Starting phenix.real_space_refine on Wed Mar 4 03:45:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vt0_32117/03_2026/7vt0_32117.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vt0_32117/03_2026/7vt0_32117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vt0_32117/03_2026/7vt0_32117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vt0_32117/03_2026/7vt0_32117.map" model { file = "/net/cci-nas-00/data/ceres_data/7vt0_32117/03_2026/7vt0_32117.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vt0_32117/03_2026/7vt0_32117.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 6690 2.51 5 N 1796 2.21 5 O 2006 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10536 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5268 Classifications: {'peptide': 663} Link IDs: {'PTRANS': 29, 'TRANS': 633} Chain: "B" Number of atoms: 5268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5268 Classifications: {'peptide': 663} Link IDs: {'CIS': 1, 'PTRANS': 29, 'TRANS': 632} Time building chain proxies: 2.50, per 1000 atoms: 0.24 Number of scatterers: 10536 At special positions: 0 Unit cell: (156.02, 100.068, 107.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 2006 8.00 N 1796 7.00 C 6690 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 625 " - pdb=" SG CYS A 660 " distance=2.03 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 736 " distance=2.02 Simple disulfide: pdb=" SG CYS A 684 " - pdb=" SG CYS A 699 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 473 " distance=2.02 Simple disulfide: pdb=" SG CYS B 625 " - pdb=" SG CYS B 660 " distance=2.03 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 736 " distance=2.05 Simple disulfide: pdb=" SG CYS B 684 " - pdb=" SG CYS B 699 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 520.5 milliseconds 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2456 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 28 sheets defined 3.8% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 149 through 152 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 617 through 622 removed outlier: 3.527A pdb=" N ALA A 620 " --> pdb=" O ALA A 617 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY A 622 " --> pdb=" O ASP A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 630 removed outlier: 3.955A pdb=" N TYR A 630 " --> pdb=" O GLU A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 706 Processing helix chain 'B' and resid 255 through 259 removed outlier: 3.679A pdb=" N TYR B 258 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP B 259 " --> pdb=" O ASP B 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 255 through 259' Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 365 through 369 removed outlier: 3.564A pdb=" N ASN B 368 " --> pdb=" O HIS B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 621 removed outlier: 3.521A pdb=" N ALA B 620 " --> pdb=" O ALA B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 682 Processing helix chain 'B' and resid 702 through 706 Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 97 removed outlier: 5.717A pdb=" N GLN A 614 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN A 95 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILE A 612 " --> pdb=" O GLN A 95 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 599 " --> pdb=" O LEU A 613 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY A 585 " --> pdb=" O PHE A 600 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 110 removed outlier: 4.398A pdb=" N VAL A 116 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA4, first strand: chain 'A' and resid 167 through 169 removed outlier: 3.818A pdb=" N TYR A 177 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR A 190 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP A 188 " --> pdb=" O PHE A 179 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 211 removed outlier: 3.613A pdb=" N ASP A 208 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 210 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 220 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP A 232 " --> pdb=" O GLY A 221 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 248 through 252 removed outlier: 3.547A pdb=" N SER A 252 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL A 277 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 299 through 303 removed outlier: 3.819A pdb=" N MET A 307 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 360 through 362 removed outlier: 3.696A pdb=" N TYR A 373 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU A 372 " --> pdb=" O SER A 385 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 415 through 416 Processing sheet with id=AB1, first strand: chain 'A' and resid 504 through 507 removed outlier: 3.645A pdb=" N ALA A 506 " --> pdb=" O TYR A 521 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 534 " --> pdb=" O VAL A 520 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 538 through 543 Processing sheet with id=AB3, first strand: chain 'A' and resid 560 through 561 Processing sheet with id=AB4, first strand: chain 'A' and resid 623 through 624 removed outlier: 7.171A pdb=" N VAL A 623 " --> pdb=" O PHE A 661 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 688 through 689 Processing sheet with id=AB6, first strand: chain 'A' and resid 722 through 724 Processing sheet with id=AB7, first strand: chain 'B' and resid 91 through 97 removed outlier: 5.018A pdb=" N VAL B 92 " --> pdb=" O ASN B 616 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASN B 616 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY B 94 " --> pdb=" O GLN B 614 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY B 585 " --> pdb=" O PHE B 600 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 106 through 110 removed outlier: 4.203A pdb=" N VAL B 116 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP B 134 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 167 through 169 removed outlier: 3.817A pdb=" N TYR B 177 " --> pdb=" O THR B 190 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE B 189 " --> pdb=" O GLN B 198 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 219 through 222 removed outlier: 4.049A pdb=" N GLN B 245 " --> pdb=" O LEU B 231 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 248 through 252 removed outlier: 4.252A pdb=" N SER B 250 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 280 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR B 276 " --> pdb=" O ARG B 268 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL B 277 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 299 through 303 Processing sheet with id=AC4, first strand: chain 'B' and resid 350 through 353 removed outlier: 6.824A pdb=" N PHE B 360 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN B 371 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU B 372 " --> pdb=" O SER B 385 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 414 through 416 Processing sheet with id=AC6, first strand: chain 'B' and resid 475 through 477 removed outlier: 3.767A pdb=" N ALA B 506 " --> pdb=" O TYR B 521 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B 534 " --> pdb=" O VAL B 520 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 538 through 543 Processing sheet with id=AC8, first strand: chain 'B' and resid 560 through 561 Processing sheet with id=AC9, first strand: chain 'B' and resid 623 through 624 removed outlier: 6.982A pdb=" N VAL B 623 " --> pdb=" O PHE B 661 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 722 through 724 162 hydrogen bonds defined for protein. 357 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.70 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1759 1.27 - 1.41: 2909 1.41 - 1.55: 6071 1.55 - 1.69: 9 1.69 - 1.83: 62 Bond restraints: 10810 Sorted by residual: bond pdb=" CA CYS A 362 " pdb=" C CYS A 362 " ideal model delta sigma weight residual 1.533 1.353 0.180 9.60e-03 1.09e+04 3.53e+02 bond pdb=" CA VAL A 363 " pdb=" C VAL A 363 " ideal model delta sigma weight residual 1.523 1.372 0.151 1.27e-02 6.20e+03 1.41e+02 bond pdb=" CA ASN B 662 " pdb=" C ASN B 662 " ideal model delta sigma weight residual 1.522 1.385 0.137 1.38e-02 5.25e+03 9.88e+01 bond pdb=" CA ASP B 667 " pdb=" C ASP B 667 " ideal model delta sigma weight residual 1.523 1.392 0.132 1.34e-02 5.57e+03 9.65e+01 bond pdb=" CA LEU A 386 " pdb=" C LEU A 386 " ideal model delta sigma weight residual 1.521 1.393 0.127 1.30e-02 5.92e+03 9.59e+01 ... (remaining 10805 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.62: 14522 5.62 - 11.24: 118 11.24 - 16.86: 14 16.86 - 22.48: 1 22.48 - 28.09: 1 Bond angle restraints: 14656 Sorted by residual: angle pdb=" N HIS A 365 " pdb=" CA HIS A 365 " pdb=" C HIS A 365 " ideal model delta sigma weight residual 111.52 83.43 28.09 1.40e+00 5.10e-01 4.03e+02 angle pdb=" N ASP B 629 " pdb=" CA ASP B 629 " pdb=" C ASP B 629 " ideal model delta sigma weight residual 114.56 100.19 14.37 1.27e+00 6.20e-01 1.28e+02 angle pdb=" C ARG B 668 " pdb=" N PRO B 669 " pdb=" CA PRO B 669 " ideal model delta sigma weight residual 119.84 105.74 14.10 1.25e+00 6.40e-01 1.27e+02 angle pdb=" CA GLU B 592 " pdb=" C GLU B 592 " pdb=" N LYS B 593 " ideal model delta sigma weight residual 116.08 103.97 12.11 1.29e+00 6.01e-01 8.82e+01 angle pdb=" N PHE B 666 " pdb=" CA PHE B 666 " pdb=" C PHE B 666 " ideal model delta sigma weight residual 110.80 129.83 -19.03 2.13e+00 2.20e-01 7.98e+01 ... (remaining 14651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 5681 17.65 - 35.30: 566 35.30 - 52.95: 109 52.95 - 70.59: 37 70.59 - 88.24: 4 Dihedral angle restraints: 6397 sinusoidal: 2557 harmonic: 3840 Sorted by residual: dihedral pdb=" CB CYS B 684 " pdb=" SG CYS B 684 " pdb=" SG CYS B 699 " pdb=" CB CYS B 699 " ideal model delta sinusoidal sigma weight residual -86.00 -19.23 -66.77 1 1.00e+01 1.00e-02 5.81e+01 dihedral pdb=" CB CYS A 677 " pdb=" SG CYS A 677 " pdb=" SG CYS A 736 " pdb=" CB CYS A 736 " ideal model delta sinusoidal sigma weight residual 93.00 36.45 56.55 1 1.00e+01 1.00e-02 4.31e+01 dihedral pdb=" CB CYS B 677 " pdb=" SG CYS B 677 " pdb=" SG CYS B 736 " pdb=" CB CYS B 736 " ideal model delta sinusoidal sigma weight residual -86.00 -32.48 -53.52 1 1.00e+01 1.00e-02 3.89e+01 ... (remaining 6394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1329 0.078 - 0.155: 188 0.155 - 0.233: 23 0.233 - 0.311: 8 0.311 - 0.388: 6 Chirality restraints: 1554 Sorted by residual: chirality pdb=" CA ASN A 388 " pdb=" N ASN A 388 " pdb=" C ASN A 388 " pdb=" CB ASN A 388 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CA SER A 364 " pdb=" N SER A 364 " pdb=" C SER A 364 " pdb=" CB SER A 364 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" CA LEU B 645 " pdb=" N LEU B 645 " pdb=" C LEU B 645 " pdb=" CB LEU B 645 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.56e+00 ... (remaining 1551 not shown) Planarity restraints: 1910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 674 " -0.033 2.00e-02 2.50e+03 6.62e-02 4.38e+01 pdb=" C ASN B 674 " 0.114 2.00e-02 2.50e+03 pdb=" O ASN B 674 " -0.043 2.00e-02 2.50e+03 pdb=" N CYS B 675 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 592 " -0.018 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C GLU B 592 " 0.074 2.00e-02 2.50e+03 pdb=" O GLU B 592 " -0.031 2.00e-02 2.50e+03 pdb=" N LYS B 593 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 673 " -0.020 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C SER A 673 " 0.068 2.00e-02 2.50e+03 pdb=" O SER A 673 " -0.026 2.00e-02 2.50e+03 pdb=" N ASN A 674 " -0.023 2.00e-02 2.50e+03 ... (remaining 1907 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 485 2.68 - 3.24: 9871 3.24 - 3.79: 14869 3.79 - 4.35: 20121 4.35 - 4.90: 33649 Nonbonded interactions: 78995 Sorted by model distance: nonbonded pdb=" CB VAL A 363 " pdb=" N SER A 364 " model vdw 2.126 2.840 nonbonded pdb=" OE2 GLU B 356 " pdb=" OH TYR B 424 " model vdw 2.196 3.040 nonbonded pdb=" OG SER B 170 " pdb=" O ASP B 173 " model vdw 2.206 3.040 nonbonded pdb=" O LYS A 260 " pdb=" OG1 THR A 263 " model vdw 2.227 3.040 nonbonded pdb=" O GLU A 697 " pdb=" OH TYR A 728 " model vdw 2.229 3.040 ... (remaining 78990 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 2.370 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.850 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 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 : 0.011 0.180 10817 Z= 0.762 Angle : 1.310 28.095 14670 Z= 0.802 Chirality : 0.061 0.388 1554 Planarity : 0.007 0.090 1910 Dihedral : 14.914 88.243 3920 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 3.10 % Allowed : 14.30 % Favored : 82.60 % Rotamer: Outliers : 3.65 % Allowed : 3.13 % Favored : 93.22 % Cbeta Deviations : 1.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: -4.14 (0.21), residues: 1322 helix: -5.13 (0.27), residues: 6 sheet: -2.70 (0.28), residues: 327 loop : -2.99 (0.18), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 439 TYR 0.024 0.002 TYR B 630 PHE 0.043 0.002 PHE B 661 TRP 0.020 0.002 TRP B 542 HIS 0.011 0.001 HIS B 545 Details of bonding type rmsd covalent geometry : bond 0.01069 (10810) covalent geometry : angle 1.30877 (14656) SS BOND : bond 0.00959 ( 7) SS BOND : angle 1.96862 ( 14) hydrogen bonds : bond 0.23216 ( 162) hydrogen bonds : angle 8.71413 ( 357) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 279 ARG cc_start: 0.7161 (ttp-110) cc_final: 0.6924 (ttp-110) REVERT: A 304 ASP cc_start: 0.7700 (t0) cc_final: 0.7481 (t0) REVERT: A 348 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7370 (mp0) REVERT: A 394 PRO cc_start: 0.6890 (Cg_endo) cc_final: 0.6518 (Cg_exo) REVERT: A 438 MET cc_start: 0.7938 (mmt) cc_final: 0.5777 (ptm) REVERT: A 690 MET cc_start: -0.1204 (mmp) cc_final: -0.3495 (ttm) REVERT: A 730 LYS cc_start: 0.3115 (OUTLIER) cc_final: 0.2839 (pttt) REVERT: B 593 LYS cc_start: 0.7234 (OUTLIER) cc_final: 0.6857 (mtmm) REVERT: B 638 GLU cc_start: 0.5393 (OUTLIER) cc_final: 0.4930 (tp30) REVERT: B 647 HIS cc_start: 0.7599 (OUTLIER) cc_final: 0.7129 (m90) outliers start: 42 outliers final: 17 residues processed: 164 average time/residue: 0.0956 time to fit residues: 22.3937 Evaluate side-chains 127 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 367 ASN Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 647 HIS Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 675 CYS Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 683 GLU Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 700 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 0.0370 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS A 388 ASN ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 GLN B 269 HIS B 566 ASN B 662 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.214606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.174684 restraints weight = 11409.722| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 3.18 r_work: 0.3599 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10817 Z= 0.155 Angle : 0.733 7.864 14670 Z= 0.391 Chirality : 0.047 0.192 1554 Planarity : 0.005 0.091 1910 Dihedral : 8.003 69.749 1494 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 1.13 % Allowed : 14.30 % Favored : 84.57 % Rotamer: Outliers : 2.09 % Allowed : 9.74 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.67 (0.21), residues: 1322 helix: None (None), residues: 0 sheet: -2.22 (0.28), residues: 329 loop : -2.73 (0.18), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 439 TYR 0.019 0.001 TYR B 392 PHE 0.017 0.002 PHE B 661 TRP 0.019 0.001 TRP A 542 HIS 0.006 0.001 HIS B 608 Details of bonding type rmsd covalent geometry : bond 0.00341 (10810) covalent geometry : angle 0.73167 (14656) SS BOND : bond 0.00313 ( 7) SS BOND : angle 1.48208 ( 14) hydrogen bonds : bond 0.03730 ( 162) hydrogen bonds : angle 5.98779 ( 357) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 279 ARG cc_start: 0.7622 (ttp-170) cc_final: 0.7405 (ttp-110) REVERT: A 304 ASP cc_start: 0.7789 (t0) cc_final: 0.7530 (t0) REVERT: A 392 TYR cc_start: 0.7042 (t80) cc_final: 0.6644 (t80) REVERT: A 394 PRO cc_start: 0.7245 (Cg_endo) cc_final: 0.6737 (Cg_exo) REVERT: A 690 MET cc_start: -0.0941 (mmp) cc_final: -0.3407 (ttm) REVERT: B 139 TYR cc_start: 0.7649 (m-80) cc_final: 0.7444 (m-80) REVERT: B 630 TYR cc_start: 0.8926 (m-80) cc_final: 0.8676 (m-80) REVERT: B 682 TYR cc_start: 0.4672 (OUTLIER) cc_final: 0.2768 (m-80) REVERT: B 683 GLU cc_start: -0.0701 (OUTLIER) cc_final: -0.0944 (pt0) outliers start: 24 outliers final: 15 residues processed: 145 average time/residue: 0.0785 time to fit residues: 17.2033 Evaluate side-chains 120 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 662 ASN Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 675 CYS Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 683 GLU Chi-restraints excluded: chain B residue 700 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 122 optimal weight: 3.9990 chunk 129 optimal weight: 20.0000 chunk 62 optimal weight: 0.0170 chunk 6 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 58 optimal weight: 0.0070 chunk 63 optimal weight: 1.9990 chunk 78 optimal weight: 0.0060 chunk 64 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 111 optimal weight: 0.4980 overall best weight: 0.5054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 GLN B 269 HIS B 647 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.215663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.171850 restraints weight = 11519.336| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 3.46 r_work: 0.3609 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10817 Z= 0.129 Angle : 0.688 9.799 14670 Z= 0.364 Chirality : 0.046 0.216 1554 Planarity : 0.005 0.087 1910 Dihedral : 6.477 59.882 1469 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 1.21 % Allowed : 12.48 % Favored : 86.31 % Rotamer: Outliers : 1.57 % Allowed : 12.00 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.37 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -1.95 (0.29), residues: 328 loop : -2.54 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 439 TYR 0.013 0.001 TYR B 186 PHE 0.014 0.001 PHE B 200 TRP 0.016 0.001 TRP A 542 HIS 0.006 0.001 HIS B 647 Details of bonding type rmsd covalent geometry : bond 0.00285 (10810) covalent geometry : angle 0.68715 (14656) SS BOND : bond 0.00234 ( 7) SS BOND : angle 1.35231 ( 14) hydrogen bonds : bond 0.03152 ( 162) hydrogen bonds : angle 5.36996 ( 357) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.372 Fit side-chains REVERT: A 90 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7899 (mm) REVERT: A 93 TYR cc_start: 0.8198 (p90) cc_final: 0.7942 (p90) REVERT: A 392 TYR cc_start: 0.7108 (t80) cc_final: 0.6596 (t80) REVERT: A 394 PRO cc_start: 0.7212 (Cg_endo) cc_final: 0.6622 (Cg_exo) REVERT: A 690 MET cc_start: -0.1058 (mmp) cc_final: -0.3583 (ttm) REVERT: B 411 PHE cc_start: 0.5514 (m-80) cc_final: 0.5254 (m-80) REVERT: B 438 MET cc_start: 0.7330 (mmt) cc_final: 0.7112 (mmt) outliers start: 18 outliers final: 10 residues processed: 127 average time/residue: 0.0814 time to fit residues: 15.8616 Evaluate side-chains 110 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 421 GLN Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 700 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 0.0970 chunk 106 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.215020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.172054 restraints weight = 11475.940| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 3.22 r_work: 0.3615 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10817 Z= 0.132 Angle : 0.672 9.832 14670 Z= 0.355 Chirality : 0.045 0.149 1554 Planarity : 0.005 0.085 1910 Dihedral : 5.724 44.717 1458 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 1.13 % Allowed : 13.24 % Favored : 85.63 % Rotamer: Outliers : 2.43 % Allowed : 13.30 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.18 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -1.77 (0.29), residues: 327 loop : -2.42 (0.19), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 439 TYR 0.020 0.001 TYR A 349 PHE 0.011 0.001 PHE A 284 TRP 0.015 0.001 TRP B 542 HIS 0.003 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00296 (10810) covalent geometry : angle 0.66946 (14656) SS BOND : bond 0.00215 ( 7) SS BOND : angle 1.90132 ( 14) hydrogen bonds : bond 0.02939 ( 162) hydrogen bonds : angle 5.07699 ( 357) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.400 Fit side-chains REVERT: A 90 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7930 (mm) REVERT: A 93 TYR cc_start: 0.8222 (p90) cc_final: 0.7956 (p90) REVERT: A 304 ASP cc_start: 0.7864 (t0) cc_final: 0.7656 (t0) REVERT: A 392 TYR cc_start: 0.7065 (t80) cc_final: 0.6585 (t80) REVERT: A 394 PRO cc_start: 0.7213 (Cg_endo) cc_final: 0.6668 (Cg_exo) REVERT: A 690 MET cc_start: -0.0967 (mmp) cc_final: -0.3501 (ttm) REVERT: B 438 MET cc_start: 0.7280 (mmt) cc_final: 0.7076 (mmt) REVERT: B 665 ASP cc_start: 0.6812 (OUTLIER) cc_final: 0.6094 (p0) outliers start: 28 outliers final: 13 residues processed: 130 average time/residue: 0.0848 time to fit residues: 16.5795 Evaluate side-chains 114 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 682 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 10 optimal weight: 2.9990 chunk 65 optimal weight: 30.0000 chunk 22 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS A 269 HIS A 476 HIS ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 GLN B 269 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.209495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.162038 restraints weight = 11686.649| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 4.52 r_work: 0.3497 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 10817 Z= 0.314 Angle : 0.818 9.875 14670 Z= 0.432 Chirality : 0.050 0.179 1554 Planarity : 0.005 0.081 1910 Dihedral : 6.547 54.669 1455 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.98 % Allowed : 17.02 % Favored : 82.00 % Rotamer: Outliers : 2.35 % Allowed : 15.13 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -3.44 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -2.10 (0.28), residues: 350 loop : -2.54 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 122 TYR 0.025 0.002 TYR A 563 PHE 0.021 0.002 PHE B 576 TRP 0.026 0.002 TRP B 542 HIS 0.008 0.002 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00733 (10810) covalent geometry : angle 0.81670 (14656) SS BOND : bond 0.00380 ( 7) SS BOND : angle 1.92970 ( 14) hydrogen bonds : bond 0.04040 ( 162) hydrogen bonds : angle 5.41097 ( 357) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.392 Fit side-chains REVERT: A 100 ASP cc_start: 0.7761 (m-30) cc_final: 0.7534 (m-30) REVERT: A 253 TRP cc_start: 0.9257 (m100) cc_final: 0.9045 (m100) REVERT: A 304 ASP cc_start: 0.7957 (t0) cc_final: 0.7674 (t0) REVERT: A 394 PRO cc_start: 0.7352 (Cg_endo) cc_final: 0.7049 (Cg_exo) REVERT: A 690 MET cc_start: -0.0375 (mmp) cc_final: -0.3149 (ttm) REVERT: B 159 ARG cc_start: 0.8288 (mmp-170) cc_final: 0.8005 (mmp-170) REVERT: B 189 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8702 (mt) REVERT: B 269 HIS cc_start: 0.8086 (OUTLIER) cc_final: 0.7864 (t-170) REVERT: B 438 MET cc_start: 0.7435 (mmt) cc_final: 0.7144 (mmt) outliers start: 27 outliers final: 19 residues processed: 133 average time/residue: 0.0908 time to fit residues: 17.8892 Evaluate side-chains 120 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 269 HIS Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 682 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 15 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.205236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.151807 restraints weight = 11921.690| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 3.30 r_work: 0.3532 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10817 Z= 0.153 Angle : 0.698 10.964 14670 Z= 0.369 Chirality : 0.046 0.165 1554 Planarity : 0.005 0.079 1910 Dihedral : 6.022 44.632 1455 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 1.06 % Allowed : 12.33 % Favored : 86.61 % Rotamer: Outliers : 2.43 % Allowed : 16.43 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.27 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -1.98 (0.28), residues: 337 loop : -2.42 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 480 TYR 0.017 0.001 TYR A 349 PHE 0.030 0.002 PHE A 382 TRP 0.017 0.001 TRP A 542 HIS 0.007 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00351 (10810) covalent geometry : angle 0.69694 (14656) SS BOND : bond 0.00400 ( 7) SS BOND : angle 1.56376 ( 14) hydrogen bonds : bond 0.03078 ( 162) hydrogen bonds : angle 5.04559 ( 357) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.373 Fit side-chains REVERT: A 304 ASP cc_start: 0.7945 (t0) cc_final: 0.7659 (t0) REVERT: A 392 TYR cc_start: 0.7101 (t80) cc_final: 0.6502 (t80) REVERT: A 394 PRO cc_start: 0.7236 (Cg_endo) cc_final: 0.6596 (Cg_exo) REVERT: A 690 MET cc_start: -0.0749 (mmp) cc_final: -0.3348 (ttm) REVERT: A 730 LYS cc_start: 0.2228 (OUTLIER) cc_final: 0.1885 (pttt) REVERT: B 243 MET cc_start: 0.8209 (tpp) cc_final: 0.7432 (tpt) REVERT: B 438 MET cc_start: 0.7271 (mmt) cc_final: 0.7015 (mmt) REVERT: B 644 LEU cc_start: 0.5000 (OUTLIER) cc_final: 0.4674 (tt) outliers start: 28 outliers final: 18 residues processed: 130 average time/residue: 0.0969 time to fit residues: 18.2379 Evaluate side-chains 119 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 682 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 30 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 77 optimal weight: 0.0570 chunk 90 optimal weight: 0.0020 chunk 82 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 overall best weight: 0.4706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.208125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.162645 restraints weight = 11885.888| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 4.07 r_work: 0.3481 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10817 Z= 0.123 Angle : 0.677 11.721 14670 Z= 0.356 Chirality : 0.046 0.240 1554 Planarity : 0.004 0.077 1910 Dihedral : 5.662 43.364 1455 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.98 % Allowed : 12.18 % Favored : 86.84 % Rotamer: Outliers : 2.17 % Allowed : 16.09 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.06 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -1.72 (0.30), residues: 318 loop : -2.32 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 343 TYR 0.017 0.001 TYR A 349 PHE 0.020 0.001 PHE A 382 TRP 0.014 0.001 TRP A 542 HIS 0.003 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00278 (10810) covalent geometry : angle 0.67559 (14656) SS BOND : bond 0.00298 ( 7) SS BOND : angle 1.39650 ( 14) hydrogen bonds : bond 0.02754 ( 162) hydrogen bonds : angle 4.89917 ( 357) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.280 Fit side-chains REVERT: A 304 ASP cc_start: 0.8061 (t0) cc_final: 0.7796 (t0) REVERT: A 307 MET cc_start: 0.8940 (ttt) cc_final: 0.8642 (tpp) REVERT: A 392 TYR cc_start: 0.7114 (t80) cc_final: 0.6568 (t80) REVERT: A 394 PRO cc_start: 0.7250 (Cg_endo) cc_final: 0.6652 (Cg_exo) REVERT: A 690 MET cc_start: -0.0834 (mmp) cc_final: -0.3354 (ttm) REVERT: A 730 LYS cc_start: 0.2018 (OUTLIER) cc_final: 0.1716 (pttt) REVERT: B 243 MET cc_start: 0.8089 (tpp) cc_final: 0.7510 (tpt) REVERT: B 438 MET cc_start: 0.7388 (mmt) cc_final: 0.7121 (mmt) REVERT: B 480 ARG cc_start: 0.6409 (mmm160) cc_final: 0.5952 (mmm160) REVERT: B 644 LEU cc_start: 0.4590 (OUTLIER) cc_final: 0.4343 (tt) outliers start: 25 outliers final: 17 residues processed: 124 average time/residue: 0.0998 time to fit residues: 17.8164 Evaluate side-chains 116 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 682 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 92 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 73 optimal weight: 0.2980 chunk 40 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.206694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.157301 restraints weight = 11845.284| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 4.56 r_work: 0.3446 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10817 Z= 0.141 Angle : 0.685 9.945 14670 Z= 0.359 Chirality : 0.046 0.231 1554 Planarity : 0.004 0.076 1910 Dihedral : 5.670 43.167 1455 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.98 % Allowed : 12.63 % Favored : 86.38 % Rotamer: Outliers : 2.35 % Allowed : 16.78 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.01 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -1.62 (0.30), residues: 316 loop : -2.31 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 439 TYR 0.032 0.001 TYR A 349 PHE 0.016 0.001 PHE A 382 TRP 0.015 0.001 TRP A 542 HIS 0.004 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00325 (10810) covalent geometry : angle 0.68377 (14656) SS BOND : bond 0.00243 ( 7) SS BOND : angle 1.41440 ( 14) hydrogen bonds : bond 0.02858 ( 162) hydrogen bonds : angle 4.83064 ( 357) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.396 Fit side-chains REVERT: A 246 GLU cc_start: 0.7619 (tp30) cc_final: 0.7381 (tp30) REVERT: A 304 ASP cc_start: 0.8084 (t0) cc_final: 0.7803 (t0) REVERT: A 307 MET cc_start: 0.8985 (ttt) cc_final: 0.8651 (tpp) REVERT: A 374 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8629 (tp) REVERT: A 392 TYR cc_start: 0.7137 (t80) cc_final: 0.6581 (t80) REVERT: A 394 PRO cc_start: 0.7247 (Cg_endo) cc_final: 0.6648 (Cg_exo) REVERT: A 690 MET cc_start: -0.0675 (mmp) cc_final: -0.3294 (ttm) REVERT: A 730 LYS cc_start: 0.2127 (OUTLIER) cc_final: 0.1774 (pttt) REVERT: B 189 ILE cc_start: 0.8858 (mt) cc_final: 0.8657 (mt) REVERT: B 243 MET cc_start: 0.8193 (tpp) cc_final: 0.7567 (tpt) REVERT: B 438 MET cc_start: 0.7400 (mmt) cc_final: 0.7121 (mmt) REVERT: B 644 LEU cc_start: 0.4523 (OUTLIER) cc_final: 0.4270 (tt) outliers start: 27 outliers final: 18 residues processed: 125 average time/residue: 0.0951 time to fit residues: 17.2505 Evaluate side-chains 118 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 682 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.204197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.146455 restraints weight = 11963.694| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 3.35 r_work: 0.3494 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10817 Z= 0.186 Angle : 0.718 8.977 14670 Z= 0.377 Chirality : 0.047 0.191 1554 Planarity : 0.005 0.075 1910 Dihedral : 5.941 45.440 1455 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.91 % Allowed : 13.69 % Favored : 85.40 % Rotamer: Outliers : 2.35 % Allowed : 16.96 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.14 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -1.81 (0.29), residues: 327 loop : -2.36 (0.19), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 439 TYR 0.029 0.002 TYR A 349 PHE 0.015 0.002 PHE B 576 TRP 0.018 0.002 TRP B 542 HIS 0.005 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00437 (10810) covalent geometry : angle 0.71697 (14656) SS BOND : bond 0.00262 ( 7) SS BOND : angle 1.46248 ( 14) hydrogen bonds : bond 0.03205 ( 162) hydrogen bonds : angle 4.97851 ( 357) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.534 Fit side-chains REVERT: A 253 TRP cc_start: 0.9216 (m100) cc_final: 0.8955 (m100) REVERT: A 304 ASP cc_start: 0.8018 (t0) cc_final: 0.7719 (t0) REVERT: A 307 MET cc_start: 0.8915 (ttt) cc_final: 0.8544 (tpp) REVERT: A 392 TYR cc_start: 0.7125 (t80) cc_final: 0.6494 (t80) REVERT: A 394 PRO cc_start: 0.7268 (Cg_endo) cc_final: 0.6611 (Cg_exo) REVERT: A 690 MET cc_start: -0.0622 (mmp) cc_final: -0.3297 (ttm) REVERT: A 730 LYS cc_start: 0.2198 (OUTLIER) cc_final: 0.1803 (pttt) REVERT: B 189 ILE cc_start: 0.8796 (mt) cc_final: 0.8587 (mt) REVERT: B 438 MET cc_start: 0.7448 (mmt) cc_final: 0.7177 (mmt) REVERT: B 644 LEU cc_start: 0.4951 (OUTLIER) cc_final: 0.4691 (tt) outliers start: 27 outliers final: 21 residues processed: 121 average time/residue: 0.1025 time to fit residues: 18.0509 Evaluate side-chains 118 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 682 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 127 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 64 optimal weight: 8.9990 chunk 110 optimal weight: 0.0270 chunk 124 optimal weight: 0.4980 chunk 122 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.205463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.147378 restraints weight = 11836.491| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 3.54 r_work: 0.3527 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10817 Z= 0.149 Angle : 0.697 12.308 14670 Z= 0.363 Chirality : 0.046 0.170 1554 Planarity : 0.004 0.074 1910 Dihedral : 5.773 43.718 1455 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.91 % Allowed : 12.41 % Favored : 86.69 % Rotamer: Outliers : 2.17 % Allowed : 17.48 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: -3.05 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -1.69 (0.29), residues: 322 loop : -2.32 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 439 TYR 0.024 0.001 TYR A 349 PHE 0.018 0.001 PHE B 200 TRP 0.015 0.001 TRP A 542 HIS 0.004 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00347 (10810) covalent geometry : angle 0.69610 (14656) SS BOND : bond 0.00267 ( 7) SS BOND : angle 1.37916 ( 14) hydrogen bonds : bond 0.02929 ( 162) hydrogen bonds : angle 4.86439 ( 357) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.284 Fit side-chains REVERT: A 246 GLU cc_start: 0.7389 (tp30) cc_final: 0.7188 (tp30) REVERT: A 304 ASP cc_start: 0.7995 (t0) cc_final: 0.7671 (t0) REVERT: A 307 MET cc_start: 0.8934 (ttt) cc_final: 0.8542 (tpp) REVERT: A 392 TYR cc_start: 0.7085 (t80) cc_final: 0.6491 (t80) REVERT: A 394 PRO cc_start: 0.7231 (Cg_endo) cc_final: 0.6597 (Cg_exo) REVERT: A 690 MET cc_start: -0.0593 (mmp) cc_final: -0.3214 (ttm) REVERT: A 730 LYS cc_start: 0.2301 (OUTLIER) cc_final: 0.1853 (pttt) REVERT: B 189 ILE cc_start: 0.8822 (mt) cc_final: 0.8622 (mt) REVERT: B 243 MET cc_start: 0.8181 (tpp) cc_final: 0.7444 (tpt) REVERT: B 438 MET cc_start: 0.7313 (mmt) cc_final: 0.7051 (mmt) REVERT: B 644 LEU cc_start: 0.4470 (OUTLIER) cc_final: 0.3640 (tp) outliers start: 25 outliers final: 19 residues processed: 122 average time/residue: 0.0934 time to fit residues: 16.6598 Evaluate side-chains 122 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 682 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 30 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 7 optimal weight: 0.0980 chunk 38 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.205713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.152731 restraints weight = 11897.333| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 3.49 r_work: 0.3525 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10817 Z= 0.141 Angle : 0.691 11.940 14670 Z= 0.358 Chirality : 0.045 0.153 1554 Planarity : 0.004 0.074 1910 Dihedral : 5.677 42.652 1455 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.91 % Allowed : 13.09 % Favored : 86.01 % Rotamer: Outliers : 2.26 % Allowed : 17.39 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: -3.03 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -1.64 (0.29), residues: 323 loop : -2.32 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 439 TYR 0.023 0.001 TYR A 349 PHE 0.028 0.001 PHE B 200 TRP 0.015 0.001 TRP A 542 HIS 0.004 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00327 (10810) covalent geometry : angle 0.69027 (14656) SS BOND : bond 0.00264 ( 7) SS BOND : angle 1.32768 ( 14) hydrogen bonds : bond 0.02854 ( 162) hydrogen bonds : angle 4.85695 ( 357) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2517.67 seconds wall clock time: 43 minutes 48.18 seconds (2628.18 seconds total)