Starting phenix.real_space_refine on Tue Jul 29 13:07:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b5d_12026/07_2025/7b5d_12026.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b5d_12026/07_2025/7b5d_12026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7b5d_12026/07_2025/7b5d_12026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b5d_12026/07_2025/7b5d_12026.map" model { file = "/net/cci-nas-00/data/ceres_data/7b5d_12026/07_2025/7b5d_12026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b5d_12026/07_2025/7b5d_12026.cif" } resolution = 3.3 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= 0.000 sd= 0.005 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 72 5.16 5 C 7470 2.51 5 N 1888 2.21 5 O 2032 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11462 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5731 Classifications: {'peptide': 701} Link IDs: {'PTRANS': 30, 'TRANS': 670} Chain breaks: 4 Restraints were copied for chains: B Time building chain proxies: 11.58, per 1000 atoms: 1.01 Number of scatterers: 11462 At special positions: 0 Unit cell: (107.272, 116.38, 115.368, 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 72 16.00 O 2032 8.00 N 1888 7.00 C 7470 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 836 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 386 " distance=2.03 Simple disulfide: pdb=" SG CYS A 625 " - pdb=" SG CYS A 630 " distance=2.04 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 836 " distance=2.04 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS B 625 " - pdb=" SG CYS B 630 " distance=2.04 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: 3.37 Conformation dependent library (CDL) restraints added in 1.7 seconds 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2688 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 10 sheets defined 61.8% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 166 through 181 removed outlier: 4.157A pdb=" N MET A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 242 through 257 Processing helix chain 'A' and resid 268 through 275 Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 316 through 325 Processing helix chain 'A' and resid 325 through 360 removed outlier: 3.923A pdb=" N ILE A 343 " --> pdb=" O THR A 339 " (cutoff:3.500A) Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 363 through 371 removed outlier: 3.594A pdb=" N MET A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET A 369 " --> pdb=" O PRO A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 406 through 439 removed outlier: 4.233A pdb=" N VAL A 410 " --> pdb=" O ASN A 406 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE A 411 " --> pdb=" O PRO A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 466 Processing helix chain 'A' and resid 490 through 519 removed outlier: 4.418A pdb=" N SER A 496 " --> pdb=" O THR A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 567 removed outlier: 4.303A pdb=" N GLU A 555 " --> pdb=" O ALA A 551 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 601 Proline residue: A 595 - end of helix Processing helix chain 'A' and resid 630 through 651 removed outlier: 4.704A pdb=" N GLN A 646 " --> pdb=" O MET A 642 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N GLN A 649 " --> pdb=" O LYS A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 692 Processing helix chain 'A' and resid 699 through 717 removed outlier: 3.876A pdb=" N MET A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 745 removed outlier: 3.507A pdb=" N PHE A 726 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE A 733 " --> pdb=" O LEU A 729 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG A 736 " --> pdb=" O ILE A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 4.199A pdb=" N ASN A 762 " --> pdb=" O GLY A 758 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 772 " --> pdb=" O GLY A 768 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 795 Processing helix chain 'A' and resid 803 through 809 Processing helix chain 'A' and resid 854 through 886 removed outlier: 3.887A pdb=" N TRP A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 910 Processing helix chain 'B' and resid 166 through 181 removed outlier: 4.157A pdb=" N MET B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Proline residue: B 177 - end of helix Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 242 through 257 Processing helix chain 'B' and resid 268 through 275 Processing helix chain 'B' and resid 296 through 305 Processing helix chain 'B' and resid 316 through 325 Processing helix chain 'B' and resid 325 through 360 removed outlier: 3.923A pdb=" N ILE B 343 " --> pdb=" O THR B 339 " (cutoff:3.500A) Proline residue: B 344 - end of helix Processing helix chain 'B' and resid 363 through 371 removed outlier: 3.594A pdb=" N MET B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET B 369 " --> pdb=" O PRO B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 406 through 439 removed outlier: 4.234A pdb=" N VAL B 410 " --> pdb=" O ASN B 406 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N PHE B 411 " --> pdb=" O PRO B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 466 Processing helix chain 'B' and resid 490 through 519 removed outlier: 4.418A pdb=" N SER B 496 " --> pdb=" O THR B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 567 removed outlier: 4.303A pdb=" N GLU B 555 " --> pdb=" O ALA B 551 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL B 556 " --> pdb=" O LEU B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 601 Proline residue: B 595 - end of helix Processing helix chain 'B' and resid 630 through 651 removed outlier: 4.704A pdb=" N GLN B 646 " --> pdb=" O MET B 642 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLN B 649 " --> pdb=" O LYS B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 692 Processing helix chain 'B' and resid 699 through 717 removed outlier: 3.876A pdb=" N MET B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 745 removed outlier: 3.507A pdb=" N PHE B 726 " --> pdb=" O LEU B 722 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE B 733 " --> pdb=" O LEU B 729 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG B 736 " --> pdb=" O ILE B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 782 removed outlier: 4.200A pdb=" N ASN B 762 " --> pdb=" O GLY B 758 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL B 772 " --> pdb=" O GLY B 768 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE B 773 " --> pdb=" O LYS B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 795 Processing helix chain 'B' and resid 803 through 809 Processing helix chain 'B' and resid 854 through 886 removed outlier: 3.887A pdb=" N TRP B 858 " --> pdb=" O SER B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 910 Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 188 removed outlier: 3.779A pdb=" N THR A 187 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP A 123 " --> pdb=" O GLN A 199 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA A 279 " --> pdb=" O PHE A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 217 through 218 Processing sheet with id=AA3, first strand: chain 'A' and resid 377 through 378 removed outlier: 4.020A pdb=" N TRP A 389 " --> pdb=" O MET A 378 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 615 through 616 removed outlier: 3.975A pdb=" N PHE A 620 " --> pdb=" O ILE A 616 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 810 through 813 Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 188 removed outlier: 3.778A pdb=" N THR B 187 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP B 123 " --> pdb=" O GLN B 199 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA B 279 " --> pdb=" O PHE B 126 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 217 through 218 Processing sheet with id=AA8, first strand: chain 'B' and resid 377 through 378 removed outlier: 4.021A pdb=" N TRP B 389 " --> pdb=" O MET B 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 615 through 616 removed outlier: 3.975A pdb=" N PHE B 620 " --> pdb=" O ILE B 616 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 810 through 813 652 hydrogen bonds defined for protein. 1944 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: 3.39 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3559 1.34 - 1.46: 2753 1.46 - 1.58: 5322 1.58 - 1.70: 0 1.70 - 1.82: 118 Bond restraints: 11752 Sorted by residual: bond pdb=" C ILE A 786 " pdb=" N PRO A 787 " ideal model delta sigma weight residual 1.335 1.350 -0.016 1.28e-02 6.10e+03 1.49e+00 bond pdb=" C ILE A 343 " pdb=" N PRO A 344 " ideal model delta sigma weight residual 1.336 1.350 -0.015 1.23e-02 6.61e+03 1.44e+00 bond pdb=" C ILE B 343 " pdb=" N PRO B 344 " ideal model delta sigma weight residual 1.336 1.350 -0.015 1.23e-02 6.61e+03 1.44e+00 bond pdb=" CB GLN A 896 " pdb=" CG GLN A 896 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.43e+00 bond pdb=" C ILE B 786 " pdb=" N PRO B 787 " ideal model delta sigma weight residual 1.335 1.350 -0.015 1.28e-02 6.10e+03 1.43e+00 ... (remaining 11747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 15754 3.25 - 6.50: 127 6.50 - 9.75: 25 9.75 - 13.00: 0 13.00 - 16.25: 2 Bond angle restraints: 15908 Sorted by residual: angle pdb=" CA LEU A 381 " pdb=" CB LEU A 381 " pdb=" CG LEU A 381 " ideal model delta sigma weight residual 116.30 132.55 -16.25 3.50e+00 8.16e-02 2.15e+01 angle pdb=" CA LEU B 381 " pdb=" CB LEU B 381 " pdb=" CG LEU B 381 " ideal model delta sigma weight residual 116.30 132.50 -16.20 3.50e+00 8.16e-02 2.14e+01 angle pdb=" CA CYS B 625 " pdb=" CB CYS B 625 " pdb=" SG CYS B 625 " ideal model delta sigma weight residual 114.40 122.49 -8.09 2.30e+00 1.89e-01 1.24e+01 angle pdb=" CA CYS A 625 " pdb=" CB CYS A 625 " pdb=" SG CYS A 625 " ideal model delta sigma weight residual 114.40 122.44 -8.04 2.30e+00 1.89e-01 1.22e+01 angle pdb=" C TYR B 288 " pdb=" N GLU B 289 " pdb=" CA GLU B 289 " ideal model delta sigma weight residual 121.54 128.04 -6.50 1.91e+00 2.74e-01 1.16e+01 ... (remaining 15903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 6166 17.68 - 35.36: 700 35.36 - 53.04: 118 53.04 - 70.72: 32 70.72 - 88.40: 6 Dihedral angle restraints: 7022 sinusoidal: 2870 harmonic: 4152 Sorted by residual: dihedral pdb=" CB CYS B 382 " pdb=" SG CYS B 382 " pdb=" SG CYS B 386 " pdb=" CB CYS B 386 " ideal model delta sinusoidal sigma weight residual -86.00 -139.55 53.55 1 1.00e+01 1.00e-02 3.90e+01 dihedral pdb=" CB CYS A 382 " pdb=" SG CYS A 382 " pdb=" SG CYS A 386 " pdb=" CB CYS A 386 " ideal model delta sinusoidal sigma weight residual -86.00 -139.55 53.55 1 1.00e+01 1.00e-02 3.90e+01 dihedral pdb=" CB CYS B 625 " pdb=" SG CYS B 625 " pdb=" SG CYS B 630 " pdb=" CB CYS B 630 " ideal model delta sinusoidal sigma weight residual -86.00 -38.37 -47.63 1 1.00e+01 1.00e-02 3.13e+01 ... (remaining 7019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1252 0.048 - 0.096: 375 0.096 - 0.144: 109 0.144 - 0.191: 14 0.191 - 0.239: 2 Chirality restraints: 1752 Sorted by residual: chirality pdb=" CB VAL B 310 " pdb=" CA VAL B 310 " pdb=" CG1 VAL B 310 " pdb=" CG2 VAL B 310 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB VAL A 310 " pdb=" CA VAL A 310 " pdb=" CG1 VAL A 310 " pdb=" CG2 VAL A 310 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB VAL B 750 " pdb=" CA VAL B 750 " pdb=" CG1 VAL B 750 " pdb=" CG2 VAL B 750 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 1749 not shown) Planarity restraints: 1998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 203 " 0.056 5.00e-02 4.00e+02 8.44e-02 1.14e+01 pdb=" N PRO B 204 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO B 204 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 204 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 203 " -0.056 5.00e-02 4.00e+02 8.44e-02 1.14e+01 pdb=" N PRO A 204 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO A 204 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 204 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 609 " 0.044 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO A 610 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 610 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 610 " 0.037 5.00e-02 4.00e+02 ... (remaining 1995 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1905 2.76 - 3.30: 10971 3.30 - 3.83: 18889 3.83 - 4.37: 21475 4.37 - 4.90: 37496 Nonbonded interactions: 90736 Sorted by model distance: nonbonded pdb=" O VAL B 590 " pdb=" OG1 THR B 594 " model vdw 2.225 3.040 nonbonded pdb=" O VAL A 590 " pdb=" OG1 THR A 594 " model vdw 2.226 3.040 nonbonded pdb=" OD1 ASN A 406 " pdb=" OG1 THR A 409 " model vdw 2.319 3.040 nonbonded pdb=" OD1 ASN B 406 " pdb=" OG1 THR B 409 " model vdw 2.320 3.040 nonbonded pdb=" OH TYR A 331 " pdb=" OD2 ASP A 738 " model vdw 2.331 3.040 ... (remaining 90731 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: 5.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.580 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 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 : 0.005 0.059 11760 Z= 0.224 Angle : 0.839 16.246 15924 Z= 0.452 Chirality : 0.049 0.239 1752 Planarity : 0.007 0.084 1998 Dihedral : 15.096 88.397 4310 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.96 % Allowed : 6.98 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -3.54 (0.18), residues: 1382 helix: -1.66 (0.14), residues: 832 sheet: -3.02 (0.66), residues: 44 loop : -3.36 (0.22), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 427 HIS 0.005 0.001 HIS B 807 PHE 0.024 0.002 PHE A 817 TYR 0.023 0.002 TYR B 119 ARG 0.001 0.000 ARG A 621 Details of bonding type rmsd hydrogen bonds : bond 0.08138 ( 652) hydrogen bonds : angle 5.32113 ( 1944) SS BOND : bond 0.00392 ( 8) SS BOND : angle 2.18447 ( 16) covalent geometry : bond 0.00515 (11752) covalent geometry : angle 0.83702 (15908) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 197 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.6995 (ttt) cc_final: 0.6536 (ttp) REVERT: A 500 MET cc_start: 0.6870 (mmt) cc_final: 0.5881 (mtp) REVERT: A 505 PHE cc_start: 0.7435 (t80) cc_final: 0.7037 (t80) REVERT: A 704 MET cc_start: 0.7669 (tpp) cc_final: 0.7168 (ttm) REVERT: A 906 GLU cc_start: 0.6719 (OUTLIER) cc_final: 0.6355 (tt0) REVERT: B 117 MET cc_start: 0.6517 (ttt) cc_final: 0.6087 (ttp) REVERT: B 233 ASP cc_start: 0.5718 (m-30) cc_final: 0.5485 (m-30) REVERT: B 462 VAL cc_start: 0.4170 (OUTLIER) cc_final: 0.3925 (t) REVERT: B 500 MET cc_start: 0.6477 (mmt) cc_final: 0.5752 (mtp) REVERT: B 706 MET cc_start: 0.8315 (mmp) cc_final: 0.8089 (mmp) REVERT: B 753 ARG cc_start: 0.7292 (mtp180) cc_final: 0.7089 (mtp180) REVERT: B 794 MET cc_start: 0.7235 (mtt) cc_final: 0.7008 (mtp) REVERT: B 876 MET cc_start: 0.6786 (mtm) cc_final: 0.6581 (ptt) outliers start: 12 outliers final: 0 residues processed: 206 average time/residue: 0.2985 time to fit residues: 82.0675 Evaluate side-chains 154 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 152 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain B residue 462 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 406 ASN A 709 GLN A 730 ASN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 ASN B 709 GLN B 730 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.160357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.129295 restraints weight = 13012.704| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.45 r_work: 0.3178 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11760 Z= 0.150 Angle : 0.616 11.537 15924 Z= 0.313 Chirality : 0.041 0.130 1752 Planarity : 0.005 0.078 1998 Dihedral : 5.233 67.343 1550 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.12 % Allowed : 13.16 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.67 (0.21), residues: 1382 helix: 0.05 (0.17), residues: 836 sheet: -3.20 (0.62), residues: 44 loop : -2.93 (0.23), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 427 HIS 0.003 0.001 HIS B 898 PHE 0.018 0.001 PHE B 505 TYR 0.018 0.001 TYR B 119 ARG 0.004 0.000 ARG A 125 Details of bonding type rmsd hydrogen bonds : bond 0.04060 ( 652) hydrogen bonds : angle 4.39868 ( 1944) SS BOND : bond 0.00335 ( 8) SS BOND : angle 1.41158 ( 16) covalent geometry : bond 0.00353 (11752) covalent geometry : angle 0.61432 (15908) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 1.462 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.7316 (ttt) cc_final: 0.6541 (ttp) REVERT: A 219 ARG cc_start: 0.4950 (mmt180) cc_final: 0.4585 (mmm160) REVERT: A 233 ASP cc_start: 0.6037 (m-30) cc_final: 0.5619 (t70) REVERT: A 416 MET cc_start: 0.8965 (tpt) cc_final: 0.8683 (tpt) REVERT: A 500 MET cc_start: 0.6636 (mmt) cc_final: 0.5264 (mtp) REVERT: A 505 PHE cc_start: 0.7828 (t80) cc_final: 0.7393 (t80) REVERT: A 704 MET cc_start: 0.8535 (tpp) cc_final: 0.8085 (ttm) REVERT: A 734 GLU cc_start: 0.8422 (tp30) cc_final: 0.8154 (tp30) REVERT: A 784 ASP cc_start: 0.8591 (t0) cc_final: 0.8297 (t0) REVERT: B 117 MET cc_start: 0.6709 (ttt) cc_final: 0.6135 (ttp) REVERT: B 416 MET cc_start: 0.8923 (tpt) cc_final: 0.8554 (mmp) REVERT: B 500 MET cc_start: 0.6475 (mmt) cc_final: 0.5334 (mtp) REVERT: B 505 PHE cc_start: 0.7347 (t80) cc_final: 0.6924 (t80) REVERT: B 753 ARG cc_start: 0.7926 (mtp180) cc_final: 0.7427 (mtp180) REVERT: B 801 MET cc_start: 0.8293 (mtm) cc_final: 0.8053 (mtm) outliers start: 14 outliers final: 4 residues processed: 177 average time/residue: 0.4355 time to fit residues: 105.9137 Evaluate side-chains 158 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 154 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 769 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 41 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 53 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 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 206 GLN A 406 ASN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** 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 = 0.3836 r_free = 0.3836 target = 0.161836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.130125 restraints weight = 13098.555| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.41 r_work: 0.3205 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11760 Z= 0.124 Angle : 0.579 11.425 15924 Z= 0.294 Chirality : 0.040 0.141 1752 Planarity : 0.005 0.076 1998 Dihedral : 4.550 21.689 1546 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.77 % Allowed : 14.45 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.91 (0.22), residues: 1382 helix: 0.76 (0.17), residues: 836 sheet: -3.24 (0.56), residues: 44 loop : -2.78 (0.24), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 427 HIS 0.003 0.001 HIS A 898 PHE 0.016 0.001 PHE B 589 TYR 0.016 0.001 TYR B 119 ARG 0.004 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.03771 ( 652) hydrogen bonds : angle 4.22533 ( 1944) SS BOND : bond 0.00339 ( 8) SS BOND : angle 2.10342 ( 16) covalent geometry : bond 0.00282 (11752) covalent geometry : angle 0.57565 (15908) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 3.864 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.7248 (ttt) cc_final: 0.6466 (ttp) REVERT: A 219 ARG cc_start: 0.5062 (mmt180) cc_final: 0.4567 (mmm160) REVERT: A 233 ASP cc_start: 0.6191 (m-30) cc_final: 0.5666 (t0) REVERT: A 416 MET cc_start: 0.8921 (tpt) cc_final: 0.8511 (tpt) REVERT: A 505 PHE cc_start: 0.7577 (t80) cc_final: 0.7140 (t80) REVERT: A 704 MET cc_start: 0.8542 (tpp) cc_final: 0.8162 (ttm) REVERT: A 734 GLU cc_start: 0.8361 (tp30) cc_final: 0.8122 (tp30) REVERT: A 769 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7416 (tttt) REVERT: A 784 ASP cc_start: 0.8738 (t0) cc_final: 0.8295 (t0) REVERT: B 117 MET cc_start: 0.6444 (ttt) cc_final: 0.6031 (ttp) REVERT: B 215 GLN cc_start: 0.7500 (pt0) cc_final: 0.7101 (mt0) REVERT: B 233 ASP cc_start: 0.5904 (m-30) cc_final: 0.5119 (t70) REVERT: B 416 MET cc_start: 0.8881 (tpt) cc_final: 0.8542 (tpt) REVERT: B 500 MET cc_start: 0.6511 (mmt) cc_final: 0.5348 (mtp) REVERT: B 505 PHE cc_start: 0.7263 (t80) cc_final: 0.6895 (t80) REVERT: B 753 ARG cc_start: 0.7907 (mtp180) cc_final: 0.7400 (mtp180) outliers start: 22 outliers final: 8 residues processed: 184 average time/residue: 0.4831 time to fit residues: 122.2881 Evaluate side-chains 171 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 162 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 795 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 45 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS A 406 ASN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** 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 = 0.3837 r_free = 0.3837 target = 0.161778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.128995 restraints weight = 13038.336| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.46 r_work: 0.3186 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11760 Z= 0.139 Angle : 0.575 11.271 15924 Z= 0.291 Chirality : 0.040 0.154 1752 Planarity : 0.004 0.074 1998 Dihedral : 4.426 17.666 1546 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.52 % Allowed : 17.01 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.61 (0.22), residues: 1382 helix: 1.03 (0.17), residues: 828 sheet: -3.23 (0.55), residues: 44 loop : -2.64 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 427 HIS 0.004 0.001 HIS B 402 PHE 0.015 0.001 PHE A 589 TYR 0.015 0.001 TYR B 119 ARG 0.005 0.000 ARG B 127 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 652) hydrogen bonds : angle 4.18149 ( 1944) SS BOND : bond 0.00261 ( 8) SS BOND : angle 1.68034 ( 16) covalent geometry : bond 0.00324 (11752) covalent geometry : angle 0.57292 (15908) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 1.451 Fit side-chains revert: symmetry clash REVERT: A 219 ARG cc_start: 0.5305 (mmt180) cc_final: 0.4798 (mmm160) REVERT: A 233 ASP cc_start: 0.6126 (m-30) cc_final: 0.5724 (t0) REVERT: A 416 MET cc_start: 0.8956 (tpt) cc_final: 0.8500 (tpt) REVERT: A 505 PHE cc_start: 0.7629 (t80) cc_final: 0.7179 (t80) REVERT: A 704 MET cc_start: 0.8625 (tpp) cc_final: 0.8188 (ttm) REVERT: A 734 GLU cc_start: 0.8303 (tp30) cc_final: 0.8071 (tp30) REVERT: A 769 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7377 (tttt) REVERT: B 215 GLN cc_start: 0.7438 (pt0) cc_final: 0.7056 (mt0) REVERT: B 233 ASP cc_start: 0.6040 (m-30) cc_final: 0.5221 (t70) REVERT: B 416 MET cc_start: 0.8937 (tpt) cc_final: 0.8529 (tpt) REVERT: B 505 PHE cc_start: 0.7287 (t80) cc_final: 0.6912 (t80) REVERT: B 753 ARG cc_start: 0.7958 (mtp180) cc_final: 0.7414 (mtp180) REVERT: B 769 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.6662 (ttpt) outliers start: 19 outliers final: 12 residues processed: 181 average time/residue: 0.3343 time to fit residues: 82.1828 Evaluate side-chains 173 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 795 TYR Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain B residue 795 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 32 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 126 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 78 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 1 optimal weight: 8.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 ASN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** 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 = 0.3837 r_free = 0.3837 target = 0.161810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.130444 restraints weight = 13037.472| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.46 r_work: 0.3178 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11760 Z= 0.142 Angle : 0.576 11.219 15924 Z= 0.292 Chirality : 0.040 0.156 1752 Planarity : 0.004 0.075 1998 Dihedral : 4.381 19.048 1546 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.61 % Allowed : 18.06 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.46 (0.22), residues: 1382 helix: 1.13 (0.17), residues: 828 sheet: -3.35 (0.54), residues: 44 loop : -2.52 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 427 HIS 0.004 0.001 HIS B 402 PHE 0.015 0.001 PHE A 589 TYR 0.015 0.001 TYR B 119 ARG 0.005 0.000 ARG B 127 Details of bonding type rmsd hydrogen bonds : bond 0.03774 ( 652) hydrogen bonds : angle 4.16624 ( 1944) SS BOND : bond 0.00272 ( 8) SS BOND : angle 1.34898 ( 16) covalent geometry : bond 0.00333 (11752) covalent geometry : angle 0.57438 (15908) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 1.234 Fit side-chains revert: symmetry clash REVERT: A 205 ILE cc_start: 0.7030 (pt) cc_final: 0.6468 (pt) REVERT: A 219 ARG cc_start: 0.5211 (mmt180) cc_final: 0.4683 (mmm160) REVERT: A 233 ASP cc_start: 0.6066 (m-30) cc_final: 0.5793 (t0) REVERT: A 416 MET cc_start: 0.8956 (tpt) cc_final: 0.8471 (tpt) REVERT: A 505 PHE cc_start: 0.7624 (t80) cc_final: 0.7175 (t80) REVERT: B 215 GLN cc_start: 0.7455 (pt0) cc_final: 0.7111 (mt0) REVERT: B 233 ASP cc_start: 0.5967 (m-30) cc_final: 0.5285 (t70) REVERT: B 416 MET cc_start: 0.8959 (tpt) cc_final: 0.8510 (tpt) REVERT: B 505 PHE cc_start: 0.7357 (t80) cc_final: 0.6956 (t80) REVERT: B 753 ARG cc_start: 0.7918 (mtp180) cc_final: 0.7413 (mtp180) REVERT: B 769 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.6700 (ttpt) outliers start: 20 outliers final: 12 residues processed: 184 average time/residue: 0.4628 time to fit residues: 119.1994 Evaluate side-chains 174 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 161 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 795 TYR Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain B residue 795 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 11 optimal weight: 0.0970 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 104 optimal weight: 0.2980 chunk 75 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 ASN ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** 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 = 0.3946 r_free = 0.3946 target = 0.170319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.136029 restraints weight = 13191.602| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.66 r_work: 0.3165 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11760 Z= 0.132 Angle : 0.575 11.034 15924 Z= 0.290 Chirality : 0.040 0.157 1752 Planarity : 0.004 0.074 1998 Dihedral : 4.348 24.007 1546 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.85 % Allowed : 18.62 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.29 (0.22), residues: 1382 helix: 1.26 (0.18), residues: 824 sheet: -3.36 (0.56), residues: 44 loop : -2.42 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 427 HIS 0.004 0.001 HIS B 402 PHE 0.015 0.001 PHE A 589 TYR 0.014 0.001 TYR B 119 ARG 0.006 0.000 ARG B 127 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 652) hydrogen bonds : angle 4.11752 ( 1944) SS BOND : bond 0.00329 ( 8) SS BOND : angle 1.82653 ( 16) covalent geometry : bond 0.00306 (11752) covalent geometry : angle 0.57233 (15908) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 1.384 Fit side-chains revert: symmetry clash REVERT: A 219 ARG cc_start: 0.5406 (mmt180) cc_final: 0.4842 (mmm160) REVERT: A 233 ASP cc_start: 0.6051 (m-30) cc_final: 0.5746 (t0) REVERT: A 416 MET cc_start: 0.8932 (tpt) cc_final: 0.8419 (tpt) REVERT: A 497 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7635 (mp) REVERT: A 505 PHE cc_start: 0.7531 (t80) cc_final: 0.7091 (t80) REVERT: B 125 ARG cc_start: 0.8072 (mtm-85) cc_final: 0.7551 (mtm-85) REVERT: B 194 ILE cc_start: 0.5722 (pt) cc_final: 0.5447 (tt) REVERT: B 215 GLN cc_start: 0.7423 (pt0) cc_final: 0.7056 (mt0) REVERT: B 219 ARG cc_start: 0.4721 (mmm160) cc_final: 0.4478 (mmm160) REVERT: B 233 ASP cc_start: 0.5818 (m-30) cc_final: 0.5171 (t70) REVERT: B 416 MET cc_start: 0.8946 (tpt) cc_final: 0.8449 (tpt) REVERT: B 505 PHE cc_start: 0.7266 (t80) cc_final: 0.6869 (t80) REVERT: B 753 ARG cc_start: 0.7930 (mtp180) cc_final: 0.7381 (mtp180) REVERT: B 769 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.6675 (ttpt) outliers start: 23 outliers final: 13 residues processed: 185 average time/residue: 0.3017 time to fit residues: 75.2317 Evaluate side-chains 175 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 795 TYR Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain B residue 795 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 20 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 128 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 121 optimal weight: 0.6980 chunk 135 optimal weight: 0.0970 chunk 24 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 95 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 ASN A 818 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** 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 = 0.3961 r_free = 0.3961 target = 0.171617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.139396 restraints weight = 13202.501| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.33 r_work: 0.3211 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11760 Z= 0.121 Angle : 0.573 10.866 15924 Z= 0.289 Chirality : 0.040 0.159 1752 Planarity : 0.004 0.075 1998 Dihedral : 4.321 25.262 1546 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.85 % Allowed : 18.62 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.15 (0.22), residues: 1382 helix: 1.39 (0.18), residues: 824 sheet: -3.35 (0.56), residues: 44 loop : -2.37 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 427 HIS 0.004 0.001 HIS B 402 PHE 0.015 0.001 PHE A 589 TYR 0.013 0.001 TYR A 119 ARG 0.006 0.000 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 652) hydrogen bonds : angle 4.07550 ( 1944) SS BOND : bond 0.00257 ( 8) SS BOND : angle 2.13091 ( 16) covalent geometry : bond 0.00275 (11752) covalent geometry : angle 0.56892 (15908) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 1.153 Fit side-chains revert: symmetry clash REVERT: A 219 ARG cc_start: 0.5380 (mmt180) cc_final: 0.4617 (mmm160) REVERT: A 233 ASP cc_start: 0.6035 (m-30) cc_final: 0.5752 (t0) REVERT: A 416 MET cc_start: 0.8864 (tpt) cc_final: 0.8336 (tpt) REVERT: A 497 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7570 (mp) REVERT: A 505 PHE cc_start: 0.7543 (t80) cc_final: 0.7125 (t80) REVERT: B 194 ILE cc_start: 0.5395 (pt) cc_final: 0.5068 (tt) REVERT: B 215 GLN cc_start: 0.7255 (pt0) cc_final: 0.6980 (mt0) REVERT: B 219 ARG cc_start: 0.4524 (mmm160) cc_final: 0.4129 (mmm160) REVERT: B 233 ASP cc_start: 0.5604 (m-30) cc_final: 0.5314 (t70) REVERT: B 416 MET cc_start: 0.8876 (tpt) cc_final: 0.8359 (tpt) REVERT: B 505 PHE cc_start: 0.7278 (t80) cc_final: 0.6895 (t80) REVERT: B 753 ARG cc_start: 0.7863 (mtp180) cc_final: 0.7368 (mtp180) REVERT: B 769 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.6589 (ttpt) REVERT: B 878 MET cc_start: 0.8609 (mtp) cc_final: 0.8355 (mtp) outliers start: 23 outliers final: 15 residues processed: 185 average time/residue: 0.2874 time to fit residues: 71.6351 Evaluate side-chains 177 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 795 TYR Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain B residue 795 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 111 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 74 optimal weight: 0.4980 chunk 133 optimal weight: 0.9990 chunk 131 optimal weight: 7.9990 chunk 125 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 77 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 ASN B 206 GLN ** B 215 GLN ** 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 = 0.3960 r_free = 0.3960 target = 0.171532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.140455 restraints weight = 13113.188| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.40 r_work: 0.3210 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11760 Z= 0.124 Angle : 0.579 10.764 15924 Z= 0.289 Chirality : 0.040 0.164 1752 Planarity : 0.004 0.074 1998 Dihedral : 4.267 24.178 1546 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.85 % Allowed : 19.02 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.04 (0.22), residues: 1382 helix: 1.48 (0.18), residues: 824 sheet: -3.38 (0.56), residues: 44 loop : -2.31 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 427 HIS 0.004 0.001 HIS A 402 PHE 0.015 0.001 PHE B 589 TYR 0.013 0.001 TYR A 119 ARG 0.007 0.000 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 652) hydrogen bonds : angle 4.06626 ( 1944) SS BOND : bond 0.00253 ( 8) SS BOND : angle 1.83113 ( 16) covalent geometry : bond 0.00285 (11752) covalent geometry : angle 0.57607 (15908) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 1.184 Fit side-chains revert: symmetry clash REVERT: A 219 ARG cc_start: 0.5363 (mmt180) cc_final: 0.4610 (mmm160) REVERT: A 233 ASP cc_start: 0.6104 (m-30) cc_final: 0.5817 (t0) REVERT: A 416 MET cc_start: 0.8877 (tpt) cc_final: 0.8330 (tpt) REVERT: A 505 PHE cc_start: 0.7555 (t80) cc_final: 0.7119 (t80) REVERT: B 228 LYS cc_start: 0.7935 (ttpt) cc_final: 0.7711 (ttpt) REVERT: B 233 ASP cc_start: 0.5480 (m-30) cc_final: 0.5186 (t70) REVERT: B 416 MET cc_start: 0.8899 (tpt) cc_final: 0.8360 (tpt) REVERT: B 500 MET cc_start: 0.6623 (mmt) cc_final: 0.5336 (mtp) REVERT: B 505 PHE cc_start: 0.7392 (t80) cc_final: 0.6997 (t80) REVERT: B 753 ARG cc_start: 0.7880 (mtp180) cc_final: 0.7379 (mtp180) REVERT: B 878 MET cc_start: 0.8650 (mtp) cc_final: 0.8405 (mtp) outliers start: 23 outliers final: 18 residues processed: 182 average time/residue: 0.2883 time to fit residues: 70.5310 Evaluate side-chains 174 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 795 TYR Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain B residue 795 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 72 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 121 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 ASN ** B 206 GLN ** 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 = 0.3943 r_free = 0.3943 target = 0.169969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.138855 restraints weight = 13187.212| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.35 r_work: 0.3195 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11760 Z= 0.149 Angle : 0.602 10.893 15924 Z= 0.302 Chirality : 0.041 0.172 1752 Planarity : 0.004 0.074 1998 Dihedral : 4.305 23.307 1546 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.77 % Allowed : 19.58 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.05 (0.22), residues: 1382 helix: 1.44 (0.18), residues: 824 sheet: -2.99 (0.64), residues: 38 loop : -2.34 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 427 HIS 0.004 0.001 HIS B 402 PHE 0.019 0.001 PHE A 311 TYR 0.013 0.001 TYR B 119 ARG 0.009 0.000 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 652) hydrogen bonds : angle 4.11508 ( 1944) SS BOND : bond 0.00222 ( 8) SS BOND : angle 1.86307 ( 16) covalent geometry : bond 0.00355 (11752) covalent geometry : angle 0.59973 (15908) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 1.458 Fit side-chains revert: symmetry clash REVERT: A 127 ARG cc_start: 0.8214 (mtm110) cc_final: 0.7218 (ptm-80) REVERT: A 219 ARG cc_start: 0.5419 (mmt180) cc_final: 0.4675 (mmm160) REVERT: A 233 ASP cc_start: 0.6177 (m-30) cc_final: 0.5946 (t70) REVERT: A 416 MET cc_start: 0.8921 (tpt) cc_final: 0.8361 (tpt) REVERT: A 505 PHE cc_start: 0.7542 (t80) cc_final: 0.7090 (t80) REVERT: B 233 ASP cc_start: 0.5532 (m-30) cc_final: 0.5231 (t70) REVERT: B 416 MET cc_start: 0.8948 (tpt) cc_final: 0.8387 (tpt) REVERT: B 505 PHE cc_start: 0.7421 (t80) cc_final: 0.7095 (t80) REVERT: B 753 ARG cc_start: 0.7926 (mtp180) cc_final: 0.7403 (mtp180) REVERT: B 878 MET cc_start: 0.8632 (mtp) cc_final: 0.8381 (mtp) outliers start: 22 outliers final: 19 residues processed: 174 average time/residue: 0.3239 time to fit residues: 77.5986 Evaluate side-chains 177 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 795 TYR Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain B residue 795 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 39 optimal weight: 0.0470 chunk 114 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 134 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 131 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 0.0030 chunk 61 optimal weight: 3.9990 overall best weight: 0.5090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 ASN B 206 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.172674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.138988 restraints weight = 13050.773| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.49 r_work: 0.3214 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11760 Z= 0.116 Angle : 0.575 10.635 15924 Z= 0.286 Chirality : 0.039 0.165 1752 Planarity : 0.004 0.075 1998 Dihedral : 4.207 22.832 1546 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.77 % Allowed : 18.94 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.12 (0.22), residues: 1382 helix: 1.57 (0.18), residues: 826 sheet: -2.96 (0.62), residues: 38 loop : -2.27 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 427 HIS 0.004 0.001 HIS B 402 PHE 0.019 0.001 PHE A 311 TYR 0.013 0.001 TYR A 119 ARG 0.009 0.000 ARG B 127 Details of bonding type rmsd hydrogen bonds : bond 0.03518 ( 652) hydrogen bonds : angle 4.05739 ( 1944) SS BOND : bond 0.00203 ( 8) SS BOND : angle 1.66051 ( 16) covalent geometry : bond 0.00262 (11752) covalent geometry : angle 0.57271 (15908) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 1.943 Fit side-chains revert: symmetry clash REVERT: A 127 ARG cc_start: 0.8125 (mtm110) cc_final: 0.7174 (ptm-80) REVERT: A 219 ARG cc_start: 0.5439 (mmt180) cc_final: 0.4681 (mmm160) REVERT: A 233 ASP cc_start: 0.6267 (m-30) cc_final: 0.5912 (t70) REVERT: A 416 MET cc_start: 0.8865 (tpt) cc_final: 0.8321 (tpt) REVERT: A 505 PHE cc_start: 0.7530 (t80) cc_final: 0.7114 (t80) REVERT: B 233 ASP cc_start: 0.5566 (m-30) cc_final: 0.5219 (t70) REVERT: B 416 MET cc_start: 0.8885 (tpt) cc_final: 0.8340 (tpt) REVERT: B 500 MET cc_start: 0.6420 (mmt) cc_final: 0.5111 (mtp) REVERT: B 505 PHE cc_start: 0.7404 (t80) cc_final: 0.7080 (t80) REVERT: B 543 VAL cc_start: 0.8577 (p) cc_final: 0.8160 (t) REVERT: B 753 ARG cc_start: 0.7913 (mtp180) cc_final: 0.7393 (mtp180) REVERT: B 878 MET cc_start: 0.8637 (mtp) cc_final: 0.8402 (mtp) outliers start: 22 outliers final: 20 residues processed: 180 average time/residue: 0.3266 time to fit residues: 79.4774 Evaluate side-chains 178 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 795 TYR Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain B residue 795 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 104 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 ASN A 818 GLN B 206 GLN ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.170728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.137083 restraints weight = 13112.708| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.53 r_work: 0.3184 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11760 Z= 0.138 Angle : 0.594 10.824 15924 Z= 0.297 Chirality : 0.040 0.173 1752 Planarity : 0.004 0.074 1998 Dihedral : 4.238 22.498 1546 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.93 % Allowed : 19.02 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.12 (0.22), residues: 1382 helix: 1.56 (0.18), residues: 826 sheet: -3.05 (0.60), residues: 38 loop : -2.24 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 427 HIS 0.004 0.001 HIS B 402 PHE 0.017 0.001 PHE A 311 TYR 0.013 0.001 TYR A 119 ARG 0.009 0.000 ARG B 127 Details of bonding type rmsd hydrogen bonds : bond 0.03673 ( 652) hydrogen bonds : angle 4.08033 ( 1944) SS BOND : bond 0.00216 ( 8) SS BOND : angle 1.70615 ( 16) covalent geometry : bond 0.00326 (11752) covalent geometry : angle 0.59159 (15908) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8217.92 seconds wall clock time: 152 minutes 6.07 seconds (9126.07 seconds total)