Starting phenix.real_space_refine on Thu Jul 2 03:15:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ca0_45378/07_2026/9ca0_45378_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ca0_45378/07_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_45378/07_2026/9ca0_45378_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ca0_45378/07_2026/9ca0_45378_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ca0_45378/07_2026/9ca0_45378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ca0_45378/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 1 Time building chain proxies: 1.47, per 1000 atoms: 0.23 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: 0.58 Conformation dependent library (CDL) restraints added in 339.5 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: 0.63 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: 1.02 Time building geometry restraints manager: 0.77 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 3.060 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: 3.290 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: 0.020 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.620 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.120 ------------------------------------------------------------------------------- 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 : 0.582 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 0.58234 / 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 : 0.228 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: 0.0896 time to fit residues: 21.9042 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 : 0.218 ------------------------------------------------------------------------------- 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: 0.0270 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: 0.4838 ------------------------------------------------------------------------------- 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** A 415 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.113008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.100910 restraints weight = 10120.701| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.17 r_work: 0.3143 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6412 Z= 0.161 Angle : 0.557 7.336 8715 Z= 0.292 Chirality : 0.041 0.211 977 Planarity : 0.004 0.028 1092 Dihedral : 11.537 59.466 954 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.05 % Allowed : 11.09 % Favored : 87.86 % 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: -0.60 (0.29), residues: 766 helix: 0.59 (0.29), residues: 302 sheet: -0.09 (0.47), residues: 132 loop : -1.45 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 524 TYR 0.014 0.001 TYR A 411 PHE 0.014 0.002 PHE A 265 TRP 0.008 0.001 TRP A 458 HIS 0.004 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 6411) covalent geometry : angle 0.55735 / 0.29 ( 8715) hydrogen bonds : bond 0.04876 / 3.25 ( 250) hydrogen bonds : angle 4.44485 / 3.08 ( 702) Misc. bond : bond 0.00181 / 0.10 ( 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 187 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 180 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8530 (mppt) cc_final: 0.8275 (mppt) REVERT: A 51 ARG cc_start: 0.8094 (ttp-170) cc_final: 0.7879 (ttp80) REVERT: A 171 ASP cc_start: 0.7441 (m-30) cc_final: 0.7218 (m-30) REVERT: A 214 PHE cc_start: 0.8614 (t80) cc_final: 0.8355 (t80) REVERT: A 240 TYR cc_start: 0.7741 (m-10) cc_final: 0.7536 (m-10) REVERT: A 285 VAL cc_start: 0.8922 (t) cc_final: 0.8570 (p) REVERT: A 349 ASP cc_start: 0.7767 (t0) cc_final: 0.7341 (t0) REVERT: A 393 MET cc_start: 0.8282 (mmm) cc_final: 0.7844 (mtt) REVERT: A 482 LYS cc_start: 0.7881 (ptmt) cc_final: 0.7536 (ptmt) REVERT: A 483 MET cc_start: 0.7968 (mpp) cc_final: 0.7389 (mpp) REVERT: A 552 ASP cc_start: 0.8102 (t0) cc_final: 0.7847 (t0) REVERT: A 597 VAL cc_start: 0.8911 (p) cc_final: 0.8704 (p) REVERT: B 22 GLU cc_start: 0.8064 (mp0) cc_final: 0.7266 (mp0) outliers start: 7 outliers final: 2 residues processed: 183 average time/residue: 0.0835 time to fit residues: 19.6755 Evaluate side-chains 174 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 172 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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: 0.9980 chunk 73 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3433 r_free = 0.3433 target = 0.111760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.099508 restraints weight = 9993.088| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.15 r_work: 0.3121 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6412 Z= 0.193 Angle : 0.539 7.294 8715 Z= 0.283 Chirality : 0.041 0.138 977 Planarity : 0.004 0.031 1092 Dihedral : 11.445 59.772 950 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.80 % Allowed : 13.49 % Favored : 84.71 % 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: -0.52 (0.30), residues: 766 helix: 0.77 (0.30), residues: 301 sheet: -0.19 (0.46), residues: 137 loop : -1.45 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 524 TYR 0.016 0.002 TYR A 578 PHE 0.017 0.002 PHE A 265 TRP 0.008 0.001 TRP A 458 HIS 0.004 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 ( 6411) covalent geometry : angle 0.53864 / 0.28 ( 8715) hydrogen bonds : bond 0.04507 / 2.91 ( 250) hydrogen bonds : angle 4.31296 / 2.97 ( 702) Misc. bond : bond 0.00366 / 0.19 ( 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 190 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 178 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8537 (mppt) cc_final: 0.8295 (mppt) REVERT: A 98 MET cc_start: 0.7914 (mmm) cc_final: 0.7609 (tmm) REVERT: A 171 ASP cc_start: 0.7490 (m-30) cc_final: 0.7264 (m-30) REVERT: A 240 TYR cc_start: 0.7869 (m-10) cc_final: 0.7556 (m-10) REVERT: A 258 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7301 (m-30) REVERT: A 285 VAL cc_start: 0.8930 (t) cc_final: 0.8588 (p) REVERT: A 349 ASP cc_start: 0.7781 (t0) cc_final: 0.7342 (t0) REVERT: A 393 MET cc_start: 0.8259 (mmm) cc_final: 0.7904 (mtt) REVERT: A 482 LYS cc_start: 0.7941 (ptmt) cc_final: 0.7581 (ptmt) REVERT: A 483 MET cc_start: 0.7958 (mpp) cc_final: 0.7400 (mpp) REVERT: A 551 ILE cc_start: 0.8489 (mm) cc_final: 0.8272 (mm) REVERT: A 552 ASP cc_start: 0.8082 (t0) cc_final: 0.7851 (t0) REVERT: A 597 VAL cc_start: 0.8880 (p) cc_final: 0.8645 (p) REVERT: B 120 ASN cc_start: 0.8034 (p0) cc_final: 0.7776 (p0) REVERT: B 136 LYS cc_start: 0.8006 (mmmt) cc_final: 0.7703 (mmmt) outliers start: 12 outliers final: 5 residues processed: 182 average time/residue: 0.0951 time to fit residues: 22.1462 Evaluate side-chains 175 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 169 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 494 LEU 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: 0.8980 chunk 3 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 52 optimal weight: 0.3980 chunk 12 optimal weight: 0.3980 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 63 optimal weight: 0.0370 chunk 22 optimal weight: 0.6980 overall best weight: 0.4458 ------------------------------------------------------------------------------- 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 = 0.3442 r_free = 0.3442 target = 0.112313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.099946 restraints weight = 10056.804| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.17 r_work: 0.3130 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6412 Z= 0.140 Angle : 0.518 9.510 8715 Z= 0.268 Chirality : 0.040 0.194 977 Planarity : 0.004 0.029 1092 Dihedral : 11.411 60.931 950 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.70 % Allowed : 14.09 % Favored : 83.21 % 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: -0.45 (0.30), residues: 766 helix: 0.84 (0.30), residues: 302 sheet: -0.21 (0.47), residues: 130 loop : -1.38 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 524 TYR 0.014 0.001 TYR A 578 PHE 0.013 0.001 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 0.00317 / 0.14 ( 6411) covalent geometry : angle 0.51787 / 0.27 ( 8715) hydrogen bonds : bond 0.04000 / 2.59 ( 250) hydrogen bonds : angle 4.23556 / 2.92 ( 702) Misc. bond : bond 0.00006 / 0.00 ( 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 194 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: A 7 VAL cc_start: 0.8559 (OUTLIER) cc_final: 0.8301 (m) REVERT: A 30 LYS cc_start: 0.8539 (mppt) cc_final: 0.8317 (mppt) REVERT: A 98 MET cc_start: 0.7932 (mmm) cc_final: 0.7566 (tmm) REVERT: A 171 ASP cc_start: 0.7472 (m-30) cc_final: 0.7236 (m-30) REVERT: A 240 TYR cc_start: 0.7790 (m-10) cc_final: 0.7503 (m-10) REVERT: A 258 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7298 (m-30) REVERT: A 272 MET cc_start: 0.7474 (tmm) cc_final: 0.7201 (tmm) REVERT: A 285 VAL cc_start: 0.8917 (t) cc_final: 0.8583 (p) REVERT: A 349 ASP cc_start: 0.7767 (t0) cc_final: 0.7323 (t0) REVERT: A 393 MET cc_start: 0.8260 (mmm) cc_final: 0.7912 (mtt) REVERT: A 482 LYS cc_start: 0.7923 (ptmt) cc_final: 0.7566 (ptmt) REVERT: A 483 MET cc_start: 0.7950 (mpp) cc_final: 0.7400 (mpp) REVERT: A 498 GLU cc_start: 0.7950 (tt0) cc_final: 0.7722 (mt-10) REVERT: A 551 ILE cc_start: 0.8496 (mm) cc_final: 0.8277 (mm) REVERT: A 552 ASP cc_start: 0.8029 (t0) cc_final: 0.7800 (t0) REVERT: A 597 VAL cc_start: 0.8880 (p) cc_final: 0.8640 (p) REVERT: B 22 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7473 (mp0) REVERT: B 120 ASN cc_start: 0.8024 (p0) cc_final: 0.7759 (p0) REVERT: B 136 LYS cc_start: 0.7965 (mmmt) cc_final: 0.7706 (mmmt) outliers start: 18 outliers final: 9 residues processed: 182 average time/residue: 0.0803 time to fit residues: 18.7131 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 : 0.213 ------------------------------------------------------------------------------- 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 430 THR 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: 1.9990 chunk 8 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 59 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3429 r_free = 0.3429 target = 0.111424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.099085 restraints weight = 10168.764| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.17 r_work: 0.3116 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1505 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= 0.192 Angle : 0.540 11.476 8715 Z= 0.276 Chirality : 0.041 0.142 977 Planarity : 0.004 0.032 1092 Dihedral : 11.423 61.738 950 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.30 % Allowed : 15.74 % Favored : 80.96 % 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: -0.46 (0.30), residues: 766 helix: 0.81 (0.30), residues: 302 sheet: -0.20 (0.46), residues: 136 loop : -1.40 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 524 TYR 0.014 0.002 TYR A 578 PHE 0.018 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 0.00443 / 0.19 ( 6411) covalent geometry : angle 0.54020 / 0.28 ( 8715) hydrogen bonds : bond 0.04103 / 2.63 ( 250) hydrogen bonds : angle 4.25376 / 2.93 ( 702) Misc. bond : bond 0.00142 / 0.07 ( 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 199 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 7 VAL cc_start: 0.8569 (OUTLIER) cc_final: 0.8315 (m) REVERT: A 30 LYS cc_start: 0.8545 (mppt) cc_final: 0.8334 (mppt) REVERT: A 171 ASP cc_start: 0.7471 (m-30) cc_final: 0.7243 (m-30) REVERT: A 240 TYR cc_start: 0.7880 (m-10) cc_final: 0.7554 (m-10) REVERT: A 258 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7315 (m-30) REVERT: A 272 MET cc_start: 0.7499 (tmm) cc_final: 0.7208 (tmm) REVERT: A 349 ASP cc_start: 0.7782 (t0) cc_final: 0.7366 (t0) REVERT: A 393 MET cc_start: 0.8295 (mmm) cc_final: 0.7967 (mtt) REVERT: A 482 LYS cc_start: 0.7908 (ptmt) cc_final: 0.7539 (ptmt) REVERT: A 483 MET cc_start: 0.7961 (mpp) cc_final: 0.7437 (mpp) REVERT: A 498 GLU cc_start: 0.7995 (tt0) cc_final: 0.7770 (mt-10) REVERT: A 552 ASP cc_start: 0.8058 (t0) cc_final: 0.7826 (t0) REVERT: A 597 VAL cc_start: 0.8891 (p) cc_final: 0.8645 (p) REVERT: B 22 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7494 (mp0) REVERT: B 120 ASN cc_start: 0.8007 (p0) cc_final: 0.7749 (p0) REVERT: B 136 LYS cc_start: 0.7995 (mmmt) cc_final: 0.7748 (mmmt) outliers start: 22 outliers final: 14 residues processed: 183 average time/residue: 0.0974 time to fit residues: 22.7696 Evaluate side-chains 194 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 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 430 THR 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 Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 66 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3416 r_free = 0.3416 target = 0.110949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.098592 restraints weight = 10172.031| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.18 r_work: 0.3107 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1585 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= 0.190 Angle : 0.560 11.761 8715 Z= 0.282 Chirality : 0.042 0.312 977 Planarity : 0.004 0.035 1092 Dihedral : 11.358 59.617 950 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.00 % Allowed : 17.09 % Favored : 79.91 % 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: 302 sheet: -0.22 (0.46), residues: 136 loop : -1.40 (0.32), residues: 328 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 0.018 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 0.00438 / 0.19 ( 6411) covalent geometry : angle 0.55954 / 0.28 ( 8715) hydrogen bonds : bond 0.04108 / 2.65 ( 250) hydrogen bonds : angle 4.27793 / 2.94 ( 702) Misc. bond : bond 0.00048 / 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 198 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 VAL cc_start: 0.8569 (OUTLIER) cc_final: 0.8304 (m) REVERT: A 30 LYS cc_start: 0.8587 (mppt) cc_final: 0.8385 (mppt) REVERT: A 171 ASP cc_start: 0.7482 (m-30) cc_final: 0.7260 (m-30) REVERT: A 240 TYR cc_start: 0.7909 (m-10) cc_final: 0.7556 (m-10) REVERT: A 258 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7322 (m-30) REVERT: A 349 ASP cc_start: 0.7763 (t0) cc_final: 0.7349 (t0) REVERT: A 393 MET cc_start: 0.8267 (mmm) cc_final: 0.7925 (mtt) REVERT: A 482 LYS cc_start: 0.7922 (ptmt) cc_final: 0.7533 (ptmt) REVERT: A 483 MET cc_start: 0.7939 (mpp) cc_final: 0.7417 (mpp) REVERT: A 498 GLU cc_start: 0.8001 (tt0) cc_final: 0.7794 (mt-10) REVERT: A 552 ASP cc_start: 0.8106 (t0) cc_final: 0.7863 (t0) REVERT: A 597 VAL cc_start: 0.8880 (p) cc_final: 0.8632 (p) REVERT: B 22 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7559 (mp0) REVERT: B 45 LEU cc_start: 0.8570 (tp) cc_final: 0.8369 (tp) REVERT: B 120 ASN cc_start: 0.8042 (p0) cc_final: 0.7788 (p0) REVERT: B 136 LYS cc_start: 0.7951 (mmmt) cc_final: 0.7661 (mmmt) outliers start: 20 outliers final: 14 residues processed: 185 average time/residue: 0.0929 time to fit residues: 22.0783 Evaluate side-chains 190 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 255 LEU 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 421 SER 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 Chi-restraints excluded: chain B residue 141 LEU 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: 0.8980 chunk 70 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3417 r_free = 0.3417 target = 0.110897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.098495 restraints weight = 10087.034| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.15 r_work: 0.3107 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6412 Z= 0.193 Angle : 0.556 8.160 8715 Z= 0.284 Chirality : 0.042 0.244 977 Planarity : 0.004 0.034 1092 Dihedral : 11.322 59.160 950 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.45 % Allowed : 16.94 % 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: -0.56 (0.30), residues: 766 helix: 0.70 (0.30), residues: 304 sheet: -0.24 (0.46), residues: 136 loop : -1.44 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 524 TYR 0.014 0.002 TYR A 578 PHE 0.019 0.002 PHE A 66 TRP 0.009 0.001 TRP A 458 HIS 0.004 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 ( 6411) covalent geometry : angle 0.55584 / 0.28 ( 8715) hydrogen bonds : bond 0.04097 / 2.63 ( 250) hydrogen bonds : angle 4.27137 / 2.94 ( 702) Misc. bond : bond 0.00075 / 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 199 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 VAL cc_start: 0.8585 (OUTLIER) cc_final: 0.8333 (m) REVERT: A 30 LYS cc_start: 0.8589 (mppt) cc_final: 0.8376 (mppt) REVERT: A 171 ASP cc_start: 0.7490 (m-30) cc_final: 0.7270 (m-30) REVERT: A 240 TYR cc_start: 0.7912 (m-10) cc_final: 0.7538 (m-10) REVERT: A 258 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7309 (m-30) REVERT: A 349 ASP cc_start: 0.7799 (t0) cc_final: 0.7382 (t0) REVERT: A 393 MET cc_start: 0.8285 (mmm) cc_final: 0.7947 (mtt) REVERT: A 482 LYS cc_start: 0.7925 (ptmt) cc_final: 0.7536 (ptmt) REVERT: A 483 MET cc_start: 0.7913 (mpp) cc_final: 0.7412 (mpp) REVERT: A 498 GLU cc_start: 0.7985 (tt0) cc_final: 0.7772 (mt-10) REVERT: A 552 ASP cc_start: 0.8109 (t0) cc_final: 0.7860 (t0) REVERT: A 597 VAL cc_start: 0.8865 (OUTLIER) cc_final: 0.8647 (p) REVERT: B 22 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7559 (mp0) REVERT: B 120 ASN cc_start: 0.8039 (p0) cc_final: 0.7782 (p0) REVERT: B 136 LYS cc_start: 0.7934 (mmmt) cc_final: 0.7649 (mmmt) outliers start: 23 outliers final: 17 residues processed: 183 average time/residue: 0.0928 time to fit residues: 21.7420 Evaluate side-chains 194 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 60 HIS 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 387 HIS Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 430 THR 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 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: 1.9990 chunk 66 optimal weight: 0.0040 chunk 44 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 65 optimal weight: 0.0470 chunk 45 optimal weight: 0.1980 chunk 69 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 37 optimal weight: 0.0020 overall best weight: 0.1698 ------------------------------------------------------------------------------- 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 = 0.3434 r_free = 0.3434 target = 0.112608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.099460 restraints weight = 10086.640| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.34 r_work: 0.3105 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6412 Z= 0.102 Angle : 0.510 8.453 8715 Z= 0.259 Chirality : 0.039 0.189 977 Planarity : 0.004 0.029 1092 Dihedral : 10.879 59.371 950 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.55 % Allowed : 19.04 % Favored : 78.41 % 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: -0.46 (0.30), residues: 766 helix: 0.80 (0.30), residues: 304 sheet: -0.35 (0.47), residues: 126 loop : -1.29 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 524 TYR 0.014 0.001 TYR A 411 PHE 0.010 0.001 PHE A 66 TRP 0.007 0.001 TRP A 458 HIS 0.002 0.000 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 6411) covalent geometry : angle 0.50973 / 0.26 ( 8715) hydrogen bonds : bond 0.03486 / 2.26 ( 250) hydrogen bonds : angle 4.13789 / 2.83 ( 702) Misc. bond : bond 0.00028 / 0.01 ( 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: 17 poor density : 175 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8634 (mppt) cc_final: 0.8401 (mppt) REVERT: A 171 ASP cc_start: 0.7446 (m-30) cc_final: 0.7223 (m-30) REVERT: A 240 TYR cc_start: 0.7629 (m-10) cc_final: 0.7377 (m-10) REVERT: A 258 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7328 (m-30) REVERT: A 272 MET cc_start: 0.7427 (tmm) cc_final: 0.7183 (tmm) REVERT: A 349 ASP cc_start: 0.7809 (t0) cc_final: 0.7380 (t0) REVERT: A 393 MET cc_start: 0.8156 (mmm) cc_final: 0.7794 (mtt) REVERT: A 482 LYS cc_start: 0.7937 (ptmt) cc_final: 0.7538 (ptmt) REVERT: A 483 MET cc_start: 0.7932 (mpp) cc_final: 0.7405 (mpp) REVERT: A 498 GLU cc_start: 0.7811 (tt0) cc_final: 0.7597 (mt-10) REVERT: A 552 ASP cc_start: 0.8171 (t0) cc_final: 0.7881 (t0) REVERT: A 597 VAL cc_start: 0.8856 (OUTLIER) cc_final: 0.8637 (p) REVERT: B 22 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7533 (mp0) REVERT: B 120 ASN cc_start: 0.8080 (p0) cc_final: 0.7831 (p0) outliers start: 17 outliers final: 11 residues processed: 178 average time/residue: 0.0919 time to fit residues: 20.9882 Evaluate side-chains 187 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 174 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 62 MET 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 430 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 145 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 58 optimal weight: 0.8980 chunk 3 optimal weight: 0.0980 chunk 37 optimal weight: 0.0030 chunk 59 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- 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 = 0.3416 r_free = 0.3416 target = 0.111391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.098326 restraints weight = 10144.566| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.34 r_work: 0.3087 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6412 Z= 0.139 Angle : 0.531 12.495 8715 Z= 0.267 Chirality : 0.042 0.376 977 Planarity : 0.004 0.052 1092 Dihedral : 10.764 59.433 950 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.80 % Allowed : 20.69 % 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: -0.46 (0.30), residues: 766 helix: 0.80 (0.30), residues: 304 sheet: -0.31 (0.47), residues: 129 loop : -1.31 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 524 TYR 0.012 0.001 TYR A 578 PHE 0.014 0.002 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 0.00322 / 0.14 ( 6411) covalent geometry : angle 0.53148 / 0.27 ( 8715) hydrogen bonds : bond 0.03634 / 2.33 ( 250) hydrogen bonds : angle 4.16645 / 2.85 ( 702) Misc. bond : bond 0.00038 / 0.02 ( 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 187 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8630 (mppt) cc_final: 0.8396 (mppt) REVERT: A 100 LYS cc_start: 0.8007 (mttp) cc_final: 0.7765 (mtmt) REVERT: A 171 ASP cc_start: 0.7476 (m-30) cc_final: 0.7232 (m-30) REVERT: A 240 TYR cc_start: 0.7708 (m-10) cc_final: 0.7427 (m-10) REVERT: A 258 ASP cc_start: 0.7716 (OUTLIER) cc_final: 0.7346 (m-30) REVERT: A 272 MET cc_start: 0.7470 (tmm) cc_final: 0.7202 (tmm) REVERT: A 349 ASP cc_start: 0.7825 (t0) cc_final: 0.7392 (t0) REVERT: A 393 MET cc_start: 0.8181 (mmm) cc_final: 0.7801 (mtt) REVERT: A 482 LYS cc_start: 0.7933 (ptmt) cc_final: 0.7527 (ptmt) REVERT: A 483 MET cc_start: 0.7965 (mpp) cc_final: 0.7441 (mpp) REVERT: A 498 GLU cc_start: 0.7851 (tt0) cc_final: 0.7582 (mt-10) REVERT: A 552 ASP cc_start: 0.8188 (t0) cc_final: 0.7898 (t0) REVERT: A 597 VAL cc_start: 0.8854 (OUTLIER) cc_final: 0.8631 (p) REVERT: B 22 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7555 (mp0) REVERT: B 120 ASN cc_start: 0.8070 (p0) cc_final: 0.7816 (p0) REVERT: B 136 LYS cc_start: 0.7874 (mmmt) cc_final: 0.7531 (mmmt) outliers start: 12 outliers final: 9 residues processed: 177 average time/residue: 0.0998 time to fit residues: 22.4797 Evaluate side-chains 184 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 173 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 60 HIS 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 387 HIS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain B residue 145 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.111205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.098116 restraints weight = 10057.617| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.32 r_work: 0.3085 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6412 Z= 0.165 Angle : 0.550 11.437 8715 Z= 0.277 Chirality : 0.042 0.327 977 Planarity : 0.004 0.045 1092 Dihedral : 10.739 59.691 950 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % 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: 0.77 (0.30), residues: 304 sheet: -0.41 (0.46), residues: 130 loop : -1.35 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 524 TYR 0.013 0.001 TYR A 578 PHE 0.018 0.002 PHE A 66 TRP 0.006 0.001 TRP A 458 HIS 0.003 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 ( 6411) covalent geometry : angle 0.55003 / 0.28 ( 8715) hydrogen bonds : bond 0.03804 / 2.44 ( 250) hydrogen bonds : angle 4.20519 / 2.88 ( 702) Misc. bond : bond 0.00061 / 0.03 ( 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 195 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8641 (mppt) cc_final: 0.8406 (mppt) REVERT: A 52 PHE cc_start: 0.8244 (m-80) cc_final: 0.7765 (t80) REVERT: A 100 LYS cc_start: 0.8007 (mttp) cc_final: 0.7771 (mtmt) REVERT: A 171 ASP cc_start: 0.7497 (m-30) cc_final: 0.7240 (m-30) REVERT: A 240 TYR cc_start: 0.7799 (m-10) cc_final: 0.7468 (m-10) REVERT: A 258 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7334 (m-30) REVERT: A 349 ASP cc_start: 0.7820 (t0) cc_final: 0.7389 (t0) REVERT: A 393 MET cc_start: 0.8182 (mmm) cc_final: 0.7828 (mtt) REVERT: A 424 CYS cc_start: 0.8420 (t) cc_final: 0.8173 (t) REVERT: A 482 LYS cc_start: 0.7949 (ptmt) cc_final: 0.7543 (ptmt) REVERT: A 483 MET cc_start: 0.7982 (mpp) cc_final: 0.7481 (mpp) REVERT: A 498 GLU cc_start: 0.7849 (tt0) cc_final: 0.7638 (mt-10) REVERT: A 552 ASP cc_start: 0.8220 (t0) cc_final: 0.7912 (t0) REVERT: A 597 VAL cc_start: 0.8847 (OUTLIER) cc_final: 0.8625 (p) REVERT: B 120 ASN cc_start: 0.8070 (p0) cc_final: 0.7821 (p0) outliers start: 16 outliers final: 11 residues processed: 184 average time/residue: 0.0951 time to fit residues: 22.4447 Evaluate side-chains 187 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 174 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS 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 255 LEU 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 430 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain B residue 145 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 1 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 19 optimal weight: 0.0980 chunk 47 optimal weight: 0.0010 chunk 71 optimal weight: 0.0670 chunk 33 optimal weight: 0.9990 chunk 69 optimal weight: 0.0030 chunk 20 optimal weight: 0.4980 chunk 7 optimal weight: 0.0980 chunk 22 optimal weight: 0.3980 overall best weight: 0.0534 ------------------------------------------------------------------------------- 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 = 0.3459 r_free = 0.3459 target = 0.114210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.101435 restraints weight = 10097.398| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.29 r_work: 0.3134 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6412 Z= 0.095 Angle : 0.518 11.430 8715 Z= 0.261 Chirality : 0.040 0.333 977 Planarity : 0.004 0.044 1092 Dihedral : 10.598 59.630 950 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.25 % Allowed : 20.99 % Favored : 76.76 % 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: -0.40 (0.30), residues: 766 helix: 0.86 (0.30), residues: 304 sheet: -0.42 (0.48), residues: 125 loop : -1.23 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 524 TYR 0.014 0.001 TYR A 41 PHE 0.012 0.001 PHE A 66 TRP 0.006 0.001 TRP A 363 HIS 0.001 0.000 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.10 ( 6411) covalent geometry : angle 0.51849 / 0.26 ( 8715) hydrogen bonds : bond 0.03301 / 2.15 ( 250) hydrogen bonds : angle 4.17721 / 2.86 ( 702) Misc. bond : bond 0.00003 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1724.40 seconds wall clock time: 30 minutes 23.38 seconds (1823.38 seconds total)