Starting phenix.real_space_refine on Tue Aug 4 19:06:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ca0_45378/08_2026/9ca0_45378_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ca0_45378/08_2026/9ca0_45378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ca0_45378/08_2026/9ca0_45378_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ca0_45378/08_2026/9ca0_45378_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ca0_45378/08_2026/9ca0_45378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ca0_45378/08_2026/9ca0_45378.map" } resolution = 3.48 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= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 10 5.49 5 S 39 5.16 5 C 3928 2.51 5 N 1081 2.21 5 O 1206 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6265 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4845 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 30, 'TRANS': 581} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1219 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "D" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 143 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "E" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Classifications: {'DNA': 3} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.35, per 1000 atoms: 0.22 Number of scatterers: 6265 At special positions: 0 Unit cell: (73.87, 86.32, 135.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 39 16.00 P 10 15.00 O 1206 8.00 N 1081 7.00 C 3928 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 335.2 milliseconds 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1442 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 6 sheets defined 41.1% alpha, 15.0% beta 0 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 10 through 23 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 77 through 82 removed outlier: 3.741A pdb=" N PHE A 82 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 96 Processing helix chain 'A' and resid 97 through 105 Processing helix chain 'A' and resid 122 through 134 Processing helix chain 'A' and resid 156 through 166 Processing helix chain 'A' and resid 171 through 190 removed outlier: 3.904A pdb=" N SER A 177 " --> pdb=" O ASN A 173 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ALA A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 200 removed outlier: 4.034A pdb=" N PHE A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 234 removed outlier: 3.603A pdb=" N PHE A 224 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N CYS A 225 " --> pdb=" O THR A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 276 Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 317 through 332 Processing helix chain 'A' and resid 349 through 355 Processing helix chain 'A' and resid 363 through 371 Processing helix chain 'A' and resid 404 through 421 removed outlier: 3.725A pdb=" N LEU A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE A 417 " --> pdb=" O THR A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 455 Processing helix chain 'A' and resid 496 through 507 Processing helix chain 'A' and resid 513 through 524 Processing helix chain 'A' and resid 538 through 552 Processing helix chain 'A' and resid 553 through 556 removed outlier: 3.618A pdb=" N VAL A 556 " --> pdb=" O ALA A 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 553 through 556' Processing helix chain 'A' and resid 559 through 573 removed outlier: 3.862A pdb=" N LEU A 570 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE A 571 " --> pdb=" O GLN A 567 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 598 removed outlier: 3.782A pdb=" N VAL A 581 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 611 removed outlier: 4.277A pdb=" N LEU A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL A 609 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER A 610 " --> pdb=" O LEU A 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 17 through 25 Processing helix chain 'B' and resid 32 through 43 Processing helix chain 'B' and resid 44 through 48 removed outlier: 3.656A pdb=" N THR B 47 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 5.464A pdb=" N SER A 37 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N SER A 56 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL A 4 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N THR A 55 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N MET A 6 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR A 3 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL A 113 " --> pdb=" O THR A 3 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LEU A 5 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N TRP A 115 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL A 7 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N PHE A 148 " --> pdb=" O ASP A 110 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE A 112 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 66 Processing sheet with id=AA3, first strand: chain 'A' and resid 254 through 256 removed outlier: 6.357A pdb=" N VAL A 242 " --> pdb=" O MET A 483 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N MET A 483 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLN A 244 " --> pdb=" O VAL A 481 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL A 481 " --> pdb=" O GLN A 244 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LYS A 246 " --> pdb=" O GLY A 479 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 258 through 259 removed outlier: 6.973A pdb=" N LYS A 425 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 432 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA A 287 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ARG A 434 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL A 285 " --> pdb=" O ARG A 434 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 494 through 495 removed outlier: 3.941A pdb=" N LEU A 494 " --> pdb=" O LEU A 535 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 64 through 65 removed outlier: 4.350A pdb=" N ASP B 134 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR B 107 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU B 142 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL B 109 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU B 95 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ARG B 96 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE B 76 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLN B 98 " --> pdb=" O GLN B 74 " (cutoff:3.500A) 250 hydrogen bonds defined for protein. 702 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 0.93 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1933 1.33 - 1.45: 886 1.45 - 1.57: 3513 1.57 - 1.69: 18 1.69 - 1.81: 61 Bond restraints: 6411 Sorted by residual: bond pdb=" OH PTR A 336 " pdb=" P PTR A 336 " ideal model delta sigma weight residual 1.769 1.606 0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" C SER A 335 " pdb=" N PTR A 336 " ideal model delta sigma weight residual 1.329 1.429 -0.100 1.40e-02 5.10e+03 5.15e+01 bond pdb=" O1P PTR A 336 " pdb=" P PTR A 336 " ideal model delta sigma weight residual 1.522 1.476 0.046 2.00e-02 2.50e+03 5.22e+00 bond pdb=" CZ PTR A 336 " pdb=" OH PTR A 336 " ideal model delta sigma weight residual 1.339 1.300 0.039 2.00e-02 2.50e+03 3.74e+00 bond pdb=" C3' DC D 0 " pdb=" C2' DC D 0 " ideal model delta sigma weight residual 1.516 1.530 -0.014 8.00e-03 1.56e+04 3.07e+00 ... (remaining 6406 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 8575 1.96 - 3.92: 117 3.92 - 5.89: 15 5.89 - 7.85: 5 7.85 - 9.81: 3 Bond angle restraints: 8715 Sorted by residual: angle pdb=" CA SER A 335 " pdb=" C SER A 335 " pdb=" N PTR A 336 " ideal model delta sigma weight residual 116.20 106.58 9.62 2.00e+00 2.50e-01 2.31e+01 angle pdb=" N3 DT D 1 " pdb=" C4 DT D 1 " pdb=" O4 DT D 1 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT E 6 " pdb=" C4 DT E 6 " pdb=" O4 DT E 6 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT E 7 " pdb=" C4 DT E 7 " pdb=" O4 DT E 7 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 angle pdb=" O4 DT D 1 " pdb=" C4 DT D 1 " pdb=" C5 DT D 1 " ideal model delta sigma weight residual 124.90 122.31 2.59 7.00e-01 2.04e+00 1.36e+01 ... (remaining 8710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.76: 3403 16.76 - 33.52: 356 33.52 - 50.28: 90 50.28 - 67.04: 25 67.04 - 83.80: 4 Dihedral angle restraints: 3878 sinusoidal: 1644 harmonic: 2234 Sorted by residual: dihedral pdb=" CA SER A 335 " pdb=" C SER A 335 " pdb=" N PTR A 336 " pdb=" CA PTR A 336 " ideal model delta harmonic sigma weight residual -180.00 -140.35 -39.65 0 5.00e+00 4.00e-02 6.29e+01 dihedral pdb=" CA LEU A 176 " pdb=" C LEU A 176 " pdb=" N SER A 177 " pdb=" CA SER A 177 " ideal model delta harmonic sigma weight residual 180.00 161.65 18.35 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA TYR A 240 " pdb=" C TYR A 240 " pdb=" N TRP A 241 " pdb=" CA TRP A 241 " ideal model delta harmonic sigma weight residual 180.00 162.37 17.63 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 3875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 632 0.032 - 0.065: 249 0.065 - 0.097: 57 0.097 - 0.129: 36 0.129 - 0.161: 3 Chirality restraints: 977 Sorted by residual: chirality pdb=" CA PTR A 336 " pdb=" N PTR A 336 " pdb=" C PTR A 336 " pdb=" CB PTR A 336 " both_signs ideal model delta sigma weight residual False 2.35 2.51 -0.16 2.00e-01 2.50e+01 6.52e-01 chirality pdb=" CA ILE B 135 " pdb=" N ILE B 135 " pdb=" C ILE B 135 " pdb=" CB ILE B 135 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CG LEU B 71 " pdb=" CB LEU B 71 " pdb=" CD1 LEU B 71 " pdb=" CD2 LEU B 71 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 974 not shown) Planarity restraints: 1092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 335 " 0.053 2.00e-02 2.50e+03 1.11e-01 1.23e+02 pdb=" C SER A 335 " -0.191 2.00e-02 2.50e+03 pdb=" O SER A 335 " 0.079 2.00e-02 2.50e+03 pdb=" N PTR A 336 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 137 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.13e+00 pdb=" C ASN B 137 " -0.035 2.00e-02 2.50e+03 pdb=" O ASN B 137 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY B 138 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 377 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+00 pdb=" N PRO A 378 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 378 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 378 " -0.023 5.00e-02 4.00e+02 ... (remaining 1089 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 90 2.66 - 3.22: 5685 3.22 - 3.78: 9085 3.78 - 4.34: 12231 4.34 - 4.90: 20360 Nonbonded interactions: 47451 Sorted by model distance: nonbonded pdb=" OD2 ASP A 119 " pdb="MN MN A 701 " model vdw 2.104 2.320 nonbonded pdb=" OE1 GLN A 196 " pdb=" OH TYR A 548 " model vdw 2.278 3.040 nonbonded pdb=" OE1 GLU A 326 " pdb=" NH2 ARG A 338 " model vdw 2.283 3.120 nonbonded pdb=" O CYS A 217 " pdb=" OG1 THR A 221 " model vdw 2.320 3.040 nonbonded pdb=" OE2 GLU A 496 " pdb=" NH2 ARG A 533 " model vdw 2.323 3.120 ... (remaining 47446 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: 3.960 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.740 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:0.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 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 : 0.004 0.163 6412 Z= 0.241 Angle : 0.583 9.812 8715 Z= 0.312 Chirality : 0.040 0.161 977 Planarity : 0.005 0.111 1092 Dihedral : 14.952 83.802 2436 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.15 % Allowed : 0.15 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.73 (0.29), residues: 766 helix: 0.34 (0.30), residues: 290 sheet: 0.05 (0.49), residues: 123 loop : -1.36 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 524 TYR 0.010 0.001 TYR A 411 PHE 0.012 0.001 PHE A 265 TRP 0.006 0.001 TRP A 241 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.22 ( 6411) covalent geometry : angle 0.58255 / 0.31 ( 8715) hydrogen bonds : bond 0.19064 / 13.30 ( 250) hydrogen bonds : angle 5.75668 / 3.97 ( 702) Misc. bond : bond 0.08005 / 4.21 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 0.266 Fit side-chains REVERT: A 30 LYS cc_start: 0.8183 (mppt) cc_final: 0.7976 (mppt) REVERT: A 51 ARG cc_start: 0.7325 (ttp-170) cc_final: 0.7054 (ttp80) REVERT: A 56 SER cc_start: 0.7983 (p) cc_final: 0.7750 (p) REVERT: A 77 ASP cc_start: 0.7639 (p0) cc_final: 0.7369 (p0) REVERT: A 105 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6913 (mm-30) REVERT: A 171 ASP cc_start: 0.6878 (m-30) cc_final: 0.6661 (m-30) REVERT: A 214 PHE cc_start: 0.8572 (t80) cc_final: 0.8338 (t80) REVERT: A 240 TYR cc_start: 0.6946 (m-10) cc_final: 0.6689 (m-10) REVERT: A 349 ASP cc_start: 0.7299 (t0) cc_final: 0.6878 (t0) REVERT: A 393 MET cc_start: 0.7731 (mmm) cc_final: 0.7315 (mmm) REVERT: A 482 LYS cc_start: 0.7496 (ptmt) cc_final: 0.7195 (ptmt) REVERT: A 483 MET cc_start: 0.7357 (mpp) cc_final: 0.6627 (mpp) outliers start: 1 outliers final: 1 residues processed: 190 average time/residue: 0.0797 time to fit residues: 19.4755 Evaluate side-chains 179 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 0.3980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN A 323 GLN ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.112583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.100436 restraints weight = 10109.351| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.17 r_work: 0.3133 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6412 Z= 0.184 Angle : 0.569 7.201 8715 Z= 0.298 Chirality : 0.042 0.224 977 Planarity : 0.004 0.029 1092 Dihedral : 11.551 59.582 954 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.90 % Allowed : 11.39 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.63 (0.29), residues: 766 helix: 0.58 (0.29), residues: 302 sheet: -0.10 (0.47), residues: 132 loop : -1.48 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 524 TYR 0.014 0.002 TYR A 411 PHE 0.016 0.002 PHE A 265 TRP 0.008 0.001 TRP A 458 HIS 0.005 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 ( 6411) covalent geometry : angle 0.56935 / 0.30 ( 8715) hydrogen bonds : bond 0.04973 / 3.31 ( 250) hydrogen bonds : angle 4.47494 / 3.11 ( 702) Misc. bond : bond 0.00401 / 0.21 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 183 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8541 (mppt) cc_final: 0.8287 (mppt) REVERT: A 51 ARG cc_start: 0.8103 (ttp-170) cc_final: 0.7897 (ttp80) REVERT: A 171 ASP cc_start: 0.7485 (m-30) cc_final: 0.7265 (m-30) REVERT: A 214 PHE cc_start: 0.8609 (t80) cc_final: 0.8389 (t80) REVERT: A 240 TYR cc_start: 0.7807 (m-10) cc_final: 0.7558 (m-10) REVERT: A 285 VAL cc_start: 0.8928 (t) cc_final: 0.8583 (p) REVERT: A 349 ASP cc_start: 0.7777 (t0) cc_final: 0.7350 (t0) REVERT: A 393 MET cc_start: 0.8282 (mmm) cc_final: 0.7857 (mtt) REVERT: A 482 LYS cc_start: 0.7901 (ptmt) cc_final: 0.7554 (ptmt) REVERT: A 483 MET cc_start: 0.7971 (mpp) cc_final: 0.7396 (mpp) REVERT: A 552 ASP cc_start: 0.8092 (t0) cc_final: 0.7843 (t0) REVERT: A 597 VAL cc_start: 0.8915 (p) cc_final: 0.8712 (p) REVERT: B 22 GLU cc_start: 0.8044 (mp0) cc_final: 0.7190 (mp0) outliers start: 6 outliers final: 2 residues processed: 184 average time/residue: 0.0787 time to fit residues: 18.5882 Evaluate side-chains 178 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 176 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 598 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 3 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 chunk 42 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 48 optimal weight: 0.0270 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.112554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.100213 restraints weight = 9985.313| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.15 r_work: 0.3131 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6412 Z= 0.159 Angle : 0.524 7.188 8715 Z= 0.274 Chirality : 0.041 0.136 977 Planarity : 0.004 0.031 1092 Dihedral : 11.421 59.789 950 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.65 % Allowed : 13.49 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.54 (0.30), residues: 766 helix: 0.78 (0.30), residues: 301 sheet: -0.29 (0.47), residues: 131 loop : -1.43 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 524 TYR 0.015 0.001 TYR A 578 PHE 0.014 0.002 PHE A 66 TRP 0.008 0.001 TRP A 458 HIS 0.004 0.001 HIS A 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 6411) covalent geometry : angle 0.52426 / 0.27 ( 8715) hydrogen bonds : bond 0.04340 / 2.80 ( 250) hydrogen bonds : angle 4.27974 / 2.95 ( 702) Misc. bond : bond 0.00394 / 0.21 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 181 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8527 (mppt) cc_final: 0.8286 (mppt) REVERT: A 171 ASP cc_start: 0.7470 (m-30) cc_final: 0.7249 (m-30) REVERT: A 240 TYR cc_start: 0.7811 (m-10) cc_final: 0.7523 (m-10) REVERT: A 258 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7301 (m-30) REVERT: A 272 MET cc_start: 0.7479 (tmm) cc_final: 0.7202 (tmm) REVERT: A 285 VAL cc_start: 0.8923 (t) cc_final: 0.8586 (p) REVERT: A 349 ASP cc_start: 0.7765 (t0) cc_final: 0.7335 (t0) REVERT: A 393 MET cc_start: 0.8252 (mmm) cc_final: 0.7889 (mtt) REVERT: A 482 LYS cc_start: 0.7924 (ptmt) cc_final: 0.7572 (ptmt) REVERT: A 483 MET cc_start: 0.7952 (mpp) cc_final: 0.7389 (mpp) REVERT: A 551 ILE cc_start: 0.8500 (mm) cc_final: 0.8276 (mm) REVERT: A 552 ASP cc_start: 0.8030 (t0) cc_final: 0.7804 (t0) REVERT: A 597 VAL cc_start: 0.8883 (p) cc_final: 0.8644 (p) REVERT: B 22 GLU cc_start: 0.8124 (mp0) cc_final: 0.7302 (mp0) REVERT: B 120 ASN cc_start: 0.8044 (p0) cc_final: 0.7783 (p0) REVERT: B 136 LYS cc_start: 0.7996 (mmmt) cc_final: 0.7714 (mmmt) outliers start: 11 outliers final: 5 residues processed: 185 average time/residue: 0.0697 time to fit residues: 16.6580 Evaluate side-chains 177 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 171 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 598 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 12 optimal weight: 0.3980 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.111620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.099343 restraints weight = 10056.534| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.15 r_work: 0.3112 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6412 Z= 0.183 Angle : 0.542 9.295 8715 Z= 0.280 Chirality : 0.042 0.203 977 Planarity : 0.004 0.034 1092 Dihedral : 11.426 61.654 950 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.55 % Allowed : 14.69 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.48 (0.30), residues: 766 helix: 0.84 (0.30), residues: 300 sheet: -0.20 (0.46), residues: 136 loop : -1.45 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 524 TYR 0.015 0.002 TYR A 578 PHE 0.017 0.002 PHE A 66 TRP 0.008 0.001 TRP A 458 HIS 0.004 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 ( 6411) covalent geometry : angle 0.54180 / 0.28 ( 8715) hydrogen bonds : bond 0.04228 / 2.73 ( 250) hydrogen bonds : angle 4.27710 / 2.94 ( 702) Misc. bond : bond 0.00068 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 7 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8303 (m) REVERT: A 30 LYS cc_start: 0.8538 (mppt) cc_final: 0.8312 (mppt) REVERT: A 98 MET cc_start: 0.7946 (mmm) cc_final: 0.7652 (tmm) REVERT: A 171 ASP cc_start: 0.7475 (m-30) cc_final: 0.7246 (m-30) REVERT: A 240 TYR cc_start: 0.7858 (m-10) cc_final: 0.7540 (m-10) REVERT: A 258 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7289 (m-30) REVERT: A 349 ASP cc_start: 0.7771 (t0) cc_final: 0.7331 (t0) REVERT: A 393 MET cc_start: 0.8282 (mmm) cc_final: 0.7957 (mtt) REVERT: A 482 LYS cc_start: 0.7903 (ptmt) cc_final: 0.7511 (ptmt) REVERT: A 483 MET cc_start: 0.7942 (mpp) cc_final: 0.7434 (mpp) REVERT: A 498 GLU cc_start: 0.7975 (tt0) cc_final: 0.7744 (mt-10) REVERT: A 551 ILE cc_start: 0.8506 (mm) cc_final: 0.8277 (mm) REVERT: A 552 ASP cc_start: 0.8040 (t0) cc_final: 0.7810 (t0) REVERT: A 597 VAL cc_start: 0.8887 (p) cc_final: 0.8646 (p) REVERT: B 120 ASN cc_start: 0.8031 (p0) cc_final: 0.7766 (p0) REVERT: B 136 LYS cc_start: 0.7989 (mmmt) cc_final: 0.7744 (mmmt) outliers start: 17 outliers final: 8 residues processed: 185 average time/residue: 0.0688 time to fit residues: 16.5303 Evaluate side-chains 185 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 175 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain B residue 145 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 53 optimal weight: 0.0770 chunk 8 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 70 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN A 520 ASN B 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.111985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.099149 restraints weight = 10165.285| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.23 r_work: 0.3117 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6412 Z= 0.152 Angle : 0.537 12.729 8715 Z= 0.272 Chirality : 0.041 0.130 977 Planarity : 0.004 0.053 1092 Dihedral : 11.396 61.877 950 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.25 % Allowed : 17.09 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.50 (0.30), residues: 766 helix: 0.80 (0.30), residues: 302 sheet: -0.29 (0.47), residues: 130 loop : -1.39 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 524 TYR 0.014 0.001 TYR A 578 PHE 0.015 0.002 PHE A 66 TRP 0.008 0.001 TRP A 458 HIS 0.003 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 6411) covalent geometry : angle 0.53666 / 0.27 ( 8715) hydrogen bonds : bond 0.03958 / 2.54 ( 250) hydrogen bonds : angle 4.21951 / 2.90 ( 702) Misc. bond : bond 0.00148 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 7 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8336 (m) REVERT: A 30 LYS cc_start: 0.8540 (mppt) cc_final: 0.8331 (mppt) REVERT: A 98 MET cc_start: 0.7984 (mmm) cc_final: 0.7633 (tmm) REVERT: A 171 ASP cc_start: 0.7497 (m-30) cc_final: 0.7259 (m-30) REVERT: A 240 TYR cc_start: 0.7823 (m-10) cc_final: 0.7529 (m-10) REVERT: A 258 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.7306 (m-30) REVERT: A 349 ASP cc_start: 0.7763 (t0) cc_final: 0.7353 (t0) REVERT: A 393 MET cc_start: 0.8288 (mmm) cc_final: 0.7963 (mtt) REVERT: A 482 LYS cc_start: 0.7909 (ptmt) cc_final: 0.7512 (ptmt) REVERT: A 483 MET cc_start: 0.7959 (mpp) cc_final: 0.7432 (mpp) REVERT: A 498 GLU cc_start: 0.7997 (tt0) cc_final: 0.7682 (mt-10) REVERT: A 552 ASP cc_start: 0.8049 (t0) cc_final: 0.7818 (t0) REVERT: A 597 VAL cc_start: 0.8892 (p) cc_final: 0.8641 (p) REVERT: B 120 ASN cc_start: 0.8025 (p0) cc_final: 0.7770 (p0) REVERT: B 136 LYS cc_start: 0.7973 (mmmt) cc_final: 0.7721 (mmmt) outliers start: 15 outliers final: 9 residues processed: 186 average time/residue: 0.0714 time to fit residues: 17.1536 Evaluate side-chains 183 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 172 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain B residue 105 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 66 optimal weight: 0.0040 chunk 25 optimal weight: 0.9980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN B 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.111374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.099009 restraints weight = 10175.646| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.17 r_work: 0.3115 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6412 Z= 0.180 Angle : 0.553 11.366 8715 Z= 0.280 Chirality : 0.042 0.333 977 Planarity : 0.004 0.032 1092 Dihedral : 11.382 62.623 950 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.15 % Allowed : 17.24 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.52 (0.30), residues: 766 helix: 0.73 (0.30), residues: 304 sheet: -0.22 (0.46), residues: 136 loop : -1.40 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 107 TYR 0.014 0.001 TYR A 578 PHE 0.017 0.002 PHE A 66 TRP 0.009 0.001 TRP A 458 HIS 0.004 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 ( 6411) covalent geometry : angle 0.55344 / 0.28 ( 8715) hydrogen bonds : bond 0.04032 / 2.60 ( 250) hydrogen bonds : angle 4.26588 / 2.93 ( 702) Misc. bond : bond 0.00051 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8341 (m) REVERT: A 9 GLU cc_start: 0.7366 (tt0) cc_final: 0.7160 (tt0) REVERT: A 30 LYS cc_start: 0.8580 (mppt) cc_final: 0.8373 (mppt) REVERT: A 100 LYS cc_start: 0.8090 (mttp) cc_final: 0.7862 (mtmt) REVERT: A 171 ASP cc_start: 0.7510 (m-30) cc_final: 0.7274 (m-30) REVERT: A 240 TYR cc_start: 0.7886 (m-10) cc_final: 0.7541 (m-10) REVERT: A 258 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7344 (m-30) REVERT: A 349 ASP cc_start: 0.7762 (t0) cc_final: 0.7357 (t0) REVERT: A 393 MET cc_start: 0.8262 (mmm) cc_final: 0.7937 (mtt) REVERT: A 482 LYS cc_start: 0.7903 (ptmt) cc_final: 0.7514 (ptmt) REVERT: A 483 MET cc_start: 0.7932 (mpp) cc_final: 0.7406 (mpp) REVERT: A 552 ASP cc_start: 0.8066 (t0) cc_final: 0.7833 (t0) REVERT: A 597 VAL cc_start: 0.8872 (OUTLIER) cc_final: 0.8634 (p) REVERT: B 22 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7478 (mp0) REVERT: B 120 ASN cc_start: 0.8048 (p0) cc_final: 0.7793 (p0) REVERT: B 136 LYS cc_start: 0.7942 (mmmt) cc_final: 0.7648 (mmmt) outliers start: 21 outliers final: 14 residues processed: 185 average time/residue: 0.0702 time to fit residues: 16.4960 Evaluate side-chains 191 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 12 optimal weight: 0.0670 chunk 29 optimal weight: 0.1980 chunk 75 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN B 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.111969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.099648 restraints weight = 10073.141| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.16 r_work: 0.3122 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6412 Z= 0.141 Angle : 0.524 8.518 8715 Z= 0.266 Chirality : 0.040 0.234 977 Planarity : 0.004 0.030 1092 Dihedral : 11.185 62.894 950 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.85 % Allowed : 18.29 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.49 (0.30), residues: 766 helix: 0.79 (0.30), residues: 304 sheet: -0.27 (0.47), residues: 130 loop : -1.38 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 524 TYR 0.012 0.001 TYR A 411 PHE 0.014 0.001 PHE A 66 TRP 0.007 0.001 TRP A 458 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 6411) covalent geometry : angle 0.52432 / 0.27 ( 8715) hydrogen bonds : bond 0.03782 / 2.43 ( 250) hydrogen bonds : angle 4.20475 / 2.89 ( 702) Misc. bond : bond 0.00080 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: A 7 VAL cc_start: 0.8536 (OUTLIER) cc_final: 0.8332 (m) REVERT: A 30 LYS cc_start: 0.8573 (mppt) cc_final: 0.8361 (mppt) REVERT: A 171 ASP cc_start: 0.7507 (m-30) cc_final: 0.7278 (m-30) REVERT: A 240 TYR cc_start: 0.7765 (m-10) cc_final: 0.7494 (m-10) REVERT: A 258 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7361 (m-30) REVERT: A 349 ASP cc_start: 0.7758 (t0) cc_final: 0.7354 (t0) REVERT: A 393 MET cc_start: 0.8249 (mmm) cc_final: 0.7895 (mtt) REVERT: A 482 LYS cc_start: 0.7896 (ptmt) cc_final: 0.7505 (ptmt) REVERT: A 483 MET cc_start: 0.7902 (mpp) cc_final: 0.7375 (mpp) REVERT: A 552 ASP cc_start: 0.8084 (t0) cc_final: 0.7849 (t0) REVERT: A 597 VAL cc_start: 0.8867 (p) cc_final: 0.8645 (p) REVERT: B 22 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7474 (mp0) REVERT: B 120 ASN cc_start: 0.8040 (p0) cc_final: 0.7782 (p0) REVERT: B 136 LYS cc_start: 0.7903 (mmmt) cc_final: 0.7587 (mmmt) outliers start: 19 outliers final: 13 residues processed: 179 average time/residue: 0.0659 time to fit residues: 15.2311 Evaluate side-chains 187 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 158 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 28 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 37 optimal weight: 0.0040 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN B 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.111009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.097935 restraints weight = 10131.374| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.33 r_work: 0.3081 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6412 Z= 0.167 Angle : 0.529 8.126 8715 Z= 0.272 Chirality : 0.041 0.186 977 Planarity : 0.004 0.031 1092 Dihedral : 10.999 64.912 950 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.40 % Allowed : 18.89 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.53 (0.30), residues: 766 helix: 0.74 (0.30), residues: 304 sheet: -0.26 (0.46), residues: 136 loop : -1.41 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 524 TYR 0.013 0.001 TYR A 578 PHE 0.017 0.002 PHE A 66 TRP 0.007 0.001 TRP A 458 HIS 0.003 0.001 HIS A 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 6411) covalent geometry : angle 0.52898 / 0.27 ( 8715) hydrogen bonds : bond 0.03874 / 2.48 ( 250) hydrogen bonds : angle 4.21697 / 2.90 ( 702) Misc. bond : bond 0.00063 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8653 (mppt) cc_final: 0.8420 (mppt) REVERT: A 100 LYS cc_start: 0.7999 (mttp) cc_final: 0.7765 (mtmt) REVERT: A 171 ASP cc_start: 0.7500 (m-30) cc_final: 0.7285 (m-30) REVERT: A 240 TYR cc_start: 0.7829 (m-10) cc_final: 0.7488 (m-10) REVERT: A 258 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7320 (m-30) REVERT: A 343 HIS cc_start: 0.8251 (t-170) cc_final: 0.7813 (t-170) REVERT: A 349 ASP cc_start: 0.7832 (t0) cc_final: 0.7408 (t0) REVERT: A 393 MET cc_start: 0.8195 (mmm) cc_final: 0.7850 (mtt) REVERT: A 482 LYS cc_start: 0.7918 (ptmt) cc_final: 0.7507 (ptmt) REVERT: A 483 MET cc_start: 0.7929 (mpp) cc_final: 0.7432 (mpp) REVERT: A 552 ASP cc_start: 0.8201 (t0) cc_final: 0.7907 (t0) REVERT: A 597 VAL cc_start: 0.8879 (p) cc_final: 0.8659 (p) REVERT: B 22 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7559 (mp0) REVERT: B 120 ASN cc_start: 0.8080 (p0) cc_final: 0.7831 (p0) REVERT: B 136 LYS cc_start: 0.7932 (mmmt) cc_final: 0.7613 (mmmt) outliers start: 16 outliers final: 11 residues processed: 181 average time/residue: 0.0691 time to fit residues: 16.0675 Evaluate side-chains 186 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 158 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 58 optimal weight: 1.9990 chunk 3 optimal weight: 0.0980 chunk 37 optimal weight: 0.0470 chunk 59 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN B 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.111668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.098540 restraints weight = 10134.722| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.33 r_work: 0.3087 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6412 Z= 0.137 Angle : 0.546 12.857 8715 Z= 0.273 Chirality : 0.042 0.374 977 Planarity : 0.004 0.030 1092 Dihedral : 10.856 64.962 950 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.15 % Allowed : 18.74 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.57 (0.30), residues: 766 helix: 0.75 (0.30), residues: 304 sheet: -0.40 (0.47), residues: 130 loop : -1.41 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 524 TYR 0.012 0.001 TYR A 578 PHE 0.015 0.002 PHE A 66 TRP 0.007 0.001 TRP A 458 HIS 0.002 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 6411) covalent geometry : angle 0.54550 / 0.27 ( 8715) hydrogen bonds : bond 0.03713 / 2.39 ( 250) hydrogen bonds : angle 4.22109 / 2.89 ( 702) Misc. bond : bond 0.00058 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8643 (mppt) cc_final: 0.8407 (mppt) REVERT: A 52 PHE cc_start: 0.8115 (m-80) cc_final: 0.7899 (t80) REVERT: A 100 LYS cc_start: 0.8008 (mttp) cc_final: 0.7767 (mtmt) REVERT: A 171 ASP cc_start: 0.7505 (m-30) cc_final: 0.7270 (m-30) REVERT: A 240 TYR cc_start: 0.7742 (m-10) cc_final: 0.7435 (m-10) REVERT: A 258 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7342 (m-30) REVERT: A 349 ASP cc_start: 0.7836 (t0) cc_final: 0.7404 (t0) REVERT: A 393 MET cc_start: 0.8183 (mmm) cc_final: 0.7838 (mtt) REVERT: A 424 CYS cc_start: 0.8412 (t) cc_final: 0.8164 (t) REVERT: A 482 LYS cc_start: 0.7901 (ptmt) cc_final: 0.7490 (ptmt) REVERT: A 483 MET cc_start: 0.7922 (mpp) cc_final: 0.7421 (mpp) REVERT: A 552 ASP cc_start: 0.8189 (t0) cc_final: 0.7897 (t0) REVERT: A 597 VAL cc_start: 0.8876 (OUTLIER) cc_final: 0.8659 (p) REVERT: B 22 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7565 (mp0) REVERT: B 120 ASN cc_start: 0.8066 (p0) cc_final: 0.7823 (p0) REVERT: B 136 LYS cc_start: 0.7905 (mmmt) cc_final: 0.7612 (mmmt) outliers start: 21 outliers final: 13 residues processed: 187 average time/residue: 0.0698 time to fit residues: 16.8262 Evaluate side-chains 188 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 158 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 0.0980 chunk 27 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 76 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.0870 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN B 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.111948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.098837 restraints weight = 10063.650| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.32 r_work: 0.3097 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6412 Z= 0.127 Angle : 0.531 11.626 8715 Z= 0.266 Chirality : 0.041 0.316 977 Planarity : 0.004 0.029 1092 Dihedral : 10.718 65.117 950 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.40 % Allowed : 20.09 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.52 (0.30), residues: 766 helix: 0.78 (0.30), residues: 304 sheet: -0.36 (0.47), residues: 129 loop : -1.38 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 524 TYR 0.013 0.001 TYR A 41 PHE 0.014 0.001 PHE A 66 TRP 0.006 0.001 TRP A 458 HIS 0.002 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 6411) covalent geometry : angle 0.53141 / 0.27 ( 8715) hydrogen bonds : bond 0.03588 / 2.30 ( 250) hydrogen bonds : angle 4.24098 / 2.92 ( 702) Misc. bond : bond 0.00038 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8646 (mppt) cc_final: 0.8402 (mppt) REVERT: A 52 PHE cc_start: 0.8166 (m-80) cc_final: 0.7545 (t80) REVERT: A 171 ASP cc_start: 0.7477 (m-30) cc_final: 0.7221 (m-30) REVERT: A 240 TYR cc_start: 0.7703 (m-10) cc_final: 0.7415 (m-10) REVERT: A 258 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7320 (m-30) REVERT: A 349 ASP cc_start: 0.7843 (t0) cc_final: 0.7432 (t0) REVERT: A 393 MET cc_start: 0.8188 (mmm) cc_final: 0.7832 (mtt) REVERT: A 482 LYS cc_start: 0.7909 (ptmt) cc_final: 0.7500 (ptmt) REVERT: A 483 MET cc_start: 0.7959 (mpp) cc_final: 0.7459 (mpp) REVERT: A 552 ASP cc_start: 0.8195 (t0) cc_final: 0.7900 (t0) REVERT: A 597 VAL cc_start: 0.8858 (OUTLIER) cc_final: 0.8628 (p) REVERT: B 22 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7519 (mp0) REVERT: B 120 ASN cc_start: 0.8063 (p0) cc_final: 0.7812 (p0) outliers start: 16 outliers final: 11 residues processed: 177 average time/residue: 0.0742 time to fit residues: 16.8880 Evaluate side-chains 185 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 158 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 1 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 0.0770 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 7 optimal weight: 0.2980 chunk 22 optimal weight: 0.1980 overall best weight: 0.2938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN B 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.112865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.099703 restraints weight = 10024.506| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.32 r_work: 0.3114 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6412 Z= 0.113 Angle : 0.523 11.398 8715 Z= 0.262 Chirality : 0.040 0.316 977 Planarity : 0.004 0.029 1092 Dihedral : 10.678 64.981 950 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.10 % Allowed : 20.69 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.51 (0.30), residues: 766 helix: 0.81 (0.30), residues: 304 sheet: -0.50 (0.47), residues: 126 loop : -1.32 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 524 TYR 0.012 0.001 TYR A 411 PHE 0.013 0.001 PHE A 52 TRP 0.006 0.001 TRP A 458 HIS 0.002 0.000 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 6411) covalent geometry : angle 0.52286 / 0.26 ( 8715) hydrogen bonds : bond 0.03480 / 2.24 ( 250) hydrogen bonds : angle 4.21374 / 2.89 ( 702) Misc. bond : bond 0.00032 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1334.73 seconds wall clock time: 23 minutes 28.66 seconds (1408.66 seconds total)