Starting phenix.real_space_refine on Fri Aug 22 17:03:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ca0_45378/08_2025/9ca0_45378_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ca0_45378/08_2025/9ca0_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_2025/9ca0_45378_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ca0_45378/08_2025/9ca0_45378_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ca0_45378/08_2025/9ca0_45378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ca0_45378/08_2025/9ca0_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-2.0-5787/lib/python3.9/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: 1.52, per 1000 atoms: 0.24 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: 0.37 Conformation dependent library (CDL) restraints added in 350.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.89 Time building geometry restraints manager: 0.50 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=" C ASP A 386 " pdb=" N HIS A 387 " ideal model delta sigma weight residual 1.331 1.307 0.024 1.48e-02 4.57e+03 2.66e+00 ... (remaining 6406 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 8581 1.96 - 3.92: 111 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=" OH PTR A 336 " pdb=" P PTR A 336 " pdb=" O2P PTR A 336 " ideal model delta sigma weight residual 99.92 109.73 -9.81 3.00e+00 1.11e-01 1.07e+01 angle pdb=" N GLN B 11 " pdb=" CA GLN B 11 " pdb=" CB GLN B 11 " ideal model delta sigma weight residual 110.41 115.56 -5.15 1.68e+00 3.54e-01 9.39e+00 angle pdb=" C SER B 10 " pdb=" N GLN B 11 " pdb=" CA GLN B 11 " ideal model delta sigma weight residual 121.58 115.81 5.77 1.95e+00 2.63e-01 8.75e+00 angle pdb=" CA LEU B 41 " pdb=" CB LEU B 41 " pdb=" CG LEU B 41 " ideal model delta sigma weight residual 116.30 124.78 -8.48 3.50e+00 8.16e-02 5.87e+00 ... (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: 640 0.032 - 0.065: 246 0.065 - 0.097: 53 0.097 - 0.129: 35 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: 4.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.330 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 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= 0.224 Angle : 0.579 9.812 8715 Z= 0.290 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 aren 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 covalent geometry : bond 0.00403 ( 6411) covalent geometry : angle 0.57879 ( 8715) hydrogen bonds : bond 0.19064 ( 250) hydrogen bonds : angle 5.75668 ( 702) Misc. bond : bond 0.08005 ( 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: 0.0945 time to fit residues: 22.7502 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 : 0.236 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3445 r_free = 0.3445 target = 0.112434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.100206 restraints weight = 10102.227| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.16 r_work: 0.3130 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6412 Z= 0.182 Angle : 0.553 7.297 8715 Z= 0.290 Chirality : 0.042 0.199 977 Planarity : 0.004 0.030 1092 Dihedral : 11.494 59.135 954 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.90 % Allowed : 11.24 % 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 aren not related in a simple way. whole: -0.59 (0.30), residues: 766 helix: 0.64 (0.30), residues: 301 sheet: -0.22 (0.48), residues: 131 loop : -1.41 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 524 TYR 0.013 0.002 TYR A 578 PHE 0.016 0.002 PHE A 265 TRP 0.008 0.001 TRP A 458 HIS 0.005 0.001 HIS A 387 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 6411) covalent geometry : angle 0.55294 ( 8715) hydrogen bonds : bond 0.04820 ( 250) hydrogen bonds : angle 4.40163 ( 702) Misc. bond : bond 0.00082 ( 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 190 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 184 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8546 (mppt) cc_final: 0.8290 (mppt) REVERT: A 51 ARG cc_start: 0.8105 (ttp-170) cc_final: 0.7892 (ttp80) REVERT: A 171 ASP cc_start: 0.7477 (m-30) cc_final: 0.7257 (m-30) REVERT: A 240 TYR cc_start: 0.7814 (m-10) cc_final: 0.7537 (m-10) REVERT: A 285 VAL cc_start: 0.8929 (t) cc_final: 0.8585 (p) REVERT: A 349 ASP cc_start: 0.7790 (t0) cc_final: 0.7361 (t0) REVERT: A 393 MET cc_start: 0.8291 (mmm) cc_final: 0.7891 (mtt) REVERT: A 482 LYS cc_start: 0.7908 (ptmt) cc_final: 0.7560 (ptmt) REVERT: A 483 MET cc_start: 0.7954 (mpp) cc_final: 0.7407 (mpp) REVERT: A 552 ASP cc_start: 0.8084 (t0) cc_final: 0.7822 (t0) REVERT: A 597 VAL cc_start: 0.8903 (p) cc_final: 0.8679 (p) REVERT: B 22 GLU cc_start: 0.8032 (mp0) cc_final: 0.7228 (mp0) outliers start: 6 outliers final: 2 residues processed: 185 average time/residue: 0.1007 time to fit residues: 23.6409 Evaluate side-chains 176 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 174 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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: 0.3980 chunk 73 optimal weight: 0.0270 chunk 70 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.112632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.100263 restraints weight = 9978.890| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.16 r_work: 0.3136 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1396 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= 0.142 Angle : 0.505 7.352 8715 Z= 0.264 Chirality : 0.040 0.140 977 Planarity : 0.004 0.030 1092 Dihedral : 11.166 61.530 950 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % 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 aren not related in a simple way. whole: -0.47 (0.30), residues: 766 helix: 0.79 (0.30), residues: 302 sheet: -0.16 (0.48), residues: 129 loop : -1.39 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 524 TYR 0.013 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 320 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 6411) covalent geometry : angle 0.50459 ( 8715) hydrogen bonds : bond 0.03990 ( 250) hydrogen bonds : angle 4.20392 ( 702) Misc. bond : bond 0.00050 ( 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 191 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 179 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8528 (mppt) cc_final: 0.8289 (mppt) REVERT: A 98 MET cc_start: 0.7969 (mmm) cc_final: 0.7574 (tmm) REVERT: A 171 ASP cc_start: 0.7466 (m-30) cc_final: 0.7224 (m-30) REVERT: A 240 TYR cc_start: 0.7774 (m-10) cc_final: 0.7493 (m-10) REVERT: A 258 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7314 (m-30) REVERT: A 272 MET cc_start: 0.7472 (tmm) cc_final: 0.7204 (tmm) REVERT: A 349 ASP cc_start: 0.7771 (t0) cc_final: 0.7337 (t0) REVERT: A 393 MET cc_start: 0.8264 (mmm) cc_final: 0.7906 (mtt) REVERT: A 482 LYS cc_start: 0.7936 (ptmt) cc_final: 0.7551 (ptmt) REVERT: A 483 MET cc_start: 0.7944 (mpp) cc_final: 0.7431 (mpp) REVERT: A 552 ASP cc_start: 0.8028 (t0) cc_final: 0.7804 (t0) REVERT: A 597 VAL cc_start: 0.8864 (p) cc_final: 0.8627 (p) REVERT: B 120 ASN cc_start: 0.8024 (p0) cc_final: 0.7764 (p0) REVERT: B 136 LYS cc_start: 0.7942 (mmmt) cc_final: 0.7656 (mmmt) outliers start: 12 outliers final: 6 residues processed: 181 average time/residue: 0.0996 time to fit residues: 22.8500 Evaluate side-chains 176 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 169 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 387 HIS Chi-restraints excluded: chain A residue 421 SER 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: 0.9980 chunk 3 optimal weight: 0.0370 chunk 73 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 63 optimal weight: 0.3980 chunk 22 optimal weight: 0.2980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3449 r_free = 0.3449 target = 0.112893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.100459 restraints weight = 10032.529| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.17 r_work: 0.3135 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1572 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= 0.134 Angle : 0.496 7.482 8715 Z= 0.257 Chirality : 0.040 0.161 977 Planarity : 0.004 0.031 1092 Dihedral : 10.766 61.275 950 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.15 % Allowed : 15.89 % 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 aren not related in a simple way. whole: -0.41 (0.30), residues: 766 helix: 0.77 (0.30), residues: 305 sheet: -0.13 (0.48), residues: 129 loop : -1.30 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 524 TYR 0.012 0.001 TYR A 578 PHE 0.014 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 covalent geometry : bond 0.00311 ( 6411) covalent geometry : angle 0.49587 ( 8715) hydrogen bonds : bond 0.03724 ( 250) hydrogen bonds : angle 4.11569 ( 702) Misc. bond : bond 0.00047 ( 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 198 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 7 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.8245 (m) REVERT: A 30 LYS cc_start: 0.8532 (mppt) cc_final: 0.8315 (mppt) REVERT: A 98 MET cc_start: 0.7995 (mmm) cc_final: 0.7619 (tmm) REVERT: A 171 ASP cc_start: 0.7479 (m-30) cc_final: 0.7225 (m-30) REVERT: A 240 TYR cc_start: 0.7718 (m-10) cc_final: 0.7453 (m-10) REVERT: A 258 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7335 (m-30) REVERT: A 349 ASP cc_start: 0.7764 (t0) cc_final: 0.7332 (t0) REVERT: A 393 MET cc_start: 0.8281 (mmm) cc_final: 0.7927 (mtt) REVERT: A 482 LYS cc_start: 0.7912 (ptmt) cc_final: 0.7518 (ptmt) REVERT: A 483 MET cc_start: 0.7943 (mpp) cc_final: 0.7433 (mpp) REVERT: A 498 GLU cc_start: 0.7915 (tt0) cc_final: 0.7686 (mt-10) REVERT: A 552 ASP cc_start: 0.8021 (t0) cc_final: 0.7795 (t0) REVERT: A 597 VAL cc_start: 0.8862 (p) cc_final: 0.8631 (p) REVERT: B 22 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7495 (mp0) REVERT: B 120 ASN cc_start: 0.7997 (p0) cc_final: 0.7733 (p0) outliers start: 21 outliers final: 11 residues processed: 182 average time/residue: 0.0976 time to fit residues: 22.5839 Evaluate side-chains 186 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 173 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 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 598 ASP Chi-restraints excluded: chain B residue 105 SER 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: 0.7980 chunk 8 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3410 r_free = 0.3410 target = 0.110499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.098061 restraints weight = 10246.258| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.17 r_work: 0.3100 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 6412 Z= 0.239 Angle : 0.567 11.488 8715 Z= 0.290 Chirality : 0.043 0.153 977 Planarity : 0.004 0.036 1092 Dihedral : 10.805 61.644 950 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.30 % Allowed : 16.79 % 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 aren not related in a simple way. whole: -0.49 (0.30), residues: 766 helix: 0.73 (0.30), residues: 303 sheet: -0.16 (0.46), residues: 136 loop : -1.38 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 524 TYR 0.019 0.002 TYR A 578 PHE 0.021 0.002 PHE A 265 TRP 0.008 0.001 TRP A 458 HIS 0.005 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00555 ( 6411) covalent geometry : angle 0.56666 ( 8715) hydrogen bonds : bond 0.04254 ( 250) hydrogen bonds : angle 4.22107 ( 702) Misc. bond : bond 0.00121 ( 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 203 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8605 (mppt) cc_final: 0.8395 (mppt) REVERT: A 171 ASP cc_start: 0.7516 (m-30) cc_final: 0.7299 (m-30) REVERT: A 240 TYR cc_start: 0.7962 (m-10) cc_final: 0.7582 (m-10) REVERT: A 258 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7394 (m-30) REVERT: A 349 ASP cc_start: 0.7812 (t0) cc_final: 0.7402 (t0) REVERT: A 393 MET cc_start: 0.8300 (mmm) cc_final: 0.7962 (mtt) REVERT: A 482 LYS cc_start: 0.7946 (ptmt) cc_final: 0.7554 (ptmt) REVERT: A 483 MET cc_start: 0.7940 (mpp) cc_final: 0.7453 (mpp) REVERT: A 498 GLU cc_start: 0.8032 (tt0) cc_final: 0.7819 (mt-10) REVERT: A 552 ASP cc_start: 0.8097 (t0) cc_final: 0.7854 (t0) REVERT: A 597 VAL cc_start: 0.8902 (OUTLIER) cc_final: 0.8657 (p) REVERT: B 22 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7557 (mp0) REVERT: B 120 ASN cc_start: 0.8036 (p0) cc_final: 0.7785 (p0) REVERT: B 136 LYS cc_start: 0.7903 (mmmt) cc_final: 0.7618 (mmmt) outliers start: 22 outliers final: 16 residues processed: 189 average time/residue: 0.0997 time to fit residues: 23.9325 Evaluate side-chains 197 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.225 ------------------------------------------------------------------------------- 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 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 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: 0.0470 chunk 73 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3422 r_free = 0.3422 target = 0.111243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.098923 restraints weight = 10153.991| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.15 r_work: 0.3112 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1731 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= 0.172 Angle : 0.544 10.409 8715 Z= 0.275 Chirality : 0.042 0.208 977 Planarity : 0.004 0.035 1092 Dihedral : 10.728 61.603 950 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.45 % Allowed : 17.69 % 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 aren not related in a simple way. whole: -0.56 (0.30), residues: 766 helix: 0.67 (0.30), residues: 305 sheet: -0.28 (0.47), residues: 130 loop : -1.36 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 524 TYR 0.014 0.001 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 covalent geometry : bond 0.00400 ( 6411) covalent geometry : angle 0.54442 ( 8715) hydrogen bonds : bond 0.03930 ( 250) hydrogen bonds : angle 4.20354 ( 702) Misc. bond : bond 0.00067 ( 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: 23 poor density : 177 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 7 VAL cc_start: 0.8563 (OUTLIER) cc_final: 0.8299 (m) REVERT: A 30 LYS cc_start: 0.8573 (mppt) cc_final: 0.8356 (mppt) REVERT: A 171 ASP cc_start: 0.7476 (m-30) cc_final: 0.7253 (m-30) REVERT: A 240 TYR cc_start: 0.7852 (m-10) cc_final: 0.7525 (m-10) REVERT: A 258 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7318 (m-30) REVERT: A 343 HIS cc_start: 0.8240 (t-170) cc_final: 0.7727 (t-170) REVERT: A 349 ASP cc_start: 0.7791 (t0) cc_final: 0.7389 (t0) REVERT: A 393 MET cc_start: 0.8278 (mmm) cc_final: 0.7927 (mtt) REVERT: A 482 LYS cc_start: 0.7904 (ptmt) cc_final: 0.7518 (ptmt) REVERT: A 483 MET cc_start: 0.7917 (mpp) cc_final: 0.7430 (mpp) REVERT: A 498 GLU cc_start: 0.7964 (tt0) cc_final: 0.7761 (mt-10) REVERT: A 552 ASP cc_start: 0.8061 (t0) cc_final: 0.7833 (t0) REVERT: A 597 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8644 (p) REVERT: B 22 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7553 (mp0) REVERT: B 120 ASN cc_start: 0.8010 (p0) cc_final: 0.7751 (p0) REVERT: B 136 LYS cc_start: 0.7872 (mmmt) cc_final: 0.7586 (mmmt) outliers start: 23 outliers final: 16 residues processed: 185 average time/residue: 0.1013 time to fit residues: 23.7900 Evaluate side-chains 194 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 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 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 A residue 598 ASP Chi-restraints excluded: chain B residue 158 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 58 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 0.2980 chunk 75 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 55 optimal weight: 0.0020 chunk 0 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3438 r_free = 0.3438 target = 0.112304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.099999 restraints weight = 10060.286| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.15 r_work: 0.3131 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1793 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= 0.134 Angle : 0.514 8.647 8715 Z= 0.262 Chirality : 0.040 0.123 977 Planarity : 0.004 0.032 1092 Dihedral : 10.632 61.947 950 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.00 % Allowed : 19.34 % Favored : 77.66 % 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 aren not related in a simple way. whole: -0.48 (0.30), residues: 766 helix: 0.75 (0.30), residues: 305 sheet: -0.28 (0.47), residues: 129 loop : -1.31 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 524 TYR 0.012 0.001 TYR A 578 PHE 0.014 0.001 PHE A 66 TRP 0.008 0.001 TRP A 458 HIS 0.003 0.001 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 6411) covalent geometry : angle 0.51376 ( 8715) hydrogen bonds : bond 0.03689 ( 250) hydrogen bonds : angle 4.10333 ( 702) Misc. bond : bond 0.00035 ( 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 193 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 7 VAL cc_start: 0.8540 (OUTLIER) cc_final: 0.8316 (m) REVERT: A 30 LYS cc_start: 0.8556 (mppt) cc_final: 0.8326 (mppt) REVERT: A 98 MET cc_start: 0.7918 (mmm) cc_final: 0.7698 (mmm) REVERT: A 171 ASP cc_start: 0.7474 (m-30) cc_final: 0.7236 (m-30) REVERT: A 240 TYR cc_start: 0.7744 (m-10) cc_final: 0.7453 (m-10) REVERT: A 258 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7335 (m-30) REVERT: A 349 ASP cc_start: 0.7779 (t0) cc_final: 0.7377 (t0) REVERT: A 393 MET cc_start: 0.8263 (mmm) cc_final: 0.7899 (mtt) REVERT: A 482 LYS cc_start: 0.7933 (ptmt) cc_final: 0.7553 (ptmt) REVERT: A 483 MET cc_start: 0.7917 (mpp) cc_final: 0.7407 (mpp) REVERT: A 498 GLU cc_start: 0.7926 (tt0) cc_final: 0.7719 (mt-10) REVERT: A 552 ASP cc_start: 0.8040 (t0) cc_final: 0.7812 (t0) REVERT: A 597 VAL cc_start: 0.8869 (p) cc_final: 0.8637 (p) REVERT: B 22 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7552 (mp0) REVERT: B 120 ASN cc_start: 0.8018 (p0) cc_final: 0.7753 (p0) outliers start: 20 outliers final: 15 residues processed: 181 average time/residue: 0.0988 time to fit residues: 22.8630 Evaluate side-chains 189 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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 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 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: 0.1980 chunk 44 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.111173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.098859 restraints weight = 10147.159| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.16 r_work: 0.3116 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6412 Z= 0.178 Angle : 0.536 8.284 8715 Z= 0.274 Chirality : 0.041 0.131 977 Planarity : 0.004 0.045 1092 Dihedral : 10.663 62.509 950 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.30 % Allowed : 19.49 % 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 aren not related in a simple way. whole: -0.54 (0.30), residues: 766 helix: 0.73 (0.30), residues: 305 sheet: -0.32 (0.46), residues: 129 loop : -1.38 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 524 TYR 0.014 0.001 TYR A 578 PHE 0.016 0.002 PHE A 265 TRP 0.008 0.001 TRP A 458 HIS 0.004 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 6411) covalent geometry : angle 0.53622 ( 8715) hydrogen bonds : bond 0.03884 ( 250) hydrogen bonds : angle 4.15535 ( 702) Misc. bond : bond 0.00075 ( 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 196 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.246 Fit side-chains REVERT: A 30 LYS cc_start: 0.8589 (mppt) cc_final: 0.8354 (mppt) REVERT: A 98 MET cc_start: 0.7934 (mmm) cc_final: 0.7591 (tmm) REVERT: A 171 ASP cc_start: 0.7486 (m-30) cc_final: 0.7245 (m-30) REVERT: A 240 TYR cc_start: 0.7844 (m-10) cc_final: 0.7525 (m-10) REVERT: A 258 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7363 (m-30) REVERT: A 349 ASP cc_start: 0.7809 (t0) cc_final: 0.7406 (t0) REVERT: A 393 MET cc_start: 0.8286 (mmm) cc_final: 0.7929 (mtt) REVERT: A 482 LYS cc_start: 0.7907 (ptmt) cc_final: 0.7521 (ptmt) REVERT: A 483 MET cc_start: 0.7938 (mpp) cc_final: 0.7447 (mpp) REVERT: A 498 GLU cc_start: 0.7949 (tt0) cc_final: 0.7745 (mt-10) REVERT: A 552 ASP cc_start: 0.8035 (t0) cc_final: 0.7798 (t0) REVERT: A 597 VAL cc_start: 0.8873 (OUTLIER) cc_final: 0.8638 (p) REVERT: B 120 ASN cc_start: 0.8030 (p0) cc_final: 0.7762 (p0) REVERT: B 136 LYS cc_start: 0.7879 (mmmt) cc_final: 0.7597 (mmmt) outliers start: 22 outliers final: 16 residues processed: 181 average time/residue: 0.0992 time to fit residues: 22.8500 Evaluate side-chains 190 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 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 455 VAL 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 158 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 58 optimal weight: 0.5980 chunk 3 optimal weight: 0.0980 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN A 343 HIS B 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.111725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.099409 restraints weight = 10163.503| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.17 r_work: 0.3118 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1901 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= 0.155 Angle : 0.524 8.413 8715 Z= 0.270 Chirality : 0.041 0.126 977 Planarity : 0.004 0.043 1092 Dihedral : 10.656 62.490 950 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.75 % Allowed : 19.49 % 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 aren not related in a simple way. whole: -0.54 (0.30), residues: 766 helix: 0.75 (0.30), residues: 305 sheet: -0.37 (0.46), residues: 129 loop : -1.37 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 524 TYR 0.013 0.001 TYR A 578 PHE 0.015 0.002 PHE A 66 TRP 0.007 0.001 TRP A 458 HIS 0.003 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 6411) covalent geometry : angle 0.52409 ( 8715) hydrogen bonds : bond 0.03778 ( 250) hydrogen bonds : angle 4.13757 ( 702) Misc. bond : bond 0.00051 ( 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 198 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.233 Fit side-chains REVERT: A 30 LYS cc_start: 0.8597 (mppt) cc_final: 0.8360 (mppt) REVERT: A 52 PHE cc_start: 0.8138 (m-80) cc_final: 0.7934 (t80) REVERT: A 171 ASP cc_start: 0.7494 (m-30) cc_final: 0.7249 (m-30) REVERT: A 240 TYR cc_start: 0.7800 (m-10) cc_final: 0.7481 (m-10) REVERT: A 258 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7365 (m-30) REVERT: A 349 ASP cc_start: 0.7805 (t0) cc_final: 0.7395 (t0) REVERT: A 393 MET cc_start: 0.8273 (mmm) cc_final: 0.7908 (mtt) REVERT: A 482 LYS cc_start: 0.7921 (ptmt) cc_final: 0.7532 (ptmt) REVERT: A 483 MET cc_start: 0.7943 (mpp) cc_final: 0.7449 (mpp) REVERT: A 498 GLU cc_start: 0.7941 (tt0) cc_final: 0.7730 (mt-10) REVERT: A 552 ASP cc_start: 0.8033 (t0) cc_final: 0.7800 (t0) REVERT: A 597 VAL cc_start: 0.8854 (OUTLIER) cc_final: 0.8620 (p) REVERT: B 22 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7391 (mp0) REVERT: B 120 ASN cc_start: 0.8022 (p0) cc_final: 0.7753 (p0) outliers start: 25 outliers final: 18 residues processed: 180 average time/residue: 0.0981 time to fit residues: 22.5034 Evaluate side-chains 193 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 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 455 VAL 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 137 ASN 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: 1.9990 chunk 27 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 76 optimal weight: 0.0770 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3437 r_free = 0.3437 target = 0.112128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.099713 restraints weight = 10087.081| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.16 r_work: 0.3126 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1947 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= 0.138 Angle : 0.535 10.719 8715 Z= 0.269 Chirality : 0.041 0.253 977 Planarity : 0.004 0.042 1092 Dihedral : 10.618 62.911 950 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.00 % Allowed : 20.24 % 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 aren not related in a simple way. whole: -0.54 (0.30), residues: 766 helix: 0.74 (0.30), residues: 305 sheet: -0.40 (0.46), residues: 129 loop : -1.36 (0.32), 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 41 PHE 0.015 0.001 PHE A 66 TRP 0.006 0.001 TRP A 458 HIS 0.002 0.001 HIS A 387 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 6411) covalent geometry : angle 0.53546 ( 8715) hydrogen bonds : bond 0.03660 ( 250) hydrogen bonds : angle 4.17404 ( 702) Misc. bond : bond 0.00042 ( 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 190 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.242 Fit side-chains REVERT: A 6 MET cc_start: 0.7750 (mtm) cc_final: 0.7517 (mtt) REVERT: A 30 LYS cc_start: 0.8592 (mppt) cc_final: 0.8356 (mppt) REVERT: A 52 PHE cc_start: 0.8179 (m-80) cc_final: 0.7573 (t80) REVERT: A 171 ASP cc_start: 0.7461 (m-30) cc_final: 0.7209 (m-30) REVERT: A 240 TYR cc_start: 0.7733 (m-10) cc_final: 0.7439 (m-10) REVERT: A 258 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.7343 (m-30) REVERT: A 349 ASP cc_start: 0.7799 (t0) cc_final: 0.7390 (t0) REVERT: A 393 MET cc_start: 0.8280 (mmm) cc_final: 0.7913 (mtt) REVERT: A 482 LYS cc_start: 0.7946 (ptmt) cc_final: 0.7565 (ptmt) REVERT: A 483 MET cc_start: 0.7962 (mpp) cc_final: 0.7479 (mpp) REVERT: A 498 GLU cc_start: 0.7935 (tt0) cc_final: 0.7721 (mt-10) REVERT: A 552 ASP cc_start: 0.8023 (t0) cc_final: 0.7788 (t0) REVERT: A 597 VAL cc_start: 0.8844 (OUTLIER) cc_final: 0.8604 (p) REVERT: B 22 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7382 (mp0) REVERT: B 120 ASN cc_start: 0.8007 (p0) cc_final: 0.7738 (p0) outliers start: 20 outliers final: 17 residues processed: 175 average time/residue: 0.0990 time to fit residues: 22.0586 Evaluate side-chains 189 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 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 455 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 137 ASN 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: 0.9990 chunk 51 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 0.0770 chunk 7 optimal weight: 0.0970 chunk 22 optimal weight: 0.6980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3437 r_free = 0.3437 target = 0.112199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.099699 restraints weight = 10101.154| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.17 r_work: 0.3131 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6412 Z= 0.145 Angle : 0.533 9.992 8715 Z= 0.268 Chirality : 0.041 0.217 977 Planarity : 0.004 0.032 1092 Dihedral : 10.607 63.357 950 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.00 % Allowed : 20.24 % 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 aren not related in a simple way. whole: -0.55 (0.30), residues: 766 helix: 0.72 (0.30), residues: 305 sheet: -0.43 (0.46), residues: 129 loop : -1.33 (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 578 PHE 0.015 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 covalent geometry : bond 0.00339 ( 6411) covalent geometry : angle 0.53284 ( 8715) hydrogen bonds : bond 0.03674 ( 250) hydrogen bonds : angle 4.16437 ( 702) Misc. bond : bond 0.00048 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1741.65 seconds wall clock time: 30 minutes 39.02 seconds (1839.02 seconds total)