Starting phenix.real_space_refine on Wed Feb 14 02:24:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ide_35365/02_2024/8ide_35365.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ide_35365/02_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ide_35365/02_2024/8ide_35365.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ide_35365/02_2024/8ide_35365.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ide_35365/02_2024/8ide_35365.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ide_35365/02_2024/8ide_35365.pdb" } 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 Residue "A ASP 137": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 3.13, per 1000 atoms: 0.37 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 - 3.50 Amino acid : False - 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: 3.29 Conformation dependent library (CDL) restraints added in 1.7 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: 1.08 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: 3.14 Time building geometry restraints manager: 3.59 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: 99.27 - 106.25: 270 106.25 - 113.23: 4853 113.23 - 120.21: 2814 120.21 - 127.19: 3599 127.19 - 134.17: 100 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 2.520 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 2.520 ... (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 ========== 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: 6.730 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: 34.840 Check model and map are aligned: 0.000 Set scattering table: 3.970 Process input model: 23.050 Find NCS groups from input model: 0.270 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.610 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 2 poor density : 203 time to evaluate : 0.842 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: 0.2413 time to fit residues: 64.6664 Evaluate side-chains 103 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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: 0.5980 chunk 87 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 46 optimal weight: 0.0040 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 55 optimal weight: 0.4980 chunk 67 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7617 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8520 Z= 0.243 Angle : 0.699 9.857 11636 Z= 0.354 Chirality : 0.046 0.237 1419 Planarity : 0.005 0.051 1535 Dihedral : 4.848 26.382 1257 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.52 % Allowed : 14.62 % Favored : 84.87 % Rotamer: Outliers : 3.25 % Allowed : 10.47 % Favored : 86.28 % 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: -1.43 (0.25), residues: 1163 helix: 1.20 (0.23), residues: 507 sheet: -1.27 (0.55), residues: 91 loop : -3.12 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 495 HIS 0.012 0.002 HIS A 976 PHE 0.022 0.003 PHE A 370 TYR 0.016 0.001 TYR A 884 ARG 0.004 0.001 ARG B 992 *********************** 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 135 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 108 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 SER cc_start: 0.8691 (m) cc_final: 0.8144 (p) REVERT: A 98 THR cc_start: 0.8778 (p) cc_final: 0.8504 (t) REVERT: A 583 ILE cc_start: 0.8062 (mm) cc_final: 0.7756 (pt) REVERT: A 896 MET cc_start: 0.6611 (pmm) cc_final: 0.6246 (ptp) REVERT: A 900 ASN cc_start: 0.8127 (m-40) cc_final: 0.7809 (m-40) REVERT: B 759 GLU cc_start: 0.6137 (OUTLIER) cc_final: 0.5619 (tp30) REVERT: B 833 GLU cc_start: 0.7935 (pp20) cc_final: 0.7686 (pp20) REVERT: B 883 LYS cc_start: 0.8478 (tmmt) cc_final: 0.8022 (tptt) REVERT: B 961 ASN cc_start: 0.8677 (t0) cc_final: 0.8260 (t0) outliers start: 27 outliers final: 21 residues processed: 128 average time/residue: 0.1861 time to fit residues: 33.7019 Evaluate side-chains 116 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP 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 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 863 HIS Chi-restraints excluded: chain A residue 865 TYR Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain B residue 759 GLU 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 895 CYS Chi-restraints excluded: chain B residue 915 ASP Chi-restraints excluded: chain B residue 942 VAL 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: 0.0670 chunk 87 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 29 optimal weight: 0.0570 chunk 105 optimal weight: 0.0060 chunk 114 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 35 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 overall best weight: 0.3052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN A 947 HIS ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2252 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= 0.176 Angle : 0.651 8.634 11636 Z= 0.329 Chirality : 0.044 0.259 1419 Planarity : 0.005 0.050 1535 Dihedral : 4.747 25.477 1257 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.43 % Allowed : 13.33 % Favored : 86.24 % Rotamer: Outliers : 3.25 % Allowed : 12.27 % Favored : 84.48 % 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: -1.39 (0.25), residues: 1163 helix: 1.24 (0.23), residues: 507 sheet: -1.53 (0.52), residues: 103 loop : -3.06 (0.24), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 495 HIS 0.009 0.002 HIS B 863 PHE 0.016 0.002 PHE A 471 TYR 0.016 0.001 TYR A 884 ARG 0.005 0.000 ARG A 39 *********************** 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 131 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 104 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 THR cc_start: 0.8680 (p) cc_final: 0.8390 (t) REVERT: A 583 ILE cc_start: 0.8038 (mm) cc_final: 0.7753 (pt) REVERT: A 814 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7212 (mtp85) REVERT: A 896 MET cc_start: 0.6590 (pmm) cc_final: 0.6177 (ptp) REVERT: A 900 ASN cc_start: 0.8047 (m-40) cc_final: 0.7607 (t0) REVERT: A 968 MET cc_start: 0.8961 (tpt) cc_final: 0.8352 (tpt) REVERT: B 768 GLN cc_start: 0.8645 (tp40) cc_final: 0.8133 (tp40) REVERT: B 833 GLU cc_start: 0.7985 (pp20) cc_final: 0.7676 (pp20) REVERT: B 961 ASN cc_start: 0.8657 (t0) cc_final: 0.8235 (t0) outliers start: 27 outliers final: 18 residues processed: 123 average time/residue: 0.1824 time to fit residues: 32.6249 Evaluate side-chains 106 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 645 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 776 LEU Chi-restraints excluded: chain A residue 814 ARG Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 863 HIS Chi-restraints excluded: chain A residue 865 TYR Chi-restraints excluded: chain A residue 935 THR 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 895 CYS Chi-restraints excluded: chain B residue 935 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: 0.7980 chunk 79 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 105 optimal weight: 0.0020 chunk 112 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- 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 908 HIS ** 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: 0.7597 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8520 Z= 0.202 Angle : 0.643 8.035 11636 Z= 0.324 Chirality : 0.044 0.305 1419 Planarity : 0.004 0.053 1535 Dihedral : 4.673 24.990 1257 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.43 % Allowed : 13.93 % Favored : 85.64 % Rotamer: Outliers : 3.97 % Allowed : 13.96 % Favored : 82.07 % 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: -1.43 (0.25), residues: 1163 helix: 1.24 (0.23), residues: 507 sheet: -1.78 (0.47), residues: 120 loop : -3.09 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 495 HIS 0.008 0.001 HIS B 863 PHE 0.015 0.002 PHE A 370 TYR 0.015 0.001 TYR A 884 ARG 0.004 0.000 ARG A 39 *********************** 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 119 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 86 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 ILE cc_start: 0.8061 (mm) cc_final: 0.7780 (pt) REVERT: A 814 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7243 (mtp85) REVERT: A 896 MET cc_start: 0.6724 (OUTLIER) cc_final: 0.6452 (ptp) REVERT: A 900 ASN cc_start: 0.8100 (m-40) cc_final: 0.7711 (t0) REVERT: B 833 GLU cc_start: 0.7999 (pp20) cc_final: 0.7726 (pp20) REVERT: B 961 ASN cc_start: 0.8677 (t0) cc_final: 0.8283 (t0) outliers start: 33 outliers final: 24 residues processed: 109 average time/residue: 0.2217 time to fit residues: 35.5055 Evaluate side-chains 107 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 81 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 575 ASP Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 645 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 775 VAL Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 814 ARG Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 863 HIS Chi-restraints excluded: chain A residue 865 TYR Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain B residue 789 ASP 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 895 CYS Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain B residue 942 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 83 optimal weight: 0.3980 chunk 46 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8520 Z= 0.323 Angle : 0.701 7.914 11636 Z= 0.357 Chirality : 0.046 0.285 1419 Planarity : 0.005 0.050 1535 Dihedral : 4.976 22.489 1257 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.60 % Allowed : 14.53 % Favored : 84.87 % Rotamer: Outliers : 4.45 % Allowed : 16.00 % Favored : 79.54 % 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: -1.64 (0.25), residues: 1163 helix: 1.03 (0.23), residues: 507 sheet: -1.52 (0.52), residues: 94 loop : -3.22 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 495 HIS 0.010 0.002 HIS B 863 PHE 0.019 0.002 PHE A 172 TYR 0.014 0.002 TYR A 884 ARG 0.005 0.001 ARG A 927 *********************** 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 121 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 84 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 583 ILE cc_start: 0.8056 (mm) cc_final: 0.7755 (pt) REVERT: A 814 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7320 (mtp85) REVERT: A 896 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6855 (ptp) REVERT: A 900 ASN cc_start: 0.8335 (m-40) cc_final: 0.7844 (t0) REVERT: A 989 ASP cc_start: 0.8726 (OUTLIER) cc_final: 0.8456 (p0) REVERT: B 896 MET cc_start: 0.8253 (mmm) cc_final: 0.7797 (mmm) REVERT: B 961 ASN cc_start: 0.8683 (t0) cc_final: 0.8322 (t0) outliers start: 37 outliers final: 24 residues processed: 110 average time/residue: 0.1761 time to fit residues: 28.8408 Evaluate side-chains 102 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 75 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 645 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 833 GLU 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 896 MET Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 989 ASP 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 895 CYS Chi-restraints excluded: chain B residue 915 ASP Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1001 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7710 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8520 Z= 0.307 Angle : 0.697 7.928 11636 Z= 0.353 Chirality : 0.047 0.367 1419 Planarity : 0.005 0.051 1535 Dihedral : 5.019 22.831 1257 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.60 % Allowed : 13.50 % Favored : 85.90 % Rotamer: Outliers : 4.45 % Allowed : 18.41 % Favored : 77.14 % 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: -1.65 (0.25), residues: 1163 helix: 1.03 (0.23), residues: 502 sheet: -1.51 (0.52), residues: 94 loop : -3.19 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 495 HIS 0.009 0.002 HIS B 863 PHE 0.023 0.002 PHE A 172 TYR 0.015 0.002 TYR A 884 ARG 0.005 0.000 ARG A 927 *********************** 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 122 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 85 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 ILE cc_start: 0.8071 (mm) cc_final: 0.7754 (pt) REVERT: A 814 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7454 (mtp85) REVERT: A 896 MET cc_start: 0.7225 (OUTLIER) cc_final: 0.6960 (ptp) REVERT: A 900 ASN cc_start: 0.8280 (m-40) cc_final: 0.8068 (m-40) REVERT: A 989 ASP cc_start: 0.8696 (OUTLIER) cc_final: 0.8433 (p0) REVERT: B 961 ASN cc_start: 0.8673 (t0) cc_final: 0.8370 (t0) outliers start: 37 outliers final: 27 residues processed: 114 average time/residue: 0.1667 time to fit residues: 28.4654 Evaluate side-chains 107 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 77 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 387 VAL Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 645 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 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 833 GLU 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 896 MET Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 989 ASP 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 895 CYS Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain B residue 942 VAL Chi-restraints excluded: chain B residue 1001 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.0570 chunk 63 optimal weight: 0.0070 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 51 optimal weight: 0.0870 chunk 44 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 overall best weight: 0.3694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7633 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8520 Z= 0.192 Angle : 0.657 8.205 11636 Z= 0.332 Chirality : 0.044 0.392 1419 Planarity : 0.004 0.050 1535 Dihedral : 4.784 21.286 1257 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.34 % Allowed : 13.41 % Favored : 86.24 % Rotamer: Outliers : 3.73 % Allowed : 20.34 % Favored : 75.93 % 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: 1.16 (0.23), residues: 502 sheet: -1.55 (0.50), residues: 103 loop : -3.06 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 962 HIS 0.009 0.001 HIS B 863 PHE 0.020 0.002 PHE A 172 TYR 0.014 0.001 TYR A 884 ARG 0.003 0.000 ARG A 39 *********************** 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 120 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 89 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 ILE cc_start: 0.8042 (mm) cc_final: 0.7734 (pt) REVERT: A 789 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.8111 (m-30) REVERT: A 896 MET cc_start: 0.7080 (OUTLIER) cc_final: 0.6864 (ptp) REVERT: A 900 ASN cc_start: 0.8249 (m-40) cc_final: 0.7698 (t0) REVERT: A 968 MET cc_start: 0.9073 (tpt) cc_final: 0.8486 (tpt) REVERT: A 989 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8436 (p0) REVERT: B 932 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7906 (mp0) REVERT: B 961 ASN cc_start: 0.8571 (t0) cc_final: 0.8320 (t0) outliers start: 31 outliers final: 23 residues processed: 115 average time/residue: 0.1618 time to fit residues: 27.7258 Evaluate side-chains 107 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 81 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 645 ASP 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 833 GLU 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 A residue 935 THR Chi-restraints excluded: chain A residue 989 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.0030 chunk 21 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7641 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8520 Z= 0.210 Angle : 0.655 8.743 11636 Z= 0.331 Chirality : 0.044 0.285 1419 Planarity : 0.004 0.053 1535 Dihedral : 4.764 21.220 1257 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.34 % Allowed : 13.67 % Favored : 85.98 % Rotamer: Outliers : 4.21 % Allowed : 20.34 % Favored : 75.45 % 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: -1.43 (0.25), residues: 1163 helix: 1.15 (0.23), residues: 506 sheet: -1.13 (0.54), residues: 86 loop : -3.07 (0.24), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 495 HIS 0.009 0.001 HIS B 863 PHE 0.017 0.002 PHE A 172 TYR 0.015 0.001 TYR A 884 ARG 0.003 0.000 ARG A 927 *********************** 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 120 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 85 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 ILE cc_start: 0.8040 (mm) cc_final: 0.7733 (pt) REVERT: A 789 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8144 (m-30) REVERT: A 900 ASN cc_start: 0.8256 (m-40) cc_final: 0.8026 (m-40) REVERT: A 968 MET cc_start: 0.9085 (tpt) cc_final: 0.8456 (tpt) REVERT: A 989 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8434 (p0) REVERT: B 961 ASN cc_start: 0.8582 (t0) cc_final: 0.8300 (t0) outliers start: 35 outliers final: 29 residues processed: 115 average time/residue: 0.1638 time to fit residues: 28.5892 Evaluate side-chains 112 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 81 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 161 LEU Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 645 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 833 GLU 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 A residue 935 THR Chi-restraints excluded: chain A residue 989 ASP Chi-restraints excluded: chain B residue 767 VAL 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: 0.7980 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 chunk 103 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 67 optimal weight: 0.2980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7653 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8520 Z= 0.226 Angle : 0.678 9.230 11636 Z= 0.343 Chirality : 0.045 0.281 1419 Planarity : 0.004 0.052 1535 Dihedral : 4.776 21.951 1257 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.34 % Allowed : 14.19 % Favored : 85.47 % Rotamer: Outliers : 4.09 % Allowed : 20.22 % 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: -1.41 (0.25), residues: 1163 helix: 1.15 (0.23), residues: 506 sheet: -1.09 (0.54), residues: 86 loop : -3.06 (0.24), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 495 HIS 0.009 0.001 HIS B 863 PHE 0.018 0.002 PHE A 172 TYR 0.015 0.001 TYR A 884 ARG 0.003 0.000 ARG A 927 *********************** 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 124 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 90 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 ILE cc_start: 0.8021 (mm) cc_final: 0.7706 (pt) REVERT: A 789 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.8129 (m-30) REVERT: A 900 ASN cc_start: 0.8260 (m-40) cc_final: 0.8033 (m-40) REVERT: A 915 ASP cc_start: 0.9014 (t70) cc_final: 0.8750 (t0) REVERT: A 968 MET cc_start: 0.9082 (tpt) cc_final: 0.8387 (tpt) REVERT: A 989 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.8466 (p0) REVERT: B 961 ASN cc_start: 0.8581 (t0) cc_final: 0.8304 (t0) outliers start: 34 outliers final: 30 residues processed: 118 average time/residue: 0.1566 time to fit residues: 27.9620 Evaluate side-chains 116 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 84 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 161 LEU Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 645 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 807 VAL Chi-restraints excluded: chain A residue 814 ARG Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 833 GLU 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 A residue 935 THR Chi-restraints excluded: chain A residue 989 ASP Chi-restraints excluded: chain B residue 767 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 3.9990 chunk 76 optimal weight: 0.3980 chunk 115 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 98 optimal weight: 0.2980 chunk 28 optimal weight: 0.8980 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 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7648 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8520 Z= 0.225 Angle : 0.680 9.842 11636 Z= 0.344 Chirality : 0.045 0.261 1419 Planarity : 0.004 0.048 1535 Dihedral : 4.809 22.663 1257 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.34 % Allowed : 13.84 % Favored : 85.81 % Rotamer: Outliers : 4.21 % Allowed : 21.18 % Favored : 74.61 % 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: -1.40 (0.25), residues: 1163 helix: 1.16 (0.23), residues: 505 sheet: -1.11 (0.54), residues: 86 loop : -3.04 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 495 HIS 0.009 0.001 HIS B 863 PHE 0.020 0.002 PHE A 172 TYR 0.015 0.001 TYR A 884 ARG 0.003 0.000 ARG A 306 ********************** 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 123 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 88 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 789 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.8136 (m-30) REVERT: A 900 ASN cc_start: 0.8264 (m-40) cc_final: 0.7653 (t0) REVERT: A 915 ASP cc_start: 0.9032 (t70) cc_final: 0.8738 (t0) REVERT: A 968 MET cc_start: 0.9040 (tpt) cc_final: 0.8434 (tpt) REVERT: A 989 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8450 (p0) REVERT: B 961 ASN cc_start: 0.8572 (t0) cc_final: 0.8297 (t0) outliers start: 35 outliers final: 32 residues processed: 115 average time/residue: 0.1642 time to fit residues: 28.7197 Evaluate side-chains 118 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 84 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 161 LEU Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 645 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 833 GLU 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 A residue 935 THR Chi-restraints excluded: chain A residue 989 ASP Chi-restraints excluded: chain B residue 767 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.111485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.091354 restraints weight = 21814.449| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 3.74 r_work: 0.3514 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8520 Z= 0.309 Angle : 0.718 8.734 11636 Z= 0.366 Chirality : 0.046 0.311 1419 Planarity : 0.005 0.054 1535 Dihedral : 5.012 22.967 1257 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 18.58 Ramachandran Plot: Outliers : 0.43 % Allowed : 14.53 % Favored : 85.04 % Rotamer: Outliers : 4.45 % Allowed : 21.06 % Favored : 74.49 % 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: -1.59 (0.25), residues: 1163 helix: 0.93 (0.23), residues: 512 sheet: -0.93 (0.59), residues: 77 loop : -3.13 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 495 HIS 0.010 0.002 HIS B 863 PHE 0.021 0.002 PHE A 172 TYR 0.016 0.002 TYR A 884 ARG 0.004 0.000 ARG A 927 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2346.25 seconds wall clock time: 43 minutes 38.31 seconds (2618.31 seconds total)