHE A 459 TRP 0.006 0.001 TRP A1742 HIS 0.002 0.001 HIS A 579 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 6741) covalent geometry : angle 0.65367 ( 9138) SS BOND : bond 0.00074 ( 1) SS BOND : angle 0.09917 ( 2) hydrogen bonds : bond 0.03449 ( 185) hydrogen bonds : angle 4.67743 ( 504) *********************** 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 163 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7209 (mt-10) REVERT: B 54 LEU cc_start: 0.8299 (mt) cc_final: 0.7833 (tp) REVERT: B 108 GLN cc_start: 0.8361 (pm20) cc_final: 0.7869 (pp30) REVERT: B 112 GLU cc_start: 0.8172 (mp0) cc_final: 0.7949 (mp0) REVERT: B 130 THR cc_start: 0.8628 (m) cc_final: 0.8421 (p) REVERT: A 375 ILE cc_start: 0.6841 (tp) cc_final: 0.6232 (mm) REVERT: A 384 ASN cc_start: 0.6111 (t0) cc_final: 0.5678 (t0) REVERT: A 394 TYR cc_start: 0.5984 (OUTLIER) cc_final: 0.3362 (m-80) REVERT: A 410 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7384 (mp) REVERT: A 436 MET cc_start: 0.5591 (ptp) cc_final: 0.5294 (ptm) REVERT: A 461 ASP cc_start: 0.7063 (p0) cc_final: 0.6794 (p0) REVERT: A 466 ILE cc_start: 0.8026 (tp) cc_final: 0.7761 (tp) REVERT: A 489 MET cc_start: 0.7114 (ttm) cc_final: 0.6847 (ttm) REVERT: A 766 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7561 (tt0) REVERT: A 776 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6849 (tt0) REVERT: A 818 LYS cc_start: 0.8451 (tptt) cc_final: 0.7771 (tptt) REVERT: A 1727 GLU cc_start: 0.7373 (mt-10) cc_final: 0.6570 (tp30) REVERT: A 1752 MET cc_start: 0.5356 (ttp) cc_final: 0.5119 (ttp) outliers start: 23 outliers final: 16 residues processed: 152 average time/residue: 0.0729 time to fit residues: 15.0577 Evaluate side-chains 155 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.204 ------------------------------------------------------------------------------- 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 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 656 ASP Chi-restraints excluded: chain A residue 681 LEU 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 1736 LEU 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 Chi-restraints excluded: chain A residue 1867 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 71 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 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** A1744 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.208112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.194768 restraints weight = 8856.070| |-----------------------------------------------------------------------------| r_work (start): 0.4320 rms_B_bonded: 1.97 r_work: 0.4237 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.4104 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6742 Z= 0.126 Angle : 0.658 10.649 9140 Z= 0.333 Chirality : 0.047 0.219 1031 Planarity : 0.005 0.126 1193 Dihedral : 5.740 33.577 894 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.76 % Favored : 91.76 % Rotamer: Outliers : 2.92 % Allowed : 17.40 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.30), residues: 825 helix: 0.67 (0.38), residues: 214 sheet: -2.12 (0.42), residues: 142 loop : -1.32 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1739 TYR 0.023 0.001 TYR A 742 PHE 0.023 0.001 PHE A 780 TRP 0.010 0.001 TRP A 520 HIS 0.004 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6741) covalent geometry : angle 0.65855 ( 9138) SS BOND : bond 0.00072 ( 1) SS BOND : angle 0.12247 ( 2) hydrogen bonds : bond 0.03583 ( 185) hydrogen bonds : angle 4.66855 ( 504) *********************** 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 161 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: B 53 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7331 (mt-10) REVERT: B 54 LEU cc_start: 0.8361 (mt) cc_final: 0.7900 (tp) REVERT: B 108 GLN cc_start: 0.8451 (pm20) cc_final: 0.7892 (pp30) REVERT: B 130 THR cc_start: 0.8537 (m) cc_final: 0.8241 (p) REVERT: A 375 ILE cc_start: 0.6841 (tp) cc_final: 0.6351 (tp) REVERT: A 384 ASN cc_start: 0.6152 (t0) cc_final: 0.5780 (t0) REVERT: A 394 TYR cc_start: 0.5956 (OUTLIER) cc_final: 0.2922 (m-80) REVERT: A 401 LYS cc_start: 0.6928 (mtmt) cc_final: 0.6485 (mtmt) REVERT: A 410 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7370 (mp) REVERT: A 411 ASN cc_start: 0.5772 (t0) cc_final: 0.5544 (t0) REVERT: A 436 MET cc_start: 0.5593 (ptp) cc_final: 0.5289 (ptm) REVERT: A 448 MET cc_start: 0.7080 (mtm) cc_final: 0.6265 (ttp) REVERT: A 461 ASP cc_start: 0.7074 (p0) cc_final: 0.6844 (p0) REVERT: A 466 ILE cc_start: 0.8020 (tp) cc_final: 0.7754 (tp) REVERT: A 766 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7626 (tt0) REVERT: A 776 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6931 (tt0) REVERT: A 818 LYS cc_start: 0.8473 (tptt) cc_final: 0.7840 (tptt) REVERT: A 1676 PHE cc_start: 0.1242 (OUTLIER) cc_final: 0.0747 (t80) REVERT: A 1727 GLU cc_start: 0.7402 (mt-10) cc_final: 0.6587 (tp30) REVERT: A 1752 MET cc_start: 0.5576 (ttp) cc_final: 0.5347 (ttp) outliers start: 22 outliers final: 14 residues processed: 149 average time/residue: 0.0721 time to fit residues: 14.5799 Evaluate side-chains 155 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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 A residue 394 TYR Chi-restraints excluded: chain A residue 410 LEU 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 1736 LEU 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 Chi-restraints excluded: chain A residue 1867 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 37 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 80 optimal weight: 0.0020 chunk 60 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 overall best weight: 0.6988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.210332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.197233 restraints weight = 8917.386| |-----------------------------------------------------------------------------| r_work (start): 0.4327 rms_B_bonded: 1.93 r_work: 0.4246 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.4119 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6742 Z= 0.121 Angle : 0.668 10.591 9140 Z= 0.336 Chirality : 0.048 0.214 1031 Planarity : 0.005 0.125 1193 Dihedral : 5.667 33.250 894 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.88 % Favored : 91.64 % Rotamer: Outliers : 2.52 % Allowed : 18.06 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.31), residues: 825 helix: 0.65 (0.38), residues: 214 sheet: -2.11 (0.42), residues: 142 loop : -1.26 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1739 TYR 0.014 0.001 TYR A1682 PHE 0.007 0.001 PHE A 658 TRP 0.008 0.001 TRP A 520 HIS 0.005 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 6741) covalent geometry : angle 0.66816 ( 9138) SS BOND : bond 0.00124 ( 1) SS BOND : angle 0.16066 ( 2) hydrogen bonds : bond 0.03480 ( 185) hydrogen bonds : angle 4.62764 ( 504) *********************** 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 155 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: B 54 LEU cc_start: 0.8321 (mt) cc_final: 0.7789 (tp) REVERT: B 56 LYS cc_start: 0.8397 (tttt) cc_final: 0.8130 (mtpp) REVERT: B 108 GLN cc_start: 0.8427 (pm20) cc_final: 0.7855 (pp30) REVERT: A 375 ILE cc_start: 0.6744 (tp) cc_final: 0.6138 (mm) REVERT: A 384 ASN cc_start: 0.5984 (t0) cc_final: 0.5592 (t0) REVERT: A 394 TYR cc_start: 0.6013 (OUTLIER) cc_final: 0.2947 (m-80) REVERT: A 410 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7387 (mp) REVERT: A 411 ASN cc_start: 0.5642 (t0) cc_final: 0.5437 (t0) REVERT: A 436 MET cc_start: 0.5620 (ptp) cc_final: 0.5304 (ptm) REVERT: A 448 MET cc_start: 0.7074 (mtm) cc_final: 0.6231 (ttp) REVERT: A 461 ASP cc_start: 0.7019 (p0) cc_final: 0.6801 (p0) REVERT: A 466 ILE cc_start: 0.7990 (tp) cc_final: 0.7731 (tp) REVERT: A 766 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7657 (tt0) REVERT: A 776 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6848 (tt0) REVERT: A 818 LYS cc_start: 0.8450 (tptt) cc_final: 0.7766 (tptt) REVERT: A 1676 PHE cc_start: 0.1160 (OUTLIER) cc_final: 0.0735 (t80) REVERT: A 1727 GLU cc_start: 0.7361 (mt-10) cc_final: 0.6553 (tp30) REVERT: A 1752 MET cc_start: 0.5614 (ttp) cc_final: 0.5376 (ttp) outliers start: 19 outliers final: 13 residues processed: 147 average time/residue: 0.0729 time to fit residues: 14.6754 Evaluate side-chains 148 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.165 ------------------------------------------------------------------------------- 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 394 TYR Chi-restraints excluded: chain A residue 410 LEU 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 1736 LEU 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 Chi-restraints excluded: chain A residue 1867 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 48 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 59 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 41 optimal weight: 0.1980 chunk 28 optimal weight: 0.0770 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 overall best weight: 0.5340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 GLN B 136 GLN ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1744 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.203633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.190472 restraints weight = 8934.084| |-----------------------------------------------------------------------------| r_work (start): 0.4289 rms_B_bonded: 1.93 r_work: 0.4202 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.4071 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6742 Z= 0.117 Angle : 0.659 11.177 9140 Z= 0.332 Chirality : 0.047 0.210 1031 Planarity : 0.005 0.123 1193 Dihedral : 5.550 32.732 894 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.24 % Favored : 91.27 % Rotamer: Outliers : 2.26 % Allowed : 18.46 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.31), residues: 825 helix: 0.65 (0.38), residues: 214 sheet: -2.04 (0.43), residues: 142 loop : -1.21 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 68 TYR 0.021 0.001 TYR A 742 PHE 0.024 0.001 PHE A 780 TRP 0.009 0.001 TRP A 520 HIS 0.004 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 6741) covalent geometry : angle 0.65941 ( 9138) SS BOND : bond 0.00125 ( 1) SS BOND : angle 0.29534 ( 2) hydrogen bonds : bond 0.03428 ( 185) hydrogen bonds : angle 4.69094 ( 504) ********************** 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 152 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: B 56 LYS cc_start: 0.8523 (tttt) cc_final: 0.8193 (mtpp) REVERT: B 108 GLN cc_start: 0.8312 (pm20) cc_final: 0.7799 (pp30) REVERT: A 375 ILE cc_start: 0.6714 (tp) cc_final: 0.6114 (mm) REVERT: A 384 ASN cc_start: 0.5939 (t0) cc_final: 0.5527 (t0) REVERT: A 394 TYR cc_start: 0.5851 (m-80) cc_final: 0.2931 (m-80) REVERT: A 404 GLU cc_start: 0.7386 (pm20) cc_final: 0.6761 (pm20) REVERT: A 410 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7352 (mp) REVERT: A 411 ASN cc_start: 0.5742 (t0) cc_final: 0.5507 (t0) REVERT: A 436 MET cc_start: 0.5634 (ptp) cc_final: 0.5310 (ptm) REVERT: A 448 MET cc_start: 0.7155 (mtm) cc_final: 0.6241 (ttp) REVERT: A 461 ASP cc_start: 0.6985 (p0) cc_final: 0.6777 (p0) REVERT: A 466 ILE cc_start: 0.7913 (tp) cc_final: 0.7673 (tp) REVERT: A 766 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7559 (tt0) REVERT: A 776 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6859 (tt0) REVERT: A 818 LYS cc_start: 0.8502 (tptt) cc_final: 0.7796 (tptt) REVERT: A 826 ILE cc_start: 0.8175 (mt) cc_final: 0.7911 (mm) REVERT: A 1727 GLU cc_start: 0.7302 (mt-10) cc_final: 0.6528 (tp30) REVERT: A 1752 MET cc_start: 0.5624 (ttp) cc_final: 0.5396 (ttp) REVERT: A 1850 ASN cc_start: 0.7558 (m110) cc_final: 0.7349 (m110) outliers start: 17 outliers final: 11 residues processed: 146 average time/residue: 0.0708 time to fit residues: 14.0066 Evaluate side-chains 146 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 410 LEU 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 1744 ASN Chi-restraints excluded: chain A residue 1763 VAL Chi-restraints excluded: chain A residue 1770 VAL Chi-restraints excluded: chain A residue 1867 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 82 optimal weight: 0.0370 chunk 58 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 53 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 GLN A 402 GLN ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1744 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.200886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.187836 restraints weight = 8838.328| |-----------------------------------------------------------------------------| r_work (start): 0.4269 rms_B_bonded: 1.92 r_work: 0.4181 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.4051 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6742 Z= 0.134 Angle : 0.664 10.659 9140 Z= 0.339 Chirality : 0.047 0.206 1031 Planarity : 0.005 0.123 1193 Dihedral : 5.605 32.731 894 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.61 % Favored : 90.91 % Rotamer: Outliers : 2.79 % Allowed : 18.73 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.31), residues: 825 helix: 0.72 (0.38), residues: 214 sheet: -2.09 (0.43), residues: 142 loop : -1.23 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 68 TYR 0.025 0.001 TYR A 742 PHE 0.009 0.001 PHE A 531 TRP 0.006 0.001 TRP A1742 HIS 0.005 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 6741) covalent geometry : angle 0.66426 ( 9138) SS BOND : bond 0.00038 ( 1) SS BOND : angle 0.07889 ( 2) hydrogen bonds : bond 0.03654 ( 185) hydrogen bonds : angle 4.72091 ( 504) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1584.48 seconds wall clock time: 27 minutes 49.23 seconds (1669.23 seconds total)