Starting phenix.real_space_refine on Sat Dec 28 12:36:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ide_35365/12_2024/8ide_35365.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ide_35365/12_2024/8ide_35365.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ide_35365/12_2024/8ide_35365.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ide_35365/12_2024/8ide_35365.map" model { file = "/net/cci-nas-00/data/ceres_data/8ide_35365/12_2024/8ide_35365.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ide_35365/12_2024/8ide_35365.cif" } resolution = 3.21 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= 0.026 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: 5 Type Number sf(0) Gaussians Mn 1 7.51 5 S 50 5.16 5 C 5244 2.51 5 N 1522 2.21 5 O 1576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8393 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 929, 6537 Classifications: {'peptide': 929} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 47, 'TRANS': 881} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 316 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 228 Chain: "B" Number of atoms: 1855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1855 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.68, per 1000 atoms: 0.92 Number of scatterers: 8393 At special positions: 0 Unit cell: (76.26, 110.7, 123.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 1 24.99 S 50 16.00 O 1576 8.00 N 1522 7.00 C 5244 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.1 seconds 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2132 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 10 sheets defined 46.8% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 93 through 111 removed outlier: 4.682A pdb=" N ALA A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) Proline residue: A 101 - end of helix Processing helix chain 'A' and resid 128 through 147 removed outlier: 4.099A pdb=" N ARG A 141 " --> pdb=" O ASP A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 164 Processing helix chain 'A' and resid 205 through 218 Processing helix chain 'A' and resid 225 through 234 Processing helix chain 'A' and resid 237 through 247 Processing helix chain 'A' and resid 263 through 276 removed outlier: 3.713A pdb=" N ALA A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA A 276 " --> pdb=" O ARG A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 309 Processing helix chain 'A' and resid 319 through 323 removed outlier: 3.596A pdb=" N ALA A 322 " --> pdb=" O GLY A 319 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 323 " --> pdb=" O GLY A 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 319 through 323' Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.943A pdb=" N GLY A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 348 Processing helix chain 'A' and resid 351 through 366 removed outlier: 4.335A pdb=" N ILE A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 397 removed outlier: 3.582A pdb=" N VAL A 393 " --> pdb=" O VAL A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 422 Processing helix chain 'A' and resid 442 through 454 Processing helix chain 'A' and resid 467 through 476 removed outlier: 3.950A pdb=" N PHE A 471 " --> pdb=" O SER A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 494 removed outlier: 4.224A pdb=" N CYS A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 removed outlier: 3.629A pdb=" N THR A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS A 516 " --> pdb=" O PRO A 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 511 through 516' Processing helix chain 'A' and resid 528 through 538 Processing helix chain 'A' and resid 557 through 565 Processing helix chain 'A' and resid 601 through 607 removed outlier: 4.736A pdb=" N ASP A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 606 " --> pdb=" O THR A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 666 Processing helix chain 'A' and resid 704 through 714 Processing helix chain 'A' and resid 736 through 743 Processing helix chain 'A' and resid 755 through 762 Processing helix chain 'A' and resid 763 through 773 Processing helix chain 'A' and resid 783 through 795 Processing helix chain 'A' and resid 809 through 813 removed outlier: 3.736A pdb=" N VAL A 813 " --> pdb=" O SER A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 823 removed outlier: 3.870A pdb=" N VAL A 823 " --> pdb=" O LEU A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 839 Processing helix chain 'A' and resid 855 through 865 Processing helix chain 'A' and resid 874 through 888 Processing helix chain 'A' and resid 914 through 916 No H-bonds generated for 'chain 'A' and resid 914 through 916' Processing helix chain 'A' and resid 920 through 933 Processing helix chain 'A' and resid 962 through 981 removed outlier: 3.608A pdb=" N PHE A 967 " --> pdb=" O PRO A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 995 removed outlier: 3.663A pdb=" N ASP A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 762 Processing helix chain 'B' and resid 763 through 772 Processing helix chain 'B' and resid 784 through 795 Processing helix chain 'B' and resid 808 through 815 Processing helix chain 'B' and resid 819 through 823 removed outlier: 3.779A pdb=" N VAL B 823 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 839 Processing helix chain 'B' and resid 856 through 865 Processing helix chain 'B' and resid 874 through 888 Processing helix chain 'B' and resid 914 through 916 No H-bonds generated for 'chain 'B' and resid 914 through 916' Processing helix chain 'B' and resid 919 through 933 Processing helix chain 'B' and resid 962 through 982 removed outlier: 3.818A pdb=" N TYR B 966 " --> pdb=" O TRP B 962 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE B 967 " --> pdb=" O PRO B 963 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA B 982 " --> pdb=" O LEU B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 995 removed outlier: 3.538A pdb=" N HIS B 990 " --> pdb=" O SER B 986 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 123 removed outlier: 6.628A pdb=" N VAL A 122 " --> pdb=" O VAL A 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 340 through 341 removed outlier: 6.048A pdb=" N LEU A 315 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LEU A 175 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE A 174 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU A 188 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ARG A 197 " --> pdb=" O LEU A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 377 through 379 removed outlier: 3.850A pdb=" N VAL A 377 " --> pdb=" O TYR A 689 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL A 670 " --> pdb=" O LYS A 686 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N TRP A 688 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL A 672 " --> pdb=" O TRP A 688 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG A 725 " --> pdb=" O ILE A 673 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 463 through 464 Processing sheet with id=AA6, first strand: chain 'A' and resid 499 through 500 Processing sheet with id=AA7, first strand: chain 'A' and resid 774 through 775 Processing sheet with id=AA8, first strand: chain 'A' and resid 911 through 912 Processing sheet with id=AA9, first strand: chain 'A' and resid 1004 through 1005 Processing sheet with id=AB1, first strand: chain 'B' and resid 843 through 844 removed outlier: 3.860A pdb=" N LEU B 799 " --> pdb=" O ASP B 843 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG B 774 " --> pdb=" O ILE B 867 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL B 869 " --> pdb=" O ARG B 774 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU B 776 " --> pdb=" O VAL B 869 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU B 892 " --> pdb=" O LYS B 939 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N VAL B 941 " --> pdb=" O LEU B 892 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N SER B 894 " --> pdb=" O VAL B 941 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 942 " --> pdb=" O ARG B 909 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1125 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: 3.09 Time building geometry restraints manager: 2.80 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: 2821 1.34 - 1.46: 843 1.46 - 1.58: 4784 1.58 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 8520 Sorted by residual: bond pdb=" N GLU A 138 " pdb=" CA GLU A 138 " ideal model delta sigma weight residual 1.456 1.482 -0.026 1.28e-02 6.10e+03 4.08e+00 bond pdb=" N ASP A 137 " pdb=" CA ASP A 137 " ideal model delta sigma weight residual 1.457 1.476 -0.020 1.32e-02 5.74e+03 2.20e+00 bond pdb=" C ASP A 137 " pdb=" O ASP A 137 " ideal model delta sigma weight residual 1.236 1.216 0.020 1.35e-02 5.49e+03 2.11e+00 bond pdb=" CB VAL A 316 " pdb=" CG1 VAL A 316 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.83e-01 bond pdb=" CA ILE A 409 " pdb=" CB ILE A 409 " ideal model delta sigma weight residual 1.540 1.527 0.013 1.36e-02 5.41e+03 9.78e-01 ... (remaining 8515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 11360 2.07 - 4.14: 235 4.14 - 6.20: 34 6.20 - 8.27: 5 8.27 - 10.34: 2 Bond angle restraints: 11636 Sorted by residual: angle pdb=" N GLU A 138 " pdb=" CA GLU A 138 " pdb=" C GLU A 138 " ideal model delta sigma weight residual 113.88 107.08 6.80 1.23e+00 6.61e-01 3.05e+01 angle pdb=" C GLU A 508 " pdb=" CA GLU A 508 " pdb=" CB GLU A 508 " ideal model delta sigma weight residual 117.23 110.21 7.02 1.36e+00 5.41e-01 2.67e+01 angle pdb=" N ASP A 137 " pdb=" CA ASP A 137 " pdb=" C ASP A 137 " ideal model delta sigma weight residual 113.20 108.40 4.80 1.21e+00 6.83e-01 1.58e+01 angle pdb=" C ASP A 396 " pdb=" N ARG A 397 " pdb=" CA ARG A 397 " ideal model delta sigma weight residual 121.80 130.76 -8.96 2.44e+00 1.68e-01 1.35e+01 angle pdb=" CA GLU A 508 " pdb=" C GLU A 508 " pdb=" N LYS A 509 " ideal model delta sigma weight residual 119.98 116.94 3.04 8.50e-01 1.38e+00 1.28e+01 ... (remaining 11631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4692 17.73 - 35.46: 349 35.46 - 53.19: 51 53.19 - 70.92: 15 70.92 - 88.64: 4 Dihedral angle restraints: 5111 sinusoidal: 1793 harmonic: 3318 Sorted by residual: dihedral pdb=" CA CYS A 919 " pdb=" C CYS A 919 " pdb=" N LEU A 920 " pdb=" CA LEU A 920 " ideal model delta harmonic sigma weight residual -180.00 -152.62 -27.38 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA ASP A 917 " pdb=" C ASP A 917 " pdb=" N VAL A 918 " pdb=" CA VAL A 918 " ideal model delta harmonic sigma weight residual -180.00 -156.67 -23.33 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA ALA A 682 " pdb=" C ALA A 682 " pdb=" N ARG A 683 " pdb=" CA ARG A 683 " ideal model delta harmonic sigma weight residual -180.00 -157.94 -22.06 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 5108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1035 0.044 - 0.088: 286 0.088 - 0.132: 90 0.132 - 0.176: 7 0.176 - 0.219: 1 Chirality restraints: 1419 Sorted by residual: chirality pdb=" CG LEU B 974 " pdb=" CB LEU B 974 " pdb=" CD1 LEU B 974 " pdb=" CD2 LEU B 974 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB ILE A 120 " pdb=" CA ILE A 120 " pdb=" CG1 ILE A 120 " pdb=" CG2 ILE A 120 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CB VAL A 736 " pdb=" CA VAL A 736 " pdb=" CG1 VAL A 736 " pdb=" CG2 VAL A 736 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.08e-01 ... (remaining 1416 not shown) Planarity restraints: 1535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 552 " 0.042 5.00e-02 4.00e+02 6.45e-02 6.65e+00 pdb=" N PRO A 553 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 553 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 553 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 205 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO A 206 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 206 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 206 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 172 " 0.033 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO A 173 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 173 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 173 " 0.028 5.00e-02 4.00e+02 ... (remaining 1532 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.50: 59 2.50 - 3.10: 6579 3.10 - 3.70: 13076 3.70 - 4.30: 17968 4.30 - 4.90: 29436 Nonbonded interactions: 67118 Sorted by model distance: nonbonded pdb=" OD1 ASP A 350 " pdb="MN MN A1101 " model vdw 1.906 2.320 nonbonded pdb=" NE2 HIS A 155 " pdb="MN MN A1101 " model vdw 1.920 2.400 nonbonded pdb=" OD1 ASN A 458 " pdb=" N ASN A 459 " model vdw 2.186 3.120 nonbonded pdb=" C VAL A 99 " pdb=" OE2 GLU A 138 " model vdw 2.253 3.270 nonbonded pdb=" O ARG B 760 " pdb=" NH1 ARG B 994 " model vdw 2.269 3.120 ... (remaining 67113 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.490 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: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.100 Process input model: 26.160 Find NCS groups from input model: 0.080 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 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 : 0.003 0.033 8520 Z= 0.200 Angle : 0.713 10.339 11636 Z= 0.377 Chirality : 0.044 0.219 1419 Planarity : 0.005 0.064 1535 Dihedral : 13.140 88.644 2979 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.52 % Allowed : 14.10 % Favored : 85.38 % Rotamer: Outliers : 0.24 % Allowed : 0.24 % Favored : 99.52 % 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: -1.37 (0.25), residues: 1163 helix: 1.31 (0.23), residues: 497 sheet: -1.07 (0.60), residues: 83 loop : -3.07 (0.24), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 495 HIS 0.011 0.002 HIS B 863 PHE 0.018 0.002 PHE A 172 TYR 0.014 0.002 TYR A 884 ARG 0.003 0.000 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 203 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 SER cc_start: 0.8540 (m) cc_final: 0.8135 (p) REVERT: A 525 MET cc_start: 0.7516 (ttm) cc_final: 0.7002 (tpp) REVERT: A 827 LYS cc_start: 0.8479 (ttmt) cc_final: 0.8233 (ttmm) REVERT: A 896 MET cc_start: 0.6659 (pmm) cc_final: 0.6257 (ptp) REVERT: A 947 HIS cc_start: 0.6579 (t70) cc_final: 0.6371 (t-90) REVERT: B 883 LYS cc_start: 0.8510 (tmmt) cc_final: 0.8054 (tptt) REVERT: B 902 THR cc_start: 0.7674 (m) cc_final: 0.7340 (m) outliers start: 2 outliers final: 0 residues processed: 205 average time/residue: 0.2516 time to fit residues: 67.5495 Evaluate side-chains 103 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 900 ASN ** A 976 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 976 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8520 Z= 0.340 Angle : 0.756 9.685 11636 Z= 0.387 Chirality : 0.048 0.249 1419 Planarity : 0.006 0.051 1535 Dihedral : 4.985 26.657 1257 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.60 % Allowed : 14.96 % Favored : 84.44 % Rotamer: Outliers : 2.77 % Allowed : 11.07 % Favored : 86.16 % 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: -1.56 (0.24), residues: 1163 helix: 1.09 (0.23), residues: 507 sheet: -1.04 (0.56), residues: 81 loop : -3.22 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 495 HIS 0.013 0.002 HIS A 976 PHE 0.021 0.003 PHE A 172 TYR 0.015 0.002 TYR A 884 ARG 0.006 0.001 ARG A 936 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 SER cc_start: 0.8730 (m) cc_final: 0.8125 (p) REVERT: A 98 THR cc_start: 0.8900 (p) cc_final: 0.8618 (t) REVERT: A 814 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.6976 (mtp85) REVERT: A 883 LYS cc_start: 0.8233 (ptmt) cc_final: 0.7736 (ptmt) REVERT: A 896 MET cc_start: 0.6772 (pmm) cc_final: 0.6255 (ptp) REVERT: A 900 ASN cc_start: 0.8208 (m-40) cc_final: 0.7600 (t0) REVERT: B 833 GLU cc_start: 0.7914 (pp20) cc_final: 0.7662 (pp20) REVERT: B 883 LYS cc_start: 0.8508 (tmmt) cc_final: 0.8296 (tptt) outliers start: 23 outliers final: 18 residues processed: 119 average time/residue: 0.2015 time to fit residues: 33.4691 Evaluate side-chains 105 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 814 ARG Chi-restraints excluded: chain A residue 863 HIS Chi-restraints excluded: chain A residue 865 TYR Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 852 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain B residue 942 VAL Chi-restraints excluded: chain B residue 1000 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 105 optimal weight: 0.0000 chunk 114 optimal weight: 0.4980 chunk 93 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 35 optimal weight: 0.0270 chunk 84 optimal weight: 0.5980 overall best weight: 0.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 947 HIS ** A 976 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 908 HIS ** B 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8520 Z= 0.185 Angle : 0.680 8.599 11636 Z= 0.343 Chirality : 0.045 0.200 1419 Planarity : 0.005 0.060 1535 Dihedral : 4.868 25.377 1257 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.34 % Allowed : 13.33 % Favored : 86.33 % Rotamer: Outliers : 2.53 % Allowed : 14.20 % Favored : 83.27 % 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: -1.47 (0.25), residues: 1163 helix: 1.19 (0.23), residues: 504 sheet: -1.66 (0.50), residues: 103 loop : -3.07 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 495 HIS 0.009 0.002 HIS B 863 PHE 0.020 0.002 PHE A 172 TYR 0.016 0.001 TYR A 884 ARG 0.012 0.001 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 SER cc_start: 0.8644 (m) cc_final: 0.8210 (p) REVERT: A 98 THR cc_start: 0.8694 (p) cc_final: 0.8419 (t) REVERT: A 583 ILE cc_start: 0.7952 (mm) cc_final: 0.7623 (pt) REVERT: A 811 ASN cc_start: 0.8340 (OUTLIER) cc_final: 0.8095 (t0) REVERT: A 883 LYS cc_start: 0.8150 (ptmt) cc_final: 0.7637 (ptmt) REVERT: A 896 MET cc_start: 0.6611 (pmm) cc_final: 0.6292 (ptp) REVERT: A 900 ASN cc_start: 0.8093 (m-40) cc_final: 0.7779 (t0) REVERT: A 909 ARG cc_start: 0.7412 (mmp-170) cc_final: 0.7204 (mmp80) REVERT: A 939 LYS cc_start: 0.8247 (mmmm) cc_final: 0.7629 (mmtt) REVERT: A 947 HIS cc_start: 0.6726 (t70) cc_final: 0.6445 (t-90) REVERT: B 768 GLN cc_start: 0.8641 (tp40) cc_final: 0.8142 (tp40) REVERT: B 833 GLU cc_start: 0.7959 (pp20) cc_final: 0.7640 (pp20) REVERT: B 883 LYS cc_start: 0.8588 (tmmt) cc_final: 0.8155 (tptt) REVERT: B 961 ASN cc_start: 0.8682 (t0) cc_final: 0.8286 (t0) outliers start: 21 outliers final: 12 residues processed: 126 average time/residue: 0.1878 time to fit residues: 34.3171 Evaluate side-chains 106 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 811 ASN Chi-restraints excluded: chain A residue 863 HIS Chi-restraints excluded: chain A residue 865 TYR Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 852 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 905 THR Chi-restraints excluded: chain B residue 942 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 50 optimal weight: 30.0000 chunk 70 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 976 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 8520 Z= 0.300 Angle : 0.706 7.509 11636 Z= 0.359 Chirality : 0.046 0.299 1419 Planarity : 0.005 0.047 1535 Dihedral : 4.954 22.446 1257 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.52 % Allowed : 14.88 % Favored : 84.61 % Rotamer: Outliers : 4.09 % Allowed : 15.04 % Favored : 80.87 % 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: -1.63 (0.25), residues: 1163 helix: 1.10 (0.23), residues: 503 sheet: -1.52 (0.50), residues: 100 loop : -3.26 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 495 HIS 0.009 0.002 HIS B 863 PHE 0.019 0.002 PHE A 172 TYR 0.014 0.002 TYR A 884 ARG 0.004 0.001 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 SER cc_start: 0.8810 (m) cc_final: 0.8322 (p) REVERT: A 583 ILE cc_start: 0.8057 (mm) cc_final: 0.7714 (pt) REVERT: A 814 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.6959 (mtp85) REVERT: A 896 MET cc_start: 0.7073 (OUTLIER) cc_final: 0.6719 (ptp) REVERT: A 900 ASN cc_start: 0.8215 (m-40) cc_final: 0.7833 (t0) REVERT: A 909 ARG cc_start: 0.7495 (mmp-170) cc_final: 0.7263 (mmp80) REVERT: A 939 LYS cc_start: 0.8197 (mmmm) cc_final: 0.7598 (mmtm) REVERT: A 947 HIS cc_start: 0.6903 (t70) cc_final: 0.6652 (t-90) REVERT: B 833 GLU cc_start: 0.7985 (pp20) cc_final: 0.7657 (pp20) REVERT: B 961 ASN cc_start: 0.8736 (t0) cc_final: 0.8384 (t0) outliers start: 34 outliers final: 25 residues processed: 125 average time/residue: 0.1923 time to fit residues: 34.2765 Evaluate side-chains 113 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 814 ARG Chi-restraints excluded: chain A residue 863 HIS Chi-restraints excluded: chain A residue 865 TYR Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 852 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 905 THR Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain B residue 942 VAL Chi-restraints excluded: chain B residue 1000 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 83 optimal weight: 0.3980 chunk 46 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 0 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 811 ASN ** A 976 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8520 Z= 0.227 Angle : 0.686 7.837 11636 Z= 0.349 Chirality : 0.045 0.225 1419 Planarity : 0.005 0.046 1535 Dihedral : 4.894 22.490 1257 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.34 % Allowed : 13.67 % Favored : 85.98 % Rotamer: Outliers : 3.49 % Allowed : 17.69 % Favored : 78.82 % 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: -1.56 (0.25), residues: 1163 helix: 1.16 (0.23), residues: 499 sheet: -1.72 (0.47), residues: 110 loop : -3.15 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 495 HIS 0.009 0.001 HIS B 863 PHE 0.022 0.002 PHE A 172 TYR 0.019 0.001 TYR A 884 ARG 0.004 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 SER cc_start: 0.8770 (m) cc_final: 0.8265 (p) REVERT: A 159 HIS cc_start: 0.7722 (OUTLIER) cc_final: 0.7244 (m-70) REVERT: A 583 ILE cc_start: 0.8014 (mm) cc_final: 0.7676 (pt) REVERT: A 811 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.8119 (t0) REVERT: A 814 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7001 (mtp85) REVERT: A 896 MET cc_start: 0.7002 (OUTLIER) cc_final: 0.6634 (ptp) REVERT: A 900 ASN cc_start: 0.8149 (m-40) cc_final: 0.7745 (t0) REVERT: A 909 ARG cc_start: 0.7449 (mmp-170) cc_final: 0.7240 (mmp80) REVERT: B 833 GLU cc_start: 0.7979 (pp20) cc_final: 0.7694 (pp20) REVERT: B 883 LYS cc_start: 0.7865 (mmmt) cc_final: 0.7662 (mmmt) REVERT: B 961 ASN cc_start: 0.8703 (t0) cc_final: 0.8412 (t0) outliers start: 29 outliers final: 20 residues processed: 117 average time/residue: 0.1943 time to fit residues: 32.6043 Evaluate side-chains 114 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 811 ASN Chi-restraints excluded: chain A residue 814 ARG Chi-restraints excluded: chain A residue 863 HIS Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 852 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 905 THR Chi-restraints excluded: chain B residue 932 GLU Chi-restraints excluded: chain B residue 942 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 HIS ** A 976 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 990 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 8520 Z= 0.388 Angle : 0.755 8.122 11636 Z= 0.388 Chirality : 0.048 0.437 1419 Planarity : 0.005 0.048 1535 Dihedral : 5.194 23.094 1257 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.52 % Allowed : 14.96 % Favored : 84.52 % Rotamer: Outliers : 5.54 % Allowed : 16.49 % Favored : 77.98 % 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: -1.79 (0.24), residues: 1163 helix: 0.91 (0.23), residues: 500 sheet: -1.88 (0.48), residues: 104 loop : -3.21 (0.24), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 495 HIS 0.010 0.002 HIS B 863 PHE 0.020 0.002 PHE A 172 TYR 0.018 0.002 TYR A 884 ARG 0.008 0.001 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 95 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 SER cc_start: 0.8781 (m) cc_final: 0.8362 (p) REVERT: A 159 HIS cc_start: 0.7810 (OUTLIER) cc_final: 0.7363 (m-70) REVERT: A 418 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7924 (mtm-85) REVERT: A 814 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7095 (mtp85) REVERT: A 896 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.7018 (ptp) REVERT: A 900 ASN cc_start: 0.8195 (m-40) cc_final: 0.7802 (t0) REVERT: A 909 ARG cc_start: 0.7476 (mmp-170) cc_final: 0.7267 (mmp80) REVERT: B 833 GLU cc_start: 0.8011 (pp20) cc_final: 0.7731 (pp20) REVERT: B 961 ASN cc_start: 0.8746 (t0) cc_final: 0.8412 (t0) outliers start: 46 outliers final: 23 residues processed: 129 average time/residue: 0.1909 time to fit residues: 35.0728 Evaluate side-chains 112 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 814 ARG Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 863 HIS Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 852 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 905 THR Chi-restraints excluded: chain B residue 932 GLU Chi-restraints excluded: chain B residue 935 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 111 optimal weight: 0.3980 chunk 69 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 66 optimal weight: 0.0570 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 HIS ** A 976 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8520 Z= 0.203 Angle : 0.709 11.041 11636 Z= 0.354 Chirality : 0.045 0.326 1419 Planarity : 0.004 0.042 1535 Dihedral : 4.951 24.211 1257 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.26 % Allowed : 12.81 % Favored : 86.93 % Rotamer: Outliers : 4.93 % Allowed : 18.17 % Favored : 76.90 % 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: -1.56 (0.25), residues: 1163 helix: 1.09 (0.23), residues: 500 sheet: -1.73 (0.48), residues: 103 loop : -3.07 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 962 HIS 0.009 0.001 HIS B 863 PHE 0.023 0.002 PHE A 172 TYR 0.018 0.001 TYR A 884 ARG 0.005 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 100 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 SER cc_start: 0.8778 (m) cc_final: 0.8273 (p) REVERT: A 159 HIS cc_start: 0.7687 (OUTLIER) cc_final: 0.7204 (m-70) REVERT: A 249 ASP cc_start: 0.4584 (OUTLIER) cc_final: 0.4367 (p0) REVERT: A 789 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8121 (m-30) REVERT: A 896 MET cc_start: 0.7107 (OUTLIER) cc_final: 0.6763 (ptp) REVERT: A 909 ARG cc_start: 0.7432 (mmp-170) cc_final: 0.7204 (mmp80) REVERT: B 961 ASN cc_start: 0.8614 (t0) cc_final: 0.8390 (t0) outliers start: 41 outliers final: 25 residues processed: 132 average time/residue: 0.1835 time to fit residues: 34.8535 Evaluate side-chains 120 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 814 ARG Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 863 HIS Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 852 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 905 THR Chi-restraints excluded: chain B residue 935 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 101 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 HIS ** A 976 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8520 Z= 0.308 Angle : 0.736 9.242 11636 Z= 0.373 Chirality : 0.048 0.489 1419 Planarity : 0.005 0.046 1535 Dihedral : 5.064 24.186 1257 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.43 % Allowed : 13.93 % Favored : 85.64 % Rotamer: Outliers : 4.33 % Allowed : 19.86 % Favored : 75.81 % 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: -1.71 (0.24), residues: 1163 helix: 0.98 (0.23), residues: 503 sheet: -1.84 (0.48), residues: 104 loop : -3.18 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 495 HIS 0.009 0.002 HIS B 863 PHE 0.019 0.002 PHE A 172 TYR 0.022 0.002 TYR B 884 ARG 0.005 0.000 ARG A 418 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 90 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 SER cc_start: 0.8842 (m) cc_final: 0.8366 (p) REVERT: A 159 HIS cc_start: 0.7772 (OUTLIER) cc_final: 0.7381 (m-70) REVERT: A 249 ASP cc_start: 0.4634 (OUTLIER) cc_final: 0.4425 (p0) REVERT: A 789 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.8114 (m-30) REVERT: A 896 MET cc_start: 0.7235 (pmm) cc_final: 0.7021 (ptp) REVERT: A 900 ASN cc_start: 0.8110 (m-40) cc_final: 0.7414 (t0) outliers start: 36 outliers final: 29 residues processed: 120 average time/residue: 0.1855 time to fit residues: 32.5702 Evaluate side-chains 118 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 86 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 814 ARG Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 863 HIS Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain B residue 775 VAL Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 852 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 935 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 81 optimal weight: 0.0050 chunk 31 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 0.3980 chunk 68 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8520 Z= 0.213 Angle : 0.716 10.275 11636 Z= 0.359 Chirality : 0.046 0.385 1419 Planarity : 0.004 0.042 1535 Dihedral : 4.969 24.319 1257 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.34 % Allowed : 13.16 % Favored : 86.50 % Rotamer: Outliers : 4.09 % Allowed : 19.86 % Favored : 76.05 % 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: -1.54 (0.25), residues: 1163 helix: 1.05 (0.23), residues: 499 sheet: -1.42 (0.54), residues: 87 loop : -3.02 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 962 HIS 0.009 0.002 HIS B 863 PHE 0.023 0.002 PHE A 172 TYR 0.018 0.002 TYR B 884 ARG 0.004 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 98 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 SER cc_start: 0.8766 (m) cc_final: 0.8332 (p) REVERT: A 159 HIS cc_start: 0.7703 (OUTLIER) cc_final: 0.7348 (m-70) REVERT: A 249 ASP cc_start: 0.4637 (OUTLIER) cc_final: 0.4428 (p0) REVERT: A 548 ASN cc_start: 0.7262 (t0) cc_final: 0.6624 (p0) REVERT: A 789 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8117 (m-30) REVERT: A 896 MET cc_start: 0.7152 (pmm) cc_final: 0.6896 (ptp) REVERT: A 900 ASN cc_start: 0.8078 (m-40) cc_final: 0.7349 (t0) REVERT: B 932 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7826 (mp0) outliers start: 34 outliers final: 26 residues processed: 124 average time/residue: 0.1765 time to fit residues: 32.2320 Evaluate side-chains 121 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 91 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 814 ARG Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 863 HIS Chi-restraints excluded: chain A residue 865 TYR Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 852 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 932 GLU Chi-restraints excluded: chain B residue 935 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 98 optimal weight: 0.0470 chunk 28 optimal weight: 0.3980 overall best weight: 1.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 HIS ** A 976 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8520 Z= 0.278 Angle : 0.736 10.187 11636 Z= 0.371 Chirality : 0.047 0.355 1419 Planarity : 0.005 0.046 1535 Dihedral : 5.063 24.449 1257 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.43 % Allowed : 13.93 % Favored : 85.64 % Rotamer: Outliers : 3.97 % Allowed : 20.70 % Favored : 75.33 % 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: -1.62 (0.25), residues: 1163 helix: 0.97 (0.23), residues: 503 sheet: -1.54 (0.52), residues: 93 loop : -3.08 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 495 HIS 0.009 0.002 HIS B 863 PHE 0.018 0.002 PHE A 172 TYR 0.017 0.002 TYR A 884 ARG 0.004 0.000 ARG A 927 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 SER cc_start: 0.8849 (m) cc_final: 0.8411 (p) REVERT: A 159 HIS cc_start: 0.7752 (OUTLIER) cc_final: 0.7324 (m-70) REVERT: A 249 ASP cc_start: 0.4658 (OUTLIER) cc_final: 0.4450 (p0) REVERT: A 548 ASN cc_start: 0.7315 (t0) cc_final: 0.6693 (p0) REVERT: A 789 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.8105 (m-30) REVERT: A 896 MET cc_start: 0.7253 (pmm) cc_final: 0.7051 (ptp) REVERT: A 968 MET cc_start: 0.9090 (tpt) cc_final: 0.8460 (tpt) REVERT: B 896 MET cc_start: 0.8313 (mmm) cc_final: 0.7718 (mmm) REVERT: B 932 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7852 (mp0) outliers start: 33 outliers final: 28 residues processed: 110 average time/residue: 0.1939 time to fit residues: 31.4921 Evaluate side-chains 116 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 84 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 814 ARG Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 863 HIS Chi-restraints excluded: chain A residue 865 TYR Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 852 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 932 GLU Chi-restraints excluded: chain B residue 935 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 8.9990 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 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 = 0.4021 r_free = 0.4021 target = 0.114266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.094456 restraints weight = 21585.471| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 3.76 r_work: 0.3571 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8520 Z= 0.215 Angle : 0.707 10.059 11636 Z= 0.355 Chirality : 0.045 0.277 1419 Planarity : 0.004 0.044 1535 Dihedral : 4.942 24.372 1257 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.34 % Allowed : 13.24 % Favored : 86.41 % Rotamer: Outliers : 4.21 % Allowed : 20.10 % Favored : 75.69 % 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: -1.51 (0.25), residues: 1163 helix: 1.04 (0.23), residues: 502 sheet: -1.45 (0.52), residues: 92 loop : -3.00 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 962 HIS 0.009 0.001 HIS B 863 PHE 0.021 0.002 PHE A 172 TYR 0.016 0.001 TYR A 884 ARG 0.004 0.000 ARG A 669 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2391.33 seconds wall clock time: 44 minutes 58.77 seconds (2698.77 seconds total)