Starting phenix.real_space_refine on Sat Dec 28 20:21:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wvu_37869/12_2024/8wvu_37869.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wvu_37869/12_2024/8wvu_37869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wvu_37869/12_2024/8wvu_37869.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wvu_37869/12_2024/8wvu_37869.map" model { file = "/net/cci-nas-00/data/ceres_data/8wvu_37869/12_2024/8wvu_37869.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wvu_37869/12_2024/8wvu_37869.cif" } resolution = 3.61 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= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2063 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 4783 2.51 5 N 1238 2.21 5 O 1356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 7427 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 733, 5714 Classifications: {'peptide': 733} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 37, 'TRANS': 695} Chain breaks: 3 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: "B" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 771 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 7, 'TRANS': 94} Chain breaks: 1 Chain: "C" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 942 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 10, 'TRANS': 126} Chain breaks: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 126 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 93 Time building chain proxies: 5.04, per 1000 atoms: 0.68 Number of scatterers: 7427 At special positions: 0 Unit cell: (75.65, 85.85, 160.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1356 8.00 N 1238 7.00 C 4783 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 35 " distance=2.12 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 43 " distance=2.07 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 364 " distance=2.02 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 522 " distance=1.67 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 532 " distance=2.21 Simple disulfide: pdb=" SG CYS A 618 " - pdb=" SG CYS A 693 " distance=2.14 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 47 " distance=2.30 Simple disulfide: pdb=" SG CYS B 44 " - pdb=" SG CYS B 53 " distance=1.94 Simple disulfide: pdb=" SG CYS B 56 " - pdb=" SG CYS B 75 " distance=2.03 Simple disulfide: pdb=" SG CYS B 79 " - pdb=" SG CYS B 94 " distance=1.91 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 105 " distance=2.10 Simple disulfide: pdb=" SG CYS B 102 " - pdb=" SG CYS B 111 " distance=1.88 Simple disulfide: pdb=" SG CYS B 114 " - pdb=" SG CYS B 125 " distance=2.12 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 142 " distance=2.05 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 119 " distance=2.38 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: 1.81 Conformation dependent library (CDL) restraints added in 1.1 seconds 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1834 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 12 sheets defined 29.2% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 123 through 128 removed outlier: 4.264A pdb=" N GLY A 127 " --> pdb=" O ALA A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 242 through 247 removed outlier: 3.836A pdb=" N LYS A 245 " --> pdb=" O GLN A 242 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA A 246 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 247 " --> pdb=" O ILE A 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 242 through 247' Processing helix chain 'A' and resid 337 through 342 removed outlier: 4.272A pdb=" N GLN A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 472 removed outlier: 3.559A pdb=" N GLN A 469 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS A 471 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA A 472 " --> pdb=" O GLN A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 564 removed outlier: 3.946A pdb=" N ARG A 542 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 543 " --> pdb=" O TRP A 539 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 601 removed outlier: 3.589A pdb=" N SER A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 614 Processing helix chain 'A' and resid 617 through 646 Processing helix chain 'A' and resid 661 through 683 removed outlier: 3.608A pdb=" N LEU A 671 " --> pdb=" O LEU A 667 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 673 " --> pdb=" O ALA A 669 " (cutoff:3.500A) Proline residue: A 680 - end of helix Processing helix chain 'A' and resid 703 through 731 removed outlier: 4.175A pdb=" N THR A 707 " --> pdb=" O SER A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 759 removed outlier: 4.366A pdb=" N MET A 745 " --> pdb=" O SER A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 768 removed outlier: 3.618A pdb=" N PHE A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 773 removed outlier: 3.673A pdb=" N ILE A 772 " --> pdb=" O PHE A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 790 removed outlier: 3.581A pdb=" N MET A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 804 removed outlier: 3.726A pdb=" N CYS A 795 " --> pdb=" O PRO A 791 " (cutoff:3.500A) Proline residue: A 798 - end of helix removed outlier: 3.665A pdb=" N TYR A 801 " --> pdb=" O ASN A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 818 removed outlier: 3.719A pdb=" N LYS A 809 " --> pdb=" O ASN A 805 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TRP A 812 " --> pdb=" O PHE A 808 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LYS A 813 " --> pdb=" O LYS A 809 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU A 814 " --> pdb=" O GLU A 810 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 815 " --> pdb=" O ASP A 811 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG A 817 " --> pdb=" O LYS A 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.519A pdb=" N LEU C 90 " --> pdb=" O PRO C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 132 removed outlier: 3.779A pdb=" N GLU C 131 " --> pdb=" O ARG C 127 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG C 132 " --> pdb=" O MET C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 150 removed outlier: 3.658A pdb=" N ALA C 148 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 178 Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42 removed outlier: 6.855A pdb=" N VAL A 41 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN A 87 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA3, first strand: chain 'A' and resid 157 through 159 removed outlier: 7.232A pdb=" N LEU A 158 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU A 182 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY A 254 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 192 removed outlier: 4.211A pdb=" N ILE A 192 " --> pdb=" O SER A 215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 262 through 263 Processing sheet with id=AA6, first strand: chain 'A' and resid 302 through 303 removed outlier: 3.841A pdb=" N LEU A 324 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU A 348 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU A 394 " --> pdb=" O ASP A 419 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU A 439 " --> pdb=" O SER A 463 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 44 through 46 removed outlier: 6.624A pdb=" N LYS B 55 " --> pdb=" O GLU B 45 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 64 through 66 Processing sheet with id=AA9, first strand: chain 'B' and resid 83 through 84 Processing sheet with id=AB1, first strand: chain 'B' and resid 102 through 104 removed outlier: 6.879A pdb=" N LYS B 113 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 119 through 121 Processing sheet with id=AB3, first strand: chain 'C' and resid 81 through 84 removed outlier: 7.169A pdb=" N PHE C 103 " --> pdb=" O SER C 135 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL C 137 " --> pdb=" O PHE C 103 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER C 105 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N PHE C 139 " --> pdb=" O SER C 105 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL C 107 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 9.470A pdb=" N VAL C 162 " --> pdb=" O SER C 135 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL C 137 " --> pdb=" O VAL C 162 " (cutoff:3.500A) 198 hydrogen bonds defined for protein. 573 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.99 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1298 1.31 - 1.44: 1844 1.44 - 1.56: 4386 1.56 - 1.69: 0 1.69 - 1.82: 63 Bond restraints: 7591 Sorted by residual: bond pdb=" C ARG C 117 " pdb=" N PRO C 118 " ideal model delta sigma weight residual 1.330 1.534 -0.204 1.22e-02 6.72e+03 2.79e+02 bond pdb=" C ALA B 86 " pdb=" N ARG B 87 " ideal model delta sigma weight residual 1.330 1.543 -0.213 1.31e-02 5.83e+03 2.65e+02 bond pdb=" C PRO C 112 " pdb=" N ARG C 113 " ideal model delta sigma weight residual 1.334 1.540 -0.205 1.33e-02 5.65e+03 2.39e+02 bond pdb=" C LEU A 694 " pdb=" N PRO A 695 " ideal model delta sigma weight residual 1.336 1.486 -0.151 1.25e-02 6.40e+03 1.45e+02 bond pdb=" C HIS C 86 " pdb=" N PRO C 87 " ideal model delta sigma weight residual 1.335 1.495 -0.160 1.36e-02 5.41e+03 1.38e+02 ... (remaining 7586 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.03: 10207 5.03 - 10.07: 94 10.07 - 15.10: 15 15.10 - 20.13: 0 20.13 - 25.16: 4 Bond angle restraints: 10320 Sorted by residual: angle pdb=" C ILE C 51 " pdb=" N PRO C 52 " pdb=" CA PRO C 52 " ideal model delta sigma weight residual 119.92 145.08 -25.16 1.07e+00 8.73e-01 5.53e+02 angle pdb=" O ILE C 51 " pdb=" C ILE C 51 " pdb=" N PRO C 52 " ideal model delta sigma weight residual 121.10 96.64 24.46 1.14e+00 7.69e-01 4.60e+02 angle pdb=" CA ILE C 51 " pdb=" C ILE C 51 " pdb=" N PRO C 52 " ideal model delta sigma weight residual 118.88 142.68 -23.80 1.54e+00 4.22e-01 2.39e+02 angle pdb=" O LYS C 81 " pdb=" C LYS C 81 " pdb=" N LEU C 82 " ideal model delta sigma weight residual 122.96 110.40 12.56 1.13e+00 7.83e-01 1.23e+02 angle pdb=" O GLY C 80 " pdb=" C GLY C 80 " pdb=" N LYS C 81 " ideal model delta sigma weight residual 123.55 111.31 12.24 1.19e+00 7.06e-01 1.06e+02 ... (remaining 10315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.34: 4313 12.34 - 24.69: 203 24.69 - 37.03: 52 37.03 - 49.37: 15 49.37 - 61.71: 10 Dihedral angle restraints: 4593 sinusoidal: 1779 harmonic: 2814 Sorted by residual: dihedral pdb=" C ARG A 460 " pdb=" N ARG A 460 " pdb=" CA ARG A 460 " pdb=" CB ARG A 460 " ideal model delta harmonic sigma weight residual -122.60 -134.88 12.28 0 2.50e+00 1.60e-01 2.41e+01 dihedral pdb=" N SER A 461 " pdb=" C SER A 461 " pdb=" CA SER A 461 " pdb=" CB SER A 461 " ideal model delta harmonic sigma weight residual 122.80 111.76 11.04 0 2.50e+00 1.60e-01 1.95e+01 dihedral pdb=" C THR C 58 " pdb=" N THR C 58 " pdb=" CA THR C 58 " pdb=" CB THR C 58 " ideal model delta harmonic sigma weight residual -122.00 -111.39 -10.61 0 2.50e+00 1.60e-01 1.80e+01 ... (remaining 4590 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1028 0.073 - 0.146: 146 0.146 - 0.219: 35 0.219 - 0.292: 3 0.292 - 0.365: 4 Chirality restraints: 1216 Sorted by residual: chirality pdb=" CA LEU C 163 " pdb=" N LEU C 163 " pdb=" C LEU C 163 " pdb=" CB LEU C 163 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CA ARG A 460 " pdb=" N ARG A 460 " pdb=" C ARG A 460 " pdb=" CB ARG A 460 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CA THR C 58 " pdb=" N THR C 58 " pdb=" C THR C 58 " pdb=" CB THR C 58 " both_signs ideal model delta sigma weight residual False 2.53 2.84 -0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 1213 not shown) Planarity restraints: 1315 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 184 " 0.024 2.00e-02 2.50e+03 4.85e-02 2.35e+01 pdb=" C VAL C 184 " -0.084 2.00e-02 2.50e+03 pdb=" O VAL C 184 " 0.032 2.00e-02 2.50e+03 pdb=" N ARG C 185 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 50 " -0.023 2.00e-02 2.50e+03 4.44e-02 1.97e+01 pdb=" C VAL C 50 " 0.077 2.00e-02 2.50e+03 pdb=" O VAL C 50 " -0.029 2.00e-02 2.50e+03 pdb=" N ILE C 51 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 80 " -0.022 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C GLY C 80 " 0.069 2.00e-02 2.50e+03 pdb=" O GLY C 80 " -0.024 2.00e-02 2.50e+03 pdb=" N LYS C 81 " -0.023 2.00e-02 2.50e+03 ... (remaining 1312 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 74 2.57 - 3.15: 6112 3.15 - 3.74: 10735 3.74 - 4.32: 14342 4.32 - 4.90: 23687 Nonbonded interactions: 54950 Sorted by model distance: nonbonded pdb=" ND2 ASN B 51 " pdb=" CD PRO C 87 " model vdw 1.989 3.520 nonbonded pdb=" NH2 ARG B 66 " pdb=" CD1 LEU C 99 " model vdw 2.019 3.540 nonbonded pdb=" O VAL C 50 " pdb=" O GLY C 59 " model vdw 2.132 3.040 nonbonded pdb=" ND1 HIS B 108 " pdb=" OD1 ASN B 109 " model vdw 2.153 3.120 nonbonded pdb=" OH TYR A 468 " pdb=" OE2 GLU A 613 " model vdw 2.193 3.040 ... (remaining 54945 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 group one per residue 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.190 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6076 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 : 0.012 0.213 7591 Z= 0.767 Angle : 1.320 25.163 10320 Z= 0.958 Chirality : 0.059 0.365 1216 Planarity : 0.006 0.063 1315 Dihedral : 8.443 61.713 2714 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.68 % Allowed : 5.11 % Favored : 92.21 % Cbeta Deviations : 0.33 % 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: -1.23 (0.28), residues: 956 helix: 0.71 (0.36), residues: 238 sheet: -2.09 (0.50), residues: 134 loop : -1.17 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 812 HIS 0.002 0.000 HIS C 86 PHE 0.007 0.001 PHE C 139 TYR 0.008 0.001 TYR A 687 ARG 0.001 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 268 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ILE cc_start: 0.8460 (mt) cc_final: 0.8217 (mt) REVERT: A 178 THR cc_start: 0.7354 (p) cc_final: 0.6865 (p) REVERT: A 228 GLU cc_start: 0.6483 (mt-10) cc_final: 0.6275 (mt-10) REVERT: A 265 ASP cc_start: 0.6958 (m-30) cc_final: 0.6516 (m-30) REVERT: A 309 VAL cc_start: 0.7898 (t) cc_final: 0.7639 (p) REVERT: A 373 GLN cc_start: 0.7545 (mt0) cc_final: 0.7005 (mt0) REVERT: A 379 GLN cc_start: 0.7974 (pt0) cc_final: 0.7638 (pm20) REVERT: A 402 HIS cc_start: 0.6791 (t70) cc_final: 0.6458 (t70) REVERT: A 582 VAL cc_start: 0.7540 (t) cc_final: 0.7327 (p) REVERT: A 587 MET cc_start: 0.7613 (tpp) cc_final: 0.7342 (tpp) REVERT: A 589 ILE cc_start: 0.7470 (mm) cc_final: 0.7175 (tt) REVERT: A 667 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7638 (tp) REVERT: A 799 VAL cc_start: 0.8431 (m) cc_final: 0.8223 (p) REVERT: B 113 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7551 (tmtm) REVERT: C 163 LEU cc_start: 0.7639 (mt) cc_final: 0.7406 (mt) outliers start: 22 outliers final: 5 residues processed: 281 average time/residue: 0.1893 time to fit residues: 71.9396 Evaluate side-chains 237 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 230 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 816 LYS Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 167 ASN Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 176 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 140 HIS A 154 GLN A 210 ASN A 218 GLN A 282 ASN A 310 GLN A 320 HIS A 354 ASN A 375 ASN A 417 ASN ** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 ASN ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 ASN B 71 GLN C 62 ASN C 167 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6221 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7591 Z= 0.294 Angle : 0.693 7.247 10320 Z= 0.348 Chirality : 0.047 0.157 1216 Planarity : 0.004 0.043 1315 Dihedral : 5.433 43.993 1027 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.04 % Allowed : 13.63 % Favored : 83.33 % 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: -1.17 (0.27), residues: 956 helix: 1.05 (0.35), residues: 234 sheet: -2.17 (0.47), residues: 127 loop : -1.24 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 159 HIS 0.012 0.001 HIS C 86 PHE 0.021 0.002 PHE A 768 TYR 0.015 0.002 TYR B 83 ARG 0.006 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 235 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 THR cc_start: 0.7204 (p) cc_final: 0.6947 (p) REVERT: A 308 MET cc_start: 0.7194 (mpp) cc_final: 0.6960 (mpp) REVERT: A 309 VAL cc_start: 0.7942 (t) cc_final: 0.7656 (p) REVERT: A 376 GLN cc_start: 0.8002 (mt0) cc_final: 0.7678 (mt0) REVERT: A 379 GLN cc_start: 0.8045 (pt0) cc_final: 0.7733 (pm20) REVERT: A 402 HIS cc_start: 0.6867 (t70) cc_final: 0.6563 (t70) REVERT: A 438 GLN cc_start: 0.8127 (tt0) cc_final: 0.7915 (tt0) REVERT: A 468 TYR cc_start: 0.8263 (m-80) cc_final: 0.7988 (m-80) REVERT: A 547 PHE cc_start: 0.7269 (t80) cc_final: 0.6985 (t80) REVERT: A 587 MET cc_start: 0.7527 (tpp) cc_final: 0.7092 (tpp) REVERT: A 595 THR cc_start: 0.6923 (t) cc_final: 0.5733 (p) REVERT: A 613 GLU cc_start: 0.7264 (mt-10) cc_final: 0.6793 (mt-10) REVERT: A 630 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6497 (mm-30) REVERT: A 667 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7638 (tp) REVERT: A 682 PHE cc_start: 0.7080 (t80) cc_final: 0.6829 (t80) REVERT: A 745 MET cc_start: 0.5973 (tpp) cc_final: 0.5745 (tpp) REVERT: B 113 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7454 (tmtm) REVERT: C 163 LEU cc_start: 0.7293 (mt) cc_final: 0.7060 (mt) outliers start: 25 outliers final: 12 residues processed: 250 average time/residue: 0.1837 time to fit residues: 62.3217 Evaluate side-chains 245 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 231 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 740 ASN Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 816 LYS Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 176 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 72 optimal weight: 0.0040 chunk 59 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 86 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6193 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7591 Z= 0.180 Angle : 0.588 5.729 10320 Z= 0.293 Chirality : 0.044 0.147 1216 Planarity : 0.004 0.051 1315 Dihedral : 4.699 43.491 1023 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.80 % Allowed : 17.27 % Favored : 79.93 % 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: -0.86 (0.27), residues: 956 helix: 1.44 (0.36), residues: 234 sheet: -1.81 (0.47), residues: 133 loop : -1.13 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 159 HIS 0.006 0.001 HIS A 97 PHE 0.018 0.001 PHE A 768 TYR 0.012 0.001 TYR B 83 ARG 0.005 0.001 ARG A 542 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 224 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 THR cc_start: 0.7115 (p) cc_final: 0.6860 (p) REVERT: A 308 MET cc_start: 0.7079 (tpp) cc_final: 0.6825 (mpp) REVERT: A 309 VAL cc_start: 0.7845 (t) cc_final: 0.7605 (p) REVERT: A 354 ASN cc_start: 0.7570 (m-40) cc_final: 0.7327 (t0) REVERT: A 376 GLN cc_start: 0.7950 (mt0) cc_final: 0.6542 (mt0) REVERT: A 402 HIS cc_start: 0.6892 (t70) cc_final: 0.6579 (t70) REVERT: A 468 TYR cc_start: 0.8245 (m-80) cc_final: 0.7949 (m-80) REVERT: A 547 PHE cc_start: 0.7308 (t80) cc_final: 0.7031 (t80) REVERT: A 587 MET cc_start: 0.7505 (tpp) cc_final: 0.6990 (tpp) REVERT: A 595 THR cc_start: 0.6804 (t) cc_final: 0.5638 (p) REVERT: A 613 GLU cc_start: 0.7273 (mt-10) cc_final: 0.6768 (mt-10) REVERT: A 630 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6591 (mm-30) REVERT: A 667 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7603 (tp) REVERT: A 674 THR cc_start: 0.7653 (OUTLIER) cc_final: 0.7396 (t) REVERT: A 682 PHE cc_start: 0.7103 (t80) cc_final: 0.6901 (t80) REVERT: A 706 PHE cc_start: 0.7457 (t80) cc_final: 0.6974 (t80) REVERT: A 745 MET cc_start: 0.5680 (tpp) cc_final: 0.5474 (tpp) REVERT: B 113 LYS cc_start: 0.7582 (OUTLIER) cc_final: 0.7341 (tmtm) REVERT: C 141 ILE cc_start: 0.6332 (OUTLIER) cc_final: 0.6101 (pt) outliers start: 23 outliers final: 13 residues processed: 233 average time/residue: 0.1865 time to fit residues: 58.9758 Evaluate side-chains 234 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 217 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 816 LYS Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain C residue 141 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.2980 chunk 65 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 87 optimal weight: 6.9990 chunk 92 optimal weight: 0.3980 chunk 83 optimal weight: 6.9990 chunk 25 optimal weight: 0.2980 chunk 77 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 HIS ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6184 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7591 Z= 0.164 Angle : 0.564 5.682 10320 Z= 0.280 Chirality : 0.043 0.146 1216 Planarity : 0.004 0.046 1315 Dihedral : 4.471 44.839 1020 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.53 % Allowed : 17.52 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.28), residues: 956 helix: 1.57 (0.35), residues: 235 sheet: -1.90 (0.43), residues: 149 loop : -1.03 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 159 HIS 0.006 0.001 HIS A 97 PHE 0.021 0.001 PHE A 790 TYR 0.010 0.001 TYR B 119 ARG 0.008 0.001 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 219 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.7069 (tpp) cc_final: 0.6761 (mpp) REVERT: A 309 VAL cc_start: 0.7851 (t) cc_final: 0.7591 (p) REVERT: A 354 ASN cc_start: 0.7582 (m-40) cc_final: 0.7332 (t0) REVERT: A 376 GLN cc_start: 0.7999 (mt0) cc_final: 0.6594 (mt0) REVERT: A 402 HIS cc_start: 0.6868 (t70) cc_final: 0.6596 (t70) REVERT: A 468 TYR cc_start: 0.8254 (m-80) cc_final: 0.7937 (m-80) REVERT: A 532 CYS cc_start: 0.5381 (m) cc_final: 0.5103 (m) REVERT: A 547 PHE cc_start: 0.7329 (t80) cc_final: 0.7065 (t80) REVERT: A 587 MET cc_start: 0.7500 (tpp) cc_final: 0.6983 (tpp) REVERT: A 595 THR cc_start: 0.6941 (t) cc_final: 0.5787 (p) REVERT: A 613 GLU cc_start: 0.7283 (mt-10) cc_final: 0.6780 (mt-10) REVERT: A 630 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6647 (mm-30) REVERT: A 667 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7570 (tp) REVERT: A 674 THR cc_start: 0.7558 (OUTLIER) cc_final: 0.7342 (t) REVERT: A 682 PHE cc_start: 0.7067 (t80) cc_final: 0.6842 (t80) REVERT: A 745 MET cc_start: 0.5569 (tpp) cc_final: 0.5346 (tpp) REVERT: B 83 TYR cc_start: 0.8198 (m-80) cc_final: 0.7961 (m-80) REVERT: B 113 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.7168 (tmtm) REVERT: C 141 ILE cc_start: 0.6333 (OUTLIER) cc_final: 0.6055 (pt) outliers start: 29 outliers final: 19 residues processed: 232 average time/residue: 0.1893 time to fit residues: 59.4566 Evaluate side-chains 233 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 210 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 816 LYS Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain C residue 141 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 79 optimal weight: 0.0670 chunk 64 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 23 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 overall best weight: 0.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 GLN ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7591 Z= 0.189 Angle : 0.571 6.196 10320 Z= 0.287 Chirality : 0.043 0.149 1216 Planarity : 0.004 0.044 1315 Dihedral : 4.533 44.863 1020 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.65 % Allowed : 18.00 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.28), residues: 956 helix: 1.50 (0.35), residues: 235 sheet: -1.72 (0.43), residues: 154 loop : -1.14 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 159 HIS 0.005 0.001 HIS A 97 PHE 0.023 0.001 PHE A 790 TYR 0.010 0.001 TYR B 119 ARG 0.005 0.001 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 213 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.7067 (tpp) cc_final: 0.6777 (mpp) REVERT: A 309 VAL cc_start: 0.7827 (t) cc_final: 0.7567 (p) REVERT: A 402 HIS cc_start: 0.6823 (t70) cc_final: 0.6566 (t70) REVERT: A 446 LYS cc_start: 0.8532 (mmmm) cc_final: 0.8289 (mmmm) REVERT: A 468 TYR cc_start: 0.8293 (m-80) cc_final: 0.7978 (m-80) REVERT: A 532 CYS cc_start: 0.5425 (m) cc_final: 0.5174 (m) REVERT: A 547 PHE cc_start: 0.7367 (t80) cc_final: 0.7123 (t80) REVERT: A 587 MET cc_start: 0.7507 (tpp) cc_final: 0.6898 (tpp) REVERT: A 613 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6792 (mt-10) REVERT: A 629 SER cc_start: 0.7277 (t) cc_final: 0.7037 (p) REVERT: A 667 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7531 (tp) REVERT: A 674 THR cc_start: 0.7580 (OUTLIER) cc_final: 0.7365 (t) REVERT: A 706 PHE cc_start: 0.7290 (t80) cc_final: 0.6839 (t80) REVERT: A 745 MET cc_start: 0.5565 (tpp) cc_final: 0.5362 (tpp) REVERT: B 113 LYS cc_start: 0.7403 (OUTLIER) cc_final: 0.7141 (tmtm) REVERT: C 141 ILE cc_start: 0.6447 (OUTLIER) cc_final: 0.6123 (pt) outliers start: 30 outliers final: 17 residues processed: 228 average time/residue: 0.1942 time to fit residues: 60.3117 Evaluate side-chains 232 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 211 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 539 TRP Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 816 LYS Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain C residue 141 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 89 optimal weight: 9.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6235 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7591 Z= 0.220 Angle : 0.590 6.271 10320 Z= 0.299 Chirality : 0.044 0.150 1216 Planarity : 0.004 0.042 1315 Dihedral : 4.643 45.306 1020 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.41 % Allowed : 19.71 % Favored : 76.89 % 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: -1.05 (0.27), residues: 956 helix: 1.25 (0.35), residues: 242 sheet: -1.70 (0.43), residues: 154 loop : -1.30 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 159 HIS 0.005 0.001 HIS C 86 PHE 0.023 0.001 PHE A 790 TYR 0.008 0.001 TYR B 119 ARG 0.006 0.001 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 SER cc_start: 0.7818 (p) cc_final: 0.7220 (p) REVERT: A 308 MET cc_start: 0.7110 (tpp) cc_final: 0.6670 (mpp) REVERT: A 309 VAL cc_start: 0.7896 (t) cc_final: 0.7611 (p) REVERT: A 376 GLN cc_start: 0.8077 (mt0) cc_final: 0.7806 (mt0) REVERT: A 402 HIS cc_start: 0.6832 (t70) cc_final: 0.6584 (t70) REVERT: A 446 LYS cc_start: 0.8553 (mmmm) cc_final: 0.8305 (mmmm) REVERT: A 468 TYR cc_start: 0.8305 (m-80) cc_final: 0.7962 (m-80) REVERT: A 532 CYS cc_start: 0.5415 (m) cc_final: 0.5152 (m) REVERT: A 547 PHE cc_start: 0.7366 (t80) cc_final: 0.7157 (t80) REVERT: A 587 MET cc_start: 0.7483 (tpp) cc_final: 0.6826 (tpp) REVERT: A 613 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6838 (mt-10) REVERT: A 667 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7347 (tp) REVERT: A 745 MET cc_start: 0.5553 (tpp) cc_final: 0.5323 (tpp) REVERT: B 109 ASN cc_start: 0.7516 (m-40) cc_final: 0.7272 (m-40) REVERT: C 141 ILE cc_start: 0.6648 (OUTLIER) cc_final: 0.6361 (pt) outliers start: 28 outliers final: 22 residues processed: 233 average time/residue: 0.1888 time to fit residues: 59.5264 Evaluate side-chains 242 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 218 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 539 TRP Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 816 LYS Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain C residue 141 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 78 optimal weight: 0.0670 chunk 51 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6227 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7591 Z= 0.192 Angle : 0.576 6.686 10320 Z= 0.290 Chirality : 0.043 0.173 1216 Planarity : 0.004 0.041 1315 Dihedral : 4.361 27.351 1016 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.16 % Allowed : 20.07 % Favored : 76.76 % 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: -1.02 (0.27), residues: 956 helix: 1.42 (0.35), residues: 235 sheet: -1.72 (0.47), residues: 127 loop : -1.36 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 159 HIS 0.005 0.001 HIS A 97 PHE 0.025 0.001 PHE A 790 TYR 0.009 0.001 TYR A 801 ARG 0.007 0.001 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 225 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 ILE cc_start: 0.7611 (mp) cc_final: 0.7370 (mm) REVERT: A 307 SER cc_start: 0.7779 (p) cc_final: 0.7128 (p) REVERT: A 308 MET cc_start: 0.7094 (tpp) cc_final: 0.6606 (mpp) REVERT: A 309 VAL cc_start: 0.7934 (t) cc_final: 0.7638 (p) REVERT: A 376 GLN cc_start: 0.8017 (mt0) cc_final: 0.7749 (mt0) REVERT: A 402 HIS cc_start: 0.6844 (t70) cc_final: 0.6581 (t70) REVERT: A 468 TYR cc_start: 0.8307 (m-80) cc_final: 0.7955 (m-80) REVERT: A 532 CYS cc_start: 0.5390 (m) cc_final: 0.5122 (m) REVERT: A 547 PHE cc_start: 0.7358 (t80) cc_final: 0.7143 (t80) REVERT: A 587 MET cc_start: 0.7521 (tpp) cc_final: 0.6728 (tpp) REVERT: A 613 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6811 (mt-10) REVERT: A 667 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7312 (tp) REVERT: A 745 MET cc_start: 0.5430 (tpp) cc_final: 0.5214 (tpp) REVERT: C 55 MET cc_start: 0.4733 (ppp) cc_final: 0.4424 (ppp) outliers start: 26 outliers final: 20 residues processed: 234 average time/residue: 0.1904 time to fit residues: 61.0297 Evaluate side-chains 245 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 224 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 539 TRP Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 816 LYS Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 112 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.0270 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 0.0020 chunk 63 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 84 optimal weight: 0.0030 chunk 88 optimal weight: 2.9990 chunk 80 optimal weight: 0.0970 overall best weight: 0.2054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6151 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7591 Z= 0.145 Angle : 0.566 6.441 10320 Z= 0.278 Chirality : 0.042 0.197 1216 Planarity : 0.004 0.065 1315 Dihedral : 3.997 28.696 1016 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.43 % Allowed : 21.78 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.28), residues: 956 helix: 1.89 (0.36), residues: 229 sheet: -1.72 (0.43), residues: 151 loop : -1.08 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 602 HIS 0.004 0.001 HIS A 97 PHE 0.021 0.001 PHE A 790 TYR 0.011 0.001 TYR A 725 ARG 0.008 0.001 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 217 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 ILE cc_start: 0.7533 (mp) cc_final: 0.7315 (mm) REVERT: A 307 SER cc_start: 0.7861 (p) cc_final: 0.7077 (p) REVERT: A 308 MET cc_start: 0.7006 (tpp) cc_final: 0.6443 (mpp) REVERT: A 309 VAL cc_start: 0.7797 (t) cc_final: 0.7499 (p) REVERT: A 376 GLN cc_start: 0.8055 (mt0) cc_final: 0.7814 (mt0) REVERT: A 402 HIS cc_start: 0.6813 (t70) cc_final: 0.6588 (t70) REVERT: A 468 TYR cc_start: 0.8267 (m-80) cc_final: 0.7947 (m-80) REVERT: A 532 CYS cc_start: 0.5316 (m) cc_final: 0.5033 (m) REVERT: A 536 LEU cc_start: 0.8544 (mt) cc_final: 0.8205 (mp) REVERT: A 547 PHE cc_start: 0.7322 (t80) cc_final: 0.7097 (t80) REVERT: A 587 MET cc_start: 0.7522 (tpp) cc_final: 0.6780 (tpp) REVERT: A 595 THR cc_start: 0.6891 (t) cc_final: 0.5738 (p) REVERT: A 613 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6776 (mt-10) REVERT: A 667 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7224 (tp) REVERT: A 725 TYR cc_start: 0.7096 (OUTLIER) cc_final: 0.6600 (m-80) REVERT: C 55 MET cc_start: 0.4839 (ppp) cc_final: 0.4512 (ppp) REVERT: C 141 ILE cc_start: 0.6669 (OUTLIER) cc_final: 0.6376 (pt) outliers start: 20 outliers final: 13 residues processed: 228 average time/residue: 0.1917 time to fit residues: 58.7849 Evaluate side-chains 232 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 216 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 816 LYS Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain C residue 141 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 26 optimal weight: 0.0010 chunk 77 optimal weight: 0.3980 chunk 81 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6213 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7591 Z= 0.196 Angle : 0.600 8.357 10320 Z= 0.298 Chirality : 0.043 0.172 1216 Planarity : 0.004 0.061 1315 Dihedral : 4.169 27.857 1016 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.19 % Allowed : 22.87 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.27), residues: 956 helix: 1.58 (0.34), residues: 245 sheet: -1.63 (0.45), residues: 141 loop : -1.30 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 159 HIS 0.004 0.001 HIS C 86 PHE 0.019 0.001 PHE A 80 TYR 0.010 0.001 TYR B 119 ARG 0.008 0.001 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 214 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 ILE cc_start: 0.7528 (mp) cc_final: 0.7315 (mm) REVERT: A 307 SER cc_start: 0.7859 (p) cc_final: 0.7157 (p) REVERT: A 308 MET cc_start: 0.7063 (tpp) cc_final: 0.6509 (mpp) REVERT: A 309 VAL cc_start: 0.7898 (t) cc_final: 0.7592 (p) REVERT: A 376 GLN cc_start: 0.8081 (mt0) cc_final: 0.7810 (mt0) REVERT: A 395 ASP cc_start: 0.7056 (t0) cc_final: 0.6818 (t0) REVERT: A 402 HIS cc_start: 0.6859 (t70) cc_final: 0.6616 (t70) REVERT: A 468 TYR cc_start: 0.8317 (m-80) cc_final: 0.7988 (m-80) REVERT: A 532 CYS cc_start: 0.5465 (m) cc_final: 0.5199 (m) REVERT: A 587 MET cc_start: 0.7491 (tpp) cc_final: 0.6804 (tpp) REVERT: A 613 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6787 (mt-10) REVERT: A 667 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7170 (tp) REVERT: A 745 MET cc_start: 0.5128 (tpp) cc_final: 0.4750 (tpp) REVERT: C 55 MET cc_start: 0.4807 (ppp) cc_final: 0.4486 (ppp) REVERT: C 141 ILE cc_start: 0.6786 (OUTLIER) cc_final: 0.6491 (pt) outliers start: 18 outliers final: 16 residues processed: 223 average time/residue: 0.1964 time to fit residues: 58.7837 Evaluate side-chains 231 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 213 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 816 LYS Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain C residue 141 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 60 optimal weight: 0.4980 chunk 81 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 154 GLN ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6249 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7591 Z= 0.238 Angle : 0.633 7.841 10320 Z= 0.317 Chirality : 0.045 0.170 1216 Planarity : 0.005 0.060 1315 Dihedral : 4.477 27.020 1016 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.43 % Allowed : 22.87 % Favored : 74.70 % 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: -1.13 (0.27), residues: 956 helix: 1.14 (0.34), residues: 257 sheet: -1.67 (0.44), residues: 144 loop : -1.46 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 159 HIS 0.006 0.001 HIS C 86 PHE 0.020 0.001 PHE A 790 TYR 0.012 0.001 TYR B 119 ARG 0.013 0.001 ARG A 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 218 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 ILE cc_start: 0.7571 (mp) cc_final: 0.7364 (mm) REVERT: A 307 SER cc_start: 0.7833 (p) cc_final: 0.7113 (p) REVERT: A 308 MET cc_start: 0.7126 (tpp) cc_final: 0.6627 (mpp) REVERT: A 309 VAL cc_start: 0.7919 (t) cc_final: 0.7608 (p) REVERT: A 402 HIS cc_start: 0.6876 (t70) cc_final: 0.6603 (t70) REVERT: A 468 TYR cc_start: 0.8327 (m-80) cc_final: 0.7961 (m-80) REVERT: A 532 CYS cc_start: 0.5463 (m) cc_final: 0.5226 (m) REVERT: A 587 MET cc_start: 0.7537 (tpp) cc_final: 0.6727 (tpp) REVERT: A 613 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6806 (mt-10) REVERT: A 667 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7208 (tp) REVERT: A 745 MET cc_start: 0.5239 (tpp) cc_final: 0.4844 (tpp) REVERT: C 55 MET cc_start: 0.4788 (ppp) cc_final: 0.4471 (ppp) REVERT: C 141 ILE cc_start: 0.6899 (OUTLIER) cc_final: 0.6592 (pt) outliers start: 20 outliers final: 15 residues processed: 228 average time/residue: 0.1963 time to fit residues: 60.6960 Evaluate side-chains 234 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 217 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 816 LYS Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain C residue 141 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 76 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.0030 chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.141952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.116985 restraints weight = 11876.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.120783 restraints weight = 6190.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.123272 restraints weight = 3844.642| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7591 Z= 0.214 Angle : 0.625 8.578 10320 Z= 0.313 Chirality : 0.044 0.170 1216 Planarity : 0.005 0.061 1315 Dihedral : 4.392 26.894 1016 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 2.19 % Allowed : 22.87 % Favored : 74.94 % 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: -1.06 (0.28), residues: 956 helix: 1.32 (0.35), residues: 245 sheet: -1.58 (0.45), residues: 143 loop : -1.43 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 159 HIS 0.012 0.001 HIS B 108 PHE 0.020 0.001 PHE A 80 TYR 0.012 0.001 TYR B 119 ARG 0.012 0.001 ARG A 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2067.31 seconds wall clock time: 38 minutes 1.33 seconds (2281.33 seconds total)