Starting phenix.real_space_refine on Mon Jul 28 18:37:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vt0_32117/07_2025/7vt0_32117.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vt0_32117/07_2025/7vt0_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_32117/07_2025/7vt0_32117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vt0_32117/07_2025/7vt0_32117.map" model { file = "/net/cci-nas-00/data/ceres_data/7vt0_32117/07_2025/7vt0_32117.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vt0_32117/07_2025/7vt0_32117.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.07, per 1000 atoms: 0.67 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: 3.17 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.54 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: 3.14 Time building geometry restraints manager: 3.20 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: 0.05 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: 8.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.110 Process input model: 28.420 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.400 ------------------------------------------------------------------------------- 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 : 14.86 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.020 0.002 TRP B 542 HIS 0.011 0.001 HIS B 545 PHE 0.043 0.002 PHE B 661 TYR 0.024 0.002 TYR B 630 ARG 0.008 0.000 ARG B 439 Details of bonding type rmsd hydrogen bonds : bond 0.23216 ( 162) hydrogen bonds : angle 8.71413 ( 357) SS BOND : bond 0.00959 ( 7) SS BOND : angle 1.96862 ( 14) covalent geometry : bond 0.01069 (10810) covalent geometry : angle 1.30877 (14656) *********************** 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 : 1.600 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: 0.7480 (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: 0.2641 time to fit residues: 60.7527 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 : 1.092 ------------------------------------------------------------------------------- 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 111 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 103 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 77 optimal weight: 0.0370 chunk 119 optimal weight: 0.7980 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.214855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.170970 restraints weight = 11367.984| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 3.30 r_work: 0.3610 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10817 Z= 0.149 Angle : 0.730 7.817 14670 Z= 0.389 Chirality : 0.047 0.186 1554 Planarity : 0.005 0.091 1910 Dihedral : 7.994 70.159 1494 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 1.13 % Allowed : 14.45 % Favored : 84.42 % Rotamer: Outliers : 2.00 % Allowed : 9.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.21), residues: 1322 helix: None (None), residues: 0 sheet: -2.20 (0.28), residues: 328 loop : -2.73 (0.18), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 542 HIS 0.007 0.001 HIS B 608 PHE 0.015 0.002 PHE B 661 TYR 0.020 0.001 TYR B 392 ARG 0.005 0.000 ARG B 439 Details of bonding type rmsd hydrogen bonds : bond 0.03793 ( 162) hydrogen bonds : angle 5.99475 ( 357) SS BOND : bond 0.00271 ( 7) SS BOND : angle 1.46824 ( 14) covalent geometry : bond 0.00332 (10810) covalent geometry : angle 0.72888 (14656) *********************** 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 145 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 2.157 Fit side-chains revert: symmetry clash REVERT: A 279 ARG cc_start: 0.7600 (ttp-170) cc_final: 0.7381 (ttp-110) REVERT: A 304 ASP cc_start: 0.7783 (t0) cc_final: 0.7520 (t0) REVERT: A 392 TYR cc_start: 0.7027 (t80) cc_final: 0.6626 (t80) REVERT: A 394 PRO cc_start: 0.7225 (Cg_endo) cc_final: 0.6720 (Cg_exo) REVERT: A 690 MET cc_start: -0.0642 (mmp) cc_final: -0.3139 (ttm) REVERT: B 139 TYR cc_start: 0.7635 (m-80) cc_final: 0.7430 (m-80) REVERT: B 630 TYR cc_start: 0.8908 (m-80) cc_final: 0.8656 (m-80) REVERT: B 682 TYR cc_start: 0.4664 (OUTLIER) cc_final: 0.2919 (m-80) REVERT: B 683 GLU cc_start: -0.0773 (OUTLIER) cc_final: -0.1077 (pt0) outliers start: 23 outliers final: 14 residues processed: 143 average time/residue: 0.2900 time to fit residues: 62.4713 Evaluate side-chains 118 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 2.423 ------------------------------------------------------------------------------- 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 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 61 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 17 optimal weight: 0.0010 chunk 82 optimal weight: 2.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- 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** B 269 HIS B 662 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.214030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.165861 restraints weight = 11582.208| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 4.04 r_work: 0.3533 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10817 Z= 0.188 Angle : 0.737 8.863 14670 Z= 0.390 Chirality : 0.048 0.202 1554 Planarity : 0.005 0.087 1910 Dihedral : 6.743 56.988 1469 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 1.21 % Allowed : 14.30 % Favored : 84.49 % Rotamer: Outliers : 1.91 % Allowed : 11.91 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -2.23 (0.28), residues: 356 loop : -2.61 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 542 HIS 0.006 0.001 HIS B 647 PHE 0.019 0.002 PHE B 200 TYR 0.019 0.002 TYR B 186 ARG 0.004 0.000 ARG B 439 Details of bonding type rmsd hydrogen bonds : bond 0.03677 ( 162) hydrogen bonds : angle 5.62919 ( 357) SS BOND : bond 0.00212 ( 7) SS BOND : angle 1.35194 ( 14) covalent geometry : bond 0.00436 (10810) covalent geometry : angle 0.73620 (14656) *********************** 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 132 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 2.430 Fit side-chains REVERT: A 90 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7961 (mm) REVERT: A 304 ASP cc_start: 0.7892 (t0) cc_final: 0.7671 (t0) REVERT: A 365 HIS cc_start: 0.6896 (t-170) cc_final: 0.6668 (t-90) REVERT: A 392 TYR cc_start: 0.7131 (t80) cc_final: 0.6518 (t80) REVERT: A 394 PRO cc_start: 0.7465 (Cg_endo) cc_final: 0.6834 (Cg_exo) REVERT: A 690 MET cc_start: -0.0868 (mmp) cc_final: -0.3473 (ttm) REVERT: B 243 MET cc_start: 0.8283 (tpp) cc_final: 0.7699 (tpt) REVERT: B 438 MET cc_start: 0.7371 (mmt) cc_final: 0.7133 (mmt) REVERT: B 480 ARG cc_start: 0.6545 (mmm160) cc_final: 0.5595 (ttt180) REVERT: B 644 LEU cc_start: 0.4940 (OUTLIER) cc_final: 0.4584 (tp) outliers start: 22 outliers final: 13 residues processed: 129 average time/residue: 0.2920 time to fit residues: 58.7535 Evaluate side-chains 116 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 2.219 ------------------------------------------------------------------------------- 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 B residue 92 VAL 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 510 VAL Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 662 ASN 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 40 optimal weight: 0.1980 chunk 56 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 127 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 ** A 538 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 = 0.4444 r_free = 0.4444 target = 0.212797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.169452 restraints weight = 11484.413| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 3.46 r_work: 0.3555 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10817 Z= 0.150 Angle : 0.696 9.220 14670 Z= 0.368 Chirality : 0.046 0.157 1554 Planarity : 0.005 0.085 1910 Dihedral : 5.963 45.096 1458 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 1.13 % Allowed : 13.01 % Favored : 85.85 % Rotamer: Outliers : 2.43 % Allowed : 14.00 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -1.95 (0.29), residues: 335 loop : -2.50 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 542 HIS 0.004 0.001 HIS A 169 PHE 0.016 0.002 PHE B 200 TYR 0.016 0.001 TYR B 392 ARG 0.003 0.000 ARG B 439 Details of bonding type rmsd hydrogen bonds : bond 0.03126 ( 162) hydrogen bonds : angle 5.18513 ( 357) SS BOND : bond 0.00209 ( 7) SS BOND : angle 2.20116 ( 14) covalent geometry : bond 0.00342 (10810) covalent geometry : angle 0.69269 (14656) *********************** 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 131 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 1.114 Fit side-chains REVERT: A 90 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7927 (mm) REVERT: A 304 ASP cc_start: 0.7818 (t0) cc_final: 0.7599 (t0) REVERT: A 392 TYR cc_start: 0.7096 (t80) cc_final: 0.6453 (t80) REVERT: A 394 PRO cc_start: 0.7287 (Cg_endo) cc_final: 0.6630 (Cg_exo) REVERT: A 690 MET cc_start: -0.0950 (mmp) cc_final: -0.3473 (ttm) REVERT: B 243 MET cc_start: 0.8235 (tpp) cc_final: 0.7662 (tpt) REVERT: B 438 MET cc_start: 0.7314 (mmt) cc_final: 0.7086 (mmt) REVERT: B 480 ARG cc_start: 0.6447 (mmm160) cc_final: 0.5518 (ttt180) outliers start: 28 outliers final: 13 residues processed: 127 average time/residue: 0.2406 time to fit residues: 45.4006 Evaluate side-chains 112 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 364 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 637 ASP 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 53 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 42 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 57 optimal weight: 0.0060 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.211262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.167583 restraints weight = 11443.169| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 3.65 r_work: 0.3534 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10817 Z= 0.168 Angle : 0.701 10.968 14670 Z= 0.368 Chirality : 0.046 0.156 1554 Planarity : 0.005 0.082 1910 Dihedral : 5.961 44.419 1455 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 1.13 % Allowed : 14.07 % Favored : 84.80 % Rotamer: Outliers : 2.35 % Allowed : 14.96 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -1.96 (0.29), residues: 333 loop : -2.42 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 542 HIS 0.004 0.001 HIS A 169 PHE 0.020 0.002 PHE B 200 TYR 0.026 0.001 TYR A 349 ARG 0.002 0.000 ARG A 122 Details of bonding type rmsd hydrogen bonds : bond 0.03170 ( 162) hydrogen bonds : angle 5.05788 ( 357) SS BOND : bond 0.00261 ( 7) SS BOND : angle 1.83985 ( 14) covalent geometry : bond 0.00389 (10810) covalent geometry : angle 0.69907 (14656) *********************** 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 131 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: A 90 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7932 (mm) REVERT: A 235 ASP cc_start: 0.8207 (t70) cc_final: 0.7965 (t0) REVERT: A 253 TRP cc_start: 0.9148 (m100) cc_final: 0.8855 (m100) REVERT: A 304 ASP cc_start: 0.7803 (t0) cc_final: 0.7563 (t0) REVERT: A 392 TYR cc_start: 0.7117 (t80) cc_final: 0.6553 (t80) REVERT: A 394 PRO cc_start: 0.7297 (Cg_endo) cc_final: 0.6685 (Cg_exo) REVERT: A 690 MET cc_start: -0.0766 (mmp) cc_final: -0.3405 (ttm) REVERT: A 730 LYS cc_start: 0.2129 (OUTLIER) cc_final: 0.1889 (pttt) REVERT: B 189 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8708 (mt) REVERT: B 243 MET cc_start: 0.8243 (tpp) cc_final: 0.7649 (tpt) REVERT: B 411 PHE cc_start: 0.4734 (m-10) cc_final: 0.4440 (m-80) REVERT: B 438 MET cc_start: 0.7338 (mmt) cc_final: 0.7098 (mmt) outliers start: 27 outliers final: 17 residues processed: 127 average time/residue: 0.2030 time to fit residues: 38.3062 Evaluate side-chains 117 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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 364 SER Chi-restraints excluded: chain A residue 436 GLU 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 189 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 297 VAL 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 50 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 64 optimal weight: 0.0570 chunk 77 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 100 optimal weight: 0.0010 overall best weight: 0.5708 ------------------------------------------------------------------------------- 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 = 0.4405 r_free = 0.4405 target = 0.207647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.160488 restraints weight = 11781.092| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 4.28 r_work: 0.3481 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10817 Z= 0.128 Angle : 0.665 10.133 14670 Z= 0.349 Chirality : 0.045 0.153 1554 Planarity : 0.004 0.080 1910 Dihedral : 5.694 43.478 1455 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 1.13 % Allowed : 12.10 % Favored : 86.76 % Rotamer: Outliers : 2.70 % Allowed : 14.70 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -1.75 (0.29), residues: 326 loop : -2.34 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 542 HIS 0.003 0.001 HIS A 169 PHE 0.014 0.001 PHE B 200 TYR 0.018 0.001 TYR A 349 ARG 0.002 0.000 ARG A 122 Details of bonding type rmsd hydrogen bonds : bond 0.02792 ( 162) hydrogen bonds : angle 4.85315 ( 357) SS BOND : bond 0.00283 ( 7) SS BOND : angle 1.58088 ( 14) covalent geometry : bond 0.00293 (10810) covalent geometry : angle 0.66337 (14656) *********************** 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 138 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 1.115 Fit side-chains revert: symmetry clash REVERT: A 90 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7960 (mm) REVERT: A 235 ASP cc_start: 0.8253 (t70) cc_final: 0.7976 (t70) REVERT: A 304 ASP cc_start: 0.7895 (t0) cc_final: 0.7568 (t0) REVERT: A 392 TYR cc_start: 0.7101 (t80) cc_final: 0.6549 (t80) REVERT: A 394 PRO cc_start: 0.7156 (Cg_endo) cc_final: 0.6585 (Cg_exo) REVERT: A 690 MET cc_start: -0.0810 (mmp) cc_final: -0.3379 (ttm) REVERT: B 159 ARG cc_start: 0.7820 (mmp-170) cc_final: 0.7564 (mmp-170) REVERT: B 243 MET cc_start: 0.8161 (tpp) cc_final: 0.7495 (tpt) REVERT: B 438 MET cc_start: 0.7366 (mmt) cc_final: 0.7104 (mmt) outliers start: 31 outliers final: 23 residues processed: 135 average time/residue: 0.2252 time to fit residues: 44.6417 Evaluate side-chains 122 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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 436 GLU Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 481 LEU 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 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 637 ASP 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 99 optimal weight: 0.0370 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 42 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.7860 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.206114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.145154 restraints weight = 11992.322| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.95 r_work: 0.3548 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10817 Z= 0.148 Angle : 0.688 11.304 14670 Z= 0.362 Chirality : 0.046 0.247 1554 Planarity : 0.004 0.077 1910 Dihedral : 5.733 43.476 1455 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.98 % Allowed : 13.69 % Favored : 85.33 % Rotamer: Outliers : 2.43 % Allowed : 15.30 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -1.66 (0.30), residues: 318 loop : -2.33 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 542 HIS 0.004 0.001 HIS A 169 PHE 0.016 0.001 PHE A 284 TYR 0.019 0.001 TYR B 93 ARG 0.002 0.000 ARG A 122 Details of bonding type rmsd hydrogen bonds : bond 0.02892 ( 162) hydrogen bonds : angle 4.83172 ( 357) SS BOND : bond 0.00256 ( 7) SS BOND : angle 1.47246 ( 14) covalent geometry : bond 0.00343 (10810) covalent geometry : angle 0.68727 (14656) *********************** 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: 28 poor density : 100 time to evaluate : 1.115 Fit side-chains revert: symmetry clash REVERT: A 90 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7910 (mm) REVERT: A 304 ASP cc_start: 0.7816 (t0) cc_final: 0.7498 (t0) REVERT: A 374 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8499 (tp) REVERT: A 394 PRO cc_start: 0.7182 (Cg_endo) cc_final: 0.6926 (Cg_exo) REVERT: A 690 MET cc_start: -0.0924 (mmp) cc_final: -0.3459 (ttm) REVERT: B 159 ARG cc_start: 0.7850 (mmp-170) cc_final: 0.7486 (mmp-170) REVERT: B 243 MET cc_start: 0.8239 (tpp) cc_final: 0.7578 (tpt) REVERT: B 438 MET cc_start: 0.7377 (mmt) cc_final: 0.7118 (mmt) outliers start: 28 outliers final: 22 residues processed: 126 average time/residue: 0.2180 time to fit residues: 40.4293 Evaluate side-chains 120 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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 374 ILE Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 481 LEU 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 77 optimal weight: 0.6980 chunk 129 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 123 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS A 476 HIS ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.201854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.142126 restraints weight = 11903.883| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 3.64 r_work: 0.3434 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 10817 Z= 0.244 Angle : 0.769 10.558 14670 Z= 0.404 Chirality : 0.048 0.234 1554 Planarity : 0.005 0.076 1910 Dihedral : 6.277 53.059 1455 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 1.06 % Allowed : 16.04 % Favored : 82.90 % Rotamer: Outliers : 2.52 % Allowed : 16.17 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -1.89 (0.28), residues: 352 loop : -2.49 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 542 HIS 0.007 0.001 HIS A 169 PHE 0.020 0.002 PHE A 284 TYR 0.020 0.002 TYR A 563 ARG 0.003 0.000 ARG B 480 Details of bonding type rmsd hydrogen bonds : bond 0.03551 ( 162) hydrogen bonds : angle 5.10515 ( 357) SS BOND : bond 0.00282 ( 7) SS BOND : angle 1.61481 ( 14) covalent geometry : bond 0.00572 (10810) covalent geometry : angle 0.76726 (14656) *********************** 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 130 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 1.173 Fit side-chains REVERT: A 90 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7989 (mm) REVERT: A 253 TRP cc_start: 0.9282 (m100) cc_final: 0.9021 (m100) REVERT: A 374 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8540 (tp) REVERT: A 392 TYR cc_start: 0.7082 (t80) cc_final: 0.6418 (t80) REVERT: A 394 PRO cc_start: 0.7279 (Cg_endo) cc_final: 0.6591 (Cg_exo) REVERT: A 436 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7974 (pt0) REVERT: A 690 MET cc_start: -0.0494 (mmp) cc_final: -0.3154 (ttm) REVERT: B 159 ARG cc_start: 0.8098 (mmp-170) cc_final: 0.7767 (mmp-170) REVERT: B 411 PHE cc_start: 0.6006 (m-80) cc_final: 0.5766 (m-80) REVERT: B 438 MET cc_start: 0.7352 (mmt) cc_final: 0.7079 (mmt) REVERT: B 480 ARG cc_start: 0.6385 (mmm160) cc_final: 0.6052 (mmm160) outliers start: 29 outliers final: 22 residues processed: 127 average time/residue: 0.2174 time to fit residues: 40.4581 Evaluate side-chains 120 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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 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 374 ILE Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 550 THR 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 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 550 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 13 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 93 optimal weight: 0.0970 chunk 116 optimal weight: 0.0770 chunk 119 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 chunk 114 optimal weight: 0.5980 overall best weight: 0.4536 ------------------------------------------------------------------------------- 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 662 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.207206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.156989 restraints weight = 11862.549| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 4.64 r_work: 0.3423 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2793 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= 0.126 Angle : 0.686 10.637 14670 Z= 0.361 Chirality : 0.045 0.215 1554 Planarity : 0.004 0.074 1910 Dihedral : 5.708 42.966 1455 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.98 % Allowed : 12.10 % Favored : 86.91 % Rotamer: Outliers : 2.26 % Allowed : 16.78 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -1.70 (0.30), residues: 320 loop : -2.35 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 542 HIS 0.003 0.001 HIS B 545 PHE 0.038 0.001 PHE A 382 TYR 0.018 0.001 TYR B 392 ARG 0.007 0.000 ARG B 439 Details of bonding type rmsd hydrogen bonds : bond 0.02714 ( 162) hydrogen bonds : angle 4.79373 ( 357) SS BOND : bond 0.00239 ( 7) SS BOND : angle 1.31262 ( 14) covalent geometry : bond 0.00288 (10810) covalent geometry : angle 0.68559 (14656) *********************** 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 128 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 1.208 Fit side-chains revert: symmetry clash REVERT: A 90 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7982 (mm) REVERT: A 392 TYR cc_start: 0.7036 (t80) cc_final: 0.6472 (t80) REVERT: A 394 PRO cc_start: 0.7140 (Cg_endo) cc_final: 0.6482 (Cg_exo) REVERT: A 690 MET cc_start: -0.0612 (mmp) cc_final: -0.3237 (ttm) REVERT: B 159 ARG cc_start: 0.7976 (mmp-170) cc_final: 0.7653 (mmp-170) REVERT: B 243 MET cc_start: 0.8117 (tpp) cc_final: 0.7512 (tpt) REVERT: B 438 MET cc_start: 0.7315 (mmt) cc_final: 0.7051 (mmt) outliers start: 26 outliers final: 22 residues processed: 125 average time/residue: 0.2288 time to fit residues: 41.3924 Evaluate side-chains 122 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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 436 GLU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 481 LEU 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 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 566 ASN Chi-restraints excluded: chain B residue 662 ASN 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 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.206580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.157335 restraints weight = 11843.636| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 4.77 r_work: 0.3444 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10817 Z= 0.140 Angle : 0.702 11.412 14670 Z= 0.366 Chirality : 0.045 0.196 1554 Planarity : 0.004 0.074 1910 Dihedral : 5.685 42.800 1455 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.91 % Allowed : 13.24 % Favored : 85.85 % Rotamer: Outliers : 2.00 % Allowed : 17.04 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -1.64 (0.30), residues: 320 loop : -2.34 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 542 HIS 0.003 0.001 HIS A 169 PHE 0.035 0.002 PHE A 382 TYR 0.020 0.001 TYR B 392 ARG 0.007 0.000 ARG B 439 Details of bonding type rmsd hydrogen bonds : bond 0.02759 ( 162) hydrogen bonds : angle 4.76231 ( 357) SS BOND : bond 0.00253 ( 7) SS BOND : angle 1.32233 ( 14) covalent geometry : bond 0.00323 (10810) covalent geometry : angle 0.70121 (14656) ********************** 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 126 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: A 90 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7951 (mm) REVERT: A 246 GLU cc_start: 0.7558 (tp30) cc_final: 0.7356 (tp30) REVERT: A 392 TYR cc_start: 0.7030 (t80) cc_final: 0.6462 (t80) REVERT: A 394 PRO cc_start: 0.7150 (Cg_endo) cc_final: 0.6502 (Cg_exo) REVERT: A 690 MET cc_start: -0.0556 (mmp) cc_final: -0.3204 (ttm) REVERT: B 243 MET cc_start: 0.8172 (tpp) cc_final: 0.7516 (tpt) REVERT: B 411 PHE cc_start: 0.5663 (m-80) cc_final: 0.5430 (m-80) REVERT: B 438 MET cc_start: 0.7341 (mmt) cc_final: 0.7079 (mmt) outliers start: 23 outliers final: 21 residues processed: 123 average time/residue: 0.2150 time to fit residues: 38.4293 Evaluate side-chains 122 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 1.142 ------------------------------------------------------------------------------- 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 436 GLU Chi-restraints excluded: chain A residue 481 LEU 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 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 566 ASN 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 110 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 77 optimal weight: 0.0980 chunk 72 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 32 optimal weight: 0.0050 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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 662 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.207731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.152769 restraints weight = 11754.843| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 3.53 r_work: 0.3547 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10817 Z= 0.130 Angle : 0.688 10.373 14670 Z= 0.358 Chirality : 0.045 0.174 1554 Planarity : 0.004 0.074 1910 Dihedral : 5.605 42.417 1455 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.91 % Allowed : 12.48 % Favored : 86.61 % Rotamer: Outliers : 2.00 % Allowed : 17.04 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -1.55 (0.30), residues: 318 loop : -2.28 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 542 HIS 0.003 0.001 HIS A 169 PHE 0.028 0.001 PHE A 382 TYR 0.019 0.001 TYR B 392 ARG 0.007 0.000 ARG B 439 Details of bonding type rmsd hydrogen bonds : bond 0.02644 ( 162) hydrogen bonds : angle 4.73488 ( 357) SS BOND : bond 0.00247 ( 7) SS BOND : angle 1.28326 ( 14) covalent geometry : bond 0.00299 (10810) covalent geometry : angle 0.68676 (14656) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5851.77 seconds wall clock time: 105 minutes 26.62 seconds (6326.62 seconds total)