Starting phenix.real_space_refine on Sun Dec 29 01:05:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dw2_27749/12_2024/8dw2_27749.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dw2_27749/12_2024/8dw2_27749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dw2_27749/12_2024/8dw2_27749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dw2_27749/12_2024/8dw2_27749.map" model { file = "/net/cci-nas-00/data/ceres_data/8dw2_27749/12_2024/8dw2_27749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dw2_27749/12_2024/8dw2_27749.cif" } resolution = 4.11 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 5906 2.51 5 N 1565 2.21 5 O 1858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9364 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1153 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "B" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1521 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 10, 'TRANS': 181} Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1624 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Chain: "D" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1715 Classifications: {'peptide': 228} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 215} Chain: "H" Number of atoms: 1609 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 216, 1607 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 216, 1607 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201} Chain breaks: 1 bond proxies already assigned to first conformer: 1646 Chain: "L" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1703 Classifications: {'peptide': 219} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.71, per 1000 atoms: 0.72 Number of scatterers: 9364 At special positions: 0 Unit cell: (79.443, 129.204, 173.727, 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 35 16.00 O 1858 8.00 N 1565 7.00 C 5906 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 89 " distance=2.04 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 194 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 210 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 200 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 Simple disulfide: pdb=" SG CYS L 140 " - pdb=" SG CYS L 200 " distance=2.03 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG E 1 " - " ASN B 343 " Time building additional restraints: 3.01 Conformation dependent library (CDL) restraints added in 1.4 seconds 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2236 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 22 sheets defined 14.2% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 16 through 25 removed outlier: 3.917A pdb=" N GLU A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 36 Processing helix chain 'A' and resid 49 through 58 Processing helix chain 'A' and resid 59 through 69 removed outlier: 3.658A pdb=" N TYR A 69 " --> pdb=" O VAL A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 91 Processing helix chain 'A' and resid 92 through 103 removed outlier: 4.045A pdb=" N VAL A 96 " --> pdb=" O HIS A 92 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 123 Processing helix chain 'A' and resid 126 through 135 removed outlier: 3.608A pdb=" N GLU A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASN A 135 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 156 removed outlier: 3.972A pdb=" N ILE A 152 " --> pdb=" O THR A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 168 removed outlier: 3.520A pdb=" N LEU A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.978A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.605A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.585A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'C' and resid 121 through 126 removed outlier: 3.695A pdb=" N LEU C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 187 removed outlier: 3.746A pdb=" N GLU C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 183 through 187' Processing helix chain 'D' and resid 87 through 91 removed outlier: 4.081A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 203 No H-bonds generated for 'chain 'D' and resid 201 through 203' Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'L' and resid 85 through 89 removed outlier: 4.127A pdb=" N VAL L 89 " --> pdb=" O ALA L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 134 removed outlier: 3.550A pdb=" N GLY L 134 " --> pdb=" O GLN L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 189 through 194 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 356 removed outlier: 3.544A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'C' and resid 4 through 5 removed outlier: 3.876A pdb=" N ARG C 24 " --> pdb=" O THR C 5 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.711A pdb=" N TYR C 50 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU C 47 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N GLN C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.711A pdb=" N TYR C 50 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU C 47 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N GLN C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 114 through 118 removed outlier: 6.373A pdb=" N TYR C 173 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 145 through 150 Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.346A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 134 through 138 Processing sheet with id=AB3, first strand: chain 'D' and resid 165 through 168 Processing sheet with id=AB4, first strand: chain 'H' and resid 2 through 6 Processing sheet with id=AB5, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.623A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL H 108 " --> pdb=" O GLY H 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.623A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 124 through 128 removed outlier: 6.227A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 124 through 128 removed outlier: 6.227A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER H 181 " --> pdb=" O VAL H 173 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 154 through 158 removed outlier: 3.847A pdb=" N TYR H 198 " --> pdb=" O VAL H 215 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'L' and resid 59 through 60 removed outlier: 6.617A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N TYR L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 120 through 124 removed outlier: 5.447A pdb=" N TYR L 179 " --> pdb=" O ASN L 144 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 150 through 156 366 hydrogen bonds defined for protein. 948 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: 2.95 Time building geometry restraints manager: 3.36 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: 3009 1.34 - 1.46: 2391 1.46 - 1.59: 4134 1.59 - 1.71: 1 1.71 - 1.83: 44 Bond restraints: 9579 Sorted by residual: bond pdb=" CA ASN D 211 " pdb=" CB ASN D 211 " ideal model delta sigma weight residual 1.530 1.565 -0.035 1.55e-02 4.16e+03 5.10e+00 bond pdb=" CB PRO C 81 " pdb=" CG PRO C 81 " ideal model delta sigma weight residual 1.492 1.604 -0.112 5.00e-02 4.00e+02 4.99e+00 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" CA ARG L 67 " pdb=" C ARG L 67 " ideal model delta sigma weight residual 1.523 1.542 -0.018 1.34e-02 5.57e+03 1.90e+00 bond pdb=" CB PRO B 384 " pdb=" CG PRO B 384 " ideal model delta sigma weight residual 1.492 1.559 -0.067 5.00e-02 4.00e+02 1.81e+00 ... (remaining 9574 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 12798 2.62 - 5.23: 189 5.23 - 7.85: 36 7.85 - 10.47: 4 10.47 - 13.09: 1 Bond angle restraints: 13028 Sorted by residual: angle pdb=" CA PRO C 81 " pdb=" N PRO C 81 " pdb=" CD PRO C 81 " ideal model delta sigma weight residual 112.00 104.54 7.46 1.40e+00 5.10e-01 2.84e+01 angle pdb=" C SER C 95 " pdb=" CA SER C 95 " pdb=" CB SER C 95 " ideal model delta sigma weight residual 116.54 111.33 5.21 1.15e+00 7.56e-01 2.05e+01 angle pdb=" CB MET H 40 " pdb=" CG MET H 40 " pdb=" SD MET H 40 " ideal model delta sigma weight residual 112.70 125.79 -13.09 3.00e+00 1.11e-01 1.90e+01 angle pdb=" N ALA D 92 " pdb=" CA ALA D 92 " pdb=" C ALA D 92 " ideal model delta sigma weight residual 108.24 113.74 -5.50 1.32e+00 5.74e-01 1.74e+01 angle pdb=" CA LYS B 444 " pdb=" CB LYS B 444 " pdb=" CG LYS B 444 " ideal model delta sigma weight residual 114.10 122.22 -8.12 2.00e+00 2.50e-01 1.65e+01 ... (remaining 13023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.73: 5045 21.73 - 43.47: 592 43.47 - 65.20: 79 65.20 - 86.94: 17 86.94 - 108.67: 5 Dihedral angle restraints: 5738 sinusoidal: 2226 harmonic: 3512 Sorted by residual: dihedral pdb=" CB CYS C 134 " pdb=" SG CYS C 134 " pdb=" SG CYS C 194 " pdb=" CB CYS C 194 " ideal model delta sinusoidal sigma weight residual 93.00 151.64 -58.64 1 1.00e+01 1.00e-02 4.60e+01 dihedral pdb=" CA CYS B 361 " pdb=" C CYS B 361 " pdb=" N VAL B 362 " pdb=" CA VAL B 362 " ideal model delta harmonic sigma weight residual 180.00 148.89 31.11 0 5.00e+00 4.00e-02 3.87e+01 dihedral pdb=" CA ASP B 420 " pdb=" C ASP B 420 " pdb=" N TYR B 421 " pdb=" CA TYR B 421 " ideal model delta harmonic sigma weight residual -180.00 -151.38 -28.62 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 5735 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1168 0.055 - 0.109: 251 0.109 - 0.164: 42 0.164 - 0.218: 4 0.218 - 0.273: 1 Chirality restraints: 1466 Sorted by residual: chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA ASN L 144 " pdb=" N ASN L 144 " pdb=" C ASN L 144 " pdb=" CB ASN L 144 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.46e-01 chirality pdb=" CA VAL H 117 " pdb=" N VAL H 117 " pdb=" C VAL H 117 " pdb=" CB VAL H 117 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.76e-01 ... (remaining 1463 not shown) Planarity restraints: 1672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " -0.062 5.00e-02 4.00e+02 9.55e-02 1.46e+01 pdb=" N PRO B 521 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 158 " -0.021 2.00e-02 2.50e+03 2.02e-02 1.02e+01 pdb=" CG TRP H 158 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP H 158 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP H 158 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP H 158 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP H 158 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP H 158 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 158 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 158 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP H 158 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE H 150 " -0.047 5.00e-02 4.00e+02 7.09e-02 8.05e+00 pdb=" N PRO H 151 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO H 151 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO H 151 " -0.035 5.00e-02 4.00e+02 ... (remaining 1669 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 338 2.68 - 3.24: 9285 3.24 - 3.79: 14814 3.79 - 4.35: 18704 4.35 - 4.90: 29833 Nonbonded interactions: 72974 Sorted by model distance: nonbonded pdb=" O TYR C 186 " pdb=" OH TYR C 192 " model vdw 2.127 3.040 nonbonded pdb=" OG SER B 514 " pdb=" OE2 GLU B 516 " model vdw 2.174 3.040 nonbonded pdb=" O SER H 192 " pdb=" OG SER H 192 " model vdw 2.199 3.040 nonbonded pdb=" OD2 ASP A 110 " pdb=" OH TYR B 489 " model vdw 2.201 3.040 nonbonded pdb=" OD1 ASP L 176 " pdb=" OG1 THR L 178 " model vdw 2.205 3.040 ... (remaining 72969 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 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 2 or resid 4 through 8 or resid 11 or resid 14 or resid 16 \ through 20 or resid 23 or resid 26 through 27 or resid 29 through 31 or resid 3 \ 4 through 43 or resid 45 or resid 47 through 50 or resid 52 through 53 or resid \ 55 or resid 58 or resid 60 through 77 or resid 79 or resid 82 through 83 or resi \ d 85 through 91 or resid 94 or resid 97 through 99 or resid 101 through 213)) selection = (chain 'L' and (resid 2 or resid 4 through 8 or resid 11 or resid 14 or resid 16 \ through 20 or resid 23 or resid 26 through 27 or resid 29 or resid 32 through 3 \ 3 or resid 39 through 48 or resid 50 or resid 52 through 55 or resid 57 through \ 58 or resid 60 or resid 63 or resid 65 through 82 or resid 84 or resid 87 throug \ h 88 or resid 90 through 96 or resid 100 or resid 103 through 105 or resid 107 t \ hrough 219)) } 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=0.00 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.430 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: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 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 0.112 9579 Z= 0.235 Angle : 0.812 13.087 13028 Z= 0.408 Chirality : 0.047 0.273 1466 Planarity : 0.006 0.095 1671 Dihedral : 17.647 108.673 3466 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.20 % Favored : 93.71 % Rotamer: Outliers : 0.48 % Allowed : 33.27 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.94 (0.24), residues: 1209 helix: -0.95 (0.39), residues: 146 sheet: 0.33 (0.26), residues: 427 loop : -1.22 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP H 158 HIS 0.004 0.001 HIS D 214 PHE 0.020 0.002 PHE H 150 TYR 0.017 0.001 TYR B 423 ARG 0.006 0.001 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 144 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 HIS cc_start: 0.9002 (m90) cc_final: 0.8452 (m90) REVERT: A 85 HIS cc_start: 0.8589 (m90) cc_final: 0.8090 (m90) REVERT: B 495 TYR cc_start: 0.8539 (m-80) cc_final: 0.8092 (t80) REVERT: C 179 LEU cc_start: 0.9171 (tp) cc_final: 0.8921 (tp) REVERT: H 40 MET cc_start: 0.8982 (mmm) cc_final: 0.8588 (mmt) REVERT: H 77 ASN cc_start: 0.7892 (OUTLIER) cc_final: 0.7622 (t0) outliers start: 5 outliers final: 3 residues processed: 146 average time/residue: 0.2042 time to fit residues: 42.5393 Evaluate side-chains 135 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 131 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 48 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 108 optimal weight: 0.5980 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 138 ASN C 155 GLN ** C 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 164 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9579 Z= 0.317 Angle : 0.727 7.569 13028 Z= 0.375 Chirality : 0.047 0.209 1466 Planarity : 0.006 0.076 1671 Dihedral : 7.438 66.612 1374 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.44 % Favored : 91.48 % Rotamer: Outliers : 0.10 % Allowed : 4.45 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % 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: -0.95 (0.24), residues: 1209 helix: -0.68 (0.41), residues: 141 sheet: 0.28 (0.26), residues: 415 loop : -1.23 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP D 50 HIS 0.005 0.001 HIS C 198 PHE 0.028 0.003 PHE B 464 TYR 0.024 0.002 TYR L 102 ARG 0.009 0.001 ARG L 217 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 1.082 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 52 HIS cc_start: 0.9031 (m90) cc_final: 0.8583 (m90) REVERT: A 85 HIS cc_start: 0.8784 (m90) cc_final: 0.8489 (m90) REVERT: A 94 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7427 (mm-30) REVERT: B 366 SER cc_start: 0.9145 (p) cc_final: 0.8830 (p) REVERT: C 138 ASN cc_start: 0.9184 (m-40) cc_final: 0.8913 (m110) REVERT: D 152 LEU cc_start: 0.8681 (mt) cc_final: 0.8326 (pp) REVERT: D 178 HIS cc_start: 0.8914 (m90) cc_final: 0.8553 (m90) REVERT: H 3 GLN cc_start: 0.8910 (mm110) cc_final: 0.8622 (mm-40) REVERT: H 40 MET cc_start: 0.9143 (mmm) cc_final: 0.8917 (mmm) REVERT: L 142 LEU cc_start: 0.9374 (tp) cc_final: 0.8951 (tt) REVERT: L 167 GLU cc_start: 0.8595 (tt0) cc_final: 0.8347 (tm-30) outliers start: 1 outliers final: 1 residues processed: 180 average time/residue: 0.2219 time to fit residues: 55.0869 Evaluate side-chains 128 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 73 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 116 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9579 Z= 0.209 Angle : 0.654 6.934 13028 Z= 0.336 Chirality : 0.045 0.177 1466 Planarity : 0.005 0.069 1671 Dihedral : 6.305 56.303 1374 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.87 % Favored : 93.05 % Rotamer: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.72 (0.24), residues: 1209 helix: -0.63 (0.40), residues: 142 sheet: 0.49 (0.26), residues: 416 loop : -1.10 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 50 HIS 0.003 0.001 HIS D 214 PHE 0.015 0.002 PHE L 122 TYR 0.021 0.001 TYR L 102 ARG 0.006 0.001 ARG L 217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 1.133 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: A 82 THR cc_start: 0.8958 (p) cc_final: 0.7653 (p) REVERT: A 85 HIS cc_start: 0.8801 (m90) cc_final: 0.8562 (m90) REVERT: A 94 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7381 (mm-30) REVERT: A 118 HIS cc_start: 0.8611 (t70) cc_final: 0.8399 (t-170) REVERT: B 489 TYR cc_start: 0.6783 (m-80) cc_final: 0.6319 (m-80) REVERT: B 498 GLN cc_start: 0.8326 (mm110) cc_final: 0.8097 (mm110) REVERT: C 138 ASN cc_start: 0.9162 (m-40) cc_final: 0.8909 (m110) REVERT: D 178 HIS cc_start: 0.8911 (m90) cc_final: 0.8523 (m90) REVERT: H 3 GLN cc_start: 0.8894 (mm110) cc_final: 0.8590 (mm-40) REVERT: L 41 TRP cc_start: 0.8644 (m100) cc_final: 0.7886 (m100) REVERT: L 84 LEU cc_start: 0.8851 (pt) cc_final: 0.8558 (pt) REVERT: L 167 GLU cc_start: 0.8613 (tt0) cc_final: 0.8321 (tm-30) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2068 time to fit residues: 50.8339 Evaluate side-chains 135 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 11 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 72 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 115 optimal weight: 20.0000 chunk 102 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 9579 Z= 0.310 Angle : 0.699 8.343 13028 Z= 0.358 Chirality : 0.046 0.176 1466 Planarity : 0.005 0.062 1671 Dihedral : 6.056 56.671 1374 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.44 % Favored : 91.48 % Rotamer: Outliers : 0.10 % Allowed : 4.45 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.84 (0.24), residues: 1209 helix: -0.51 (0.42), residues: 141 sheet: 0.30 (0.26), residues: 419 loop : -1.15 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 50 HIS 0.004 0.001 HIS C 198 PHE 0.023 0.003 PHE B 377 TYR 0.023 0.002 TYR H 52 ARG 0.009 0.001 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 1.062 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 49 THR cc_start: 0.8775 (p) cc_final: 0.7677 (p) REVERT: A 52 HIS cc_start: 0.9036 (m90) cc_final: 0.8713 (m90) REVERT: A 94 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7431 (mm-30) REVERT: B 421 TYR cc_start: 0.8888 (m-80) cc_final: 0.8292 (m-80) REVERT: B 498 GLN cc_start: 0.8287 (mm110) cc_final: 0.8074 (mm110) REVERT: D 70 MET cc_start: 0.7127 (mtt) cc_final: 0.6894 (mtt) REVERT: D 154 CYS cc_start: 0.6220 (m) cc_final: 0.5278 (m) REVERT: D 178 HIS cc_start: 0.8899 (m90) cc_final: 0.8500 (m90) REVERT: H 3 GLN cc_start: 0.8944 (mm110) cc_final: 0.8565 (mm-40) REVERT: H 144 CYS cc_start: 0.4969 (m) cc_final: 0.4583 (m) REVERT: H 150 PHE cc_start: 0.8275 (t80) cc_final: 0.8067 (t80) REVERT: L 41 TRP cc_start: 0.8690 (m100) cc_final: 0.8065 (m100) REVERT: L 142 LEU cc_start: 0.9417 (tt) cc_final: 0.9033 (tt) REVERT: L 167 GLU cc_start: 0.8682 (tt0) cc_final: 0.8303 (tm-30) outliers start: 1 outliers final: 1 residues processed: 150 average time/residue: 0.2128 time to fit residues: 45.0707 Evaluate side-chains 120 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 HIS L 96 GLN L 164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9579 Z= 0.291 Angle : 0.691 7.566 13028 Z= 0.357 Chirality : 0.045 0.168 1466 Planarity : 0.005 0.063 1671 Dihedral : 5.848 56.445 1374 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.19 % Favored : 91.73 % Rotamer: Outliers : 0.10 % Allowed : 3.38 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % 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: -0.92 (0.24), residues: 1209 helix: -0.81 (0.40), residues: 147 sheet: 0.30 (0.26), residues: 418 loop : -1.18 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP H 47 HIS 0.004 0.001 HIS C 198 PHE 0.020 0.002 PHE D 106 TYR 0.038 0.002 TYR L 102 ARG 0.003 0.001 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 HIS cc_start: 0.9151 (m90) cc_final: 0.8683 (m90) REVERT: A 61 GLU cc_start: 0.9086 (mp0) cc_final: 0.8864 (pm20) REVERT: A 62 ILE cc_start: 0.8717 (pt) cc_final: 0.8291 (pt) REVERT: A 82 THR cc_start: 0.8924 (p) cc_final: 0.7456 (p) REVERT: A 90 THR cc_start: 0.8304 (t) cc_final: 0.8058 (p) REVERT: A 94 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7443 (mm-30) REVERT: A 118 HIS cc_start: 0.8692 (t70) cc_final: 0.8479 (t-170) REVERT: B 421 TYR cc_start: 0.8961 (m-80) cc_final: 0.8326 (m-80) REVERT: B 498 GLN cc_start: 0.8301 (mm110) cc_final: 0.8092 (mm110) REVERT: D 70 MET cc_start: 0.7153 (mtt) cc_final: 0.6923 (mtt) REVERT: D 154 CYS cc_start: 0.6174 (m) cc_final: 0.5307 (m) REVERT: D 178 HIS cc_start: 0.8877 (m90) cc_final: 0.8459 (m90) REVERT: H 3 GLN cc_start: 0.8931 (mm110) cc_final: 0.8580 (mm-40) REVERT: H 144 CYS cc_start: 0.4856 (m) cc_final: 0.4357 (m) REVERT: H 150 PHE cc_start: 0.8392 (t80) cc_final: 0.7985 (t80) REVERT: L 41 TRP cc_start: 0.8695 (m100) cc_final: 0.8060 (m100) REVERT: L 142 LEU cc_start: 0.9431 (tt) cc_final: 0.9109 (tt) outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 0.2035 time to fit residues: 42.8325 Evaluate side-chains 113 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 53 optimal weight: 8.9990 chunk 9 optimal weight: 0.0970 chunk 38 optimal weight: 0.0470 chunk 60 optimal weight: 0.5980 chunk 111 optimal weight: 6.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 HIS L 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9579 Z= 0.174 Angle : 0.648 8.548 13028 Z= 0.327 Chirality : 0.045 0.245 1466 Planarity : 0.005 0.058 1671 Dihedral : 5.296 55.266 1374 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.78 % Favored : 93.13 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.62 (0.25), residues: 1209 helix: -0.65 (0.41), residues: 148 sheet: 0.55 (0.26), residues: 416 loop : -1.00 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 168 HIS 0.004 0.001 HIS A 59 PHE 0.016 0.001 PHE C 72 TYR 0.018 0.001 TYR H 52 ARG 0.002 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 THR cc_start: 0.8895 (p) cc_final: 0.7882 (p) REVERT: A 52 HIS cc_start: 0.9065 (m90) cc_final: 0.8823 (m90) REVERT: A 90 THR cc_start: 0.8107 (t) cc_final: 0.7840 (p) REVERT: A 94 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7327 (mm-30) REVERT: B 421 TYR cc_start: 0.8921 (m-80) cc_final: 0.8233 (m-80) REVERT: C 138 ASN cc_start: 0.9109 (m-40) cc_final: 0.8855 (m110) REVERT: D 3 GLN cc_start: 0.8864 (mm110) cc_final: 0.8514 (mp10) REVERT: D 70 MET cc_start: 0.7099 (mtt) cc_final: 0.6899 (mtt) REVERT: D 143 LYS cc_start: 0.6437 (pttt) cc_final: 0.5968 (tppt) REVERT: D 154 CYS cc_start: 0.5677 (m) cc_final: 0.4828 (m) REVERT: D 178 HIS cc_start: 0.8786 (m90) cc_final: 0.8366 (m90) REVERT: H 3 GLN cc_start: 0.8899 (mm110) cc_final: 0.8563 (mm-40) REVERT: H 144 CYS cc_start: 0.4661 (m) cc_final: 0.4241 (m) REVERT: H 150 PHE cc_start: 0.8224 (t80) cc_final: 0.7903 (t80) REVERT: L 41 TRP cc_start: 0.8619 (m100) cc_final: 0.8059 (m100) REVERT: L 142 LEU cc_start: 0.9426 (tt) cc_final: 0.9047 (tt) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.2003 time to fit residues: 47.7824 Evaluate side-chains 121 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 69 optimal weight: 30.0000 chunk 52 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN L 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 9579 Z= 0.475 Angle : 0.818 10.208 13028 Z= 0.423 Chirality : 0.048 0.238 1466 Planarity : 0.006 0.067 1671 Dihedral : 6.415 56.467 1374 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.43 % Favored : 90.49 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.18 (0.24), residues: 1209 helix: -0.92 (0.41), residues: 148 sheet: -0.02 (0.25), residues: 434 loop : -1.29 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP D 50 HIS 0.014 0.002 HIS C 198 PHE 0.022 0.003 PHE B 377 TYR 0.036 0.002 TYR L 102 ARG 0.014 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 HIS cc_start: 0.9182 (m90) cc_final: 0.8816 (m90) REVERT: A 82 THR cc_start: 0.8966 (p) cc_final: 0.7906 (p) REVERT: A 85 HIS cc_start: 0.8921 (m90) cc_final: 0.8562 (m90) REVERT: A 90 THR cc_start: 0.8269 (t) cc_final: 0.8014 (p) REVERT: A 94 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7563 (mm-30) REVERT: B 421 TYR cc_start: 0.9006 (m-80) cc_final: 0.8464 (m-80) REVERT: D 57 ASN cc_start: 0.9257 (m110) cc_final: 0.9047 (m110) REVERT: D 70 MET cc_start: 0.7140 (mtt) cc_final: 0.6925 (mtt) REVERT: D 154 CYS cc_start: 0.6364 (m) cc_final: 0.5593 (m) REVERT: D 168 TRP cc_start: 0.8300 (m-10) cc_final: 0.7779 (m-10) REVERT: D 178 HIS cc_start: 0.8891 (m90) cc_final: 0.8375 (m90) REVERT: H 3 GLN cc_start: 0.9027 (mm110) cc_final: 0.8668 (mm-40) REVERT: H 144 CYS cc_start: 0.4846 (m) cc_final: 0.4331 (m) REVERT: H 149 TYR cc_start: 0.7692 (p90) cc_final: 0.7477 (p90) REVERT: H 150 PHE cc_start: 0.8596 (t80) cc_final: 0.8197 (t80) REVERT: L 41 TRP cc_start: 0.8767 (m100) cc_final: 0.7855 (m100) REVERT: L 142 LEU cc_start: 0.9449 (tt) cc_final: 0.9045 (tt) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1846 time to fit residues: 34.9207 Evaluate side-chains 108 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 chunk 10 optimal weight: 10.0000 chunk 90 optimal weight: 0.0270 chunk 104 optimal weight: 2.9990 chunk 109 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 overall best weight: 2.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9579 Z= 0.224 Angle : 0.692 8.664 13028 Z= 0.354 Chirality : 0.046 0.234 1466 Planarity : 0.005 0.064 1671 Dihedral : 5.771 56.229 1374 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.44 % Favored : 92.47 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.24), residues: 1209 helix: -0.84 (0.40), residues: 147 sheet: 0.15 (0.25), residues: 425 loop : -1.04 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP H 158 HIS 0.005 0.001 HIS C 198 PHE 0.021 0.002 PHE C 118 TYR 0.022 0.001 TYR L 102 ARG 0.007 0.001 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 THR cc_start: 0.8875 (p) cc_final: 0.7943 (p) REVERT: A 82 THR cc_start: 0.8961 (p) cc_final: 0.7937 (p) REVERT: A 85 HIS cc_start: 0.8807 (m90) cc_final: 0.8579 (m90) REVERT: A 94 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7453 (mm-30) REVERT: B 402 ILE cc_start: 0.9174 (tp) cc_final: 0.8650 (pt) REVERT: B 406 GLU cc_start: 0.8562 (mp0) cc_final: 0.8075 (mp0) REVERT: B 421 TYR cc_start: 0.8936 (m-80) cc_final: 0.8368 (m-80) REVERT: D 143 LYS cc_start: 0.6587 (pttt) cc_final: 0.6077 (tppt) REVERT: D 154 CYS cc_start: 0.5990 (m) cc_final: 0.5119 (m) REVERT: D 168 TRP cc_start: 0.8331 (m-10) cc_final: 0.8093 (m-10) REVERT: D 178 HIS cc_start: 0.8825 (m90) cc_final: 0.8264 (m90) REVERT: H 3 GLN cc_start: 0.8920 (mm110) cc_final: 0.8574 (mm-40) REVERT: H 150 PHE cc_start: 0.8383 (t80) cc_final: 0.7973 (t80) REVERT: L 41 TRP cc_start: 0.8649 (m100) cc_final: 0.7862 (m100) REVERT: L 142 LEU cc_start: 0.9440 (tt) cc_final: 0.9058 (tt) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1932 time to fit residues: 40.6750 Evaluate side-chains 125 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 46 optimal weight: 0.0370 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9579 Z= 0.249 Angle : 0.682 9.167 13028 Z= 0.349 Chirality : 0.045 0.209 1466 Planarity : 0.005 0.062 1671 Dihedral : 5.678 55.264 1374 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.77 % Favored : 91.15 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % 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: -0.94 (0.24), residues: 1209 helix: -0.84 (0.41), residues: 147 sheet: 0.13 (0.25), residues: 423 loop : -1.07 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP H 83 HIS 0.006 0.001 HIS C 198 PHE 0.020 0.002 PHE C 118 TYR 0.022 0.001 TYR L 102 ARG 0.009 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 THR cc_start: 0.8911 (p) cc_final: 0.8169 (p) REVERT: A 82 THR cc_start: 0.8921 (p) cc_final: 0.7946 (p) REVERT: A 94 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7415 (mm-30) REVERT: B 402 ILE cc_start: 0.9176 (tp) cc_final: 0.8718 (pt) REVERT: B 406 GLU cc_start: 0.8654 (mp0) cc_final: 0.8166 (mp0) REVERT: B 421 TYR cc_start: 0.8921 (m-80) cc_final: 0.8393 (m-80) REVERT: D 143 LYS cc_start: 0.6573 (pttt) cc_final: 0.6066 (tppt) REVERT: D 154 CYS cc_start: 0.6054 (m) cc_final: 0.5388 (m) REVERT: D 168 TRP cc_start: 0.8345 (m-10) cc_final: 0.8044 (m-10) REVERT: D 178 HIS cc_start: 0.8826 (m90) cc_final: 0.8226 (m90) REVERT: H 3 GLN cc_start: 0.8940 (mm110) cc_final: 0.8592 (mm-40) REVERT: H 144 CYS cc_start: 0.4692 (m) cc_final: 0.4248 (m) REVERT: H 149 TYR cc_start: 0.7664 (p90) cc_final: 0.7340 (p90) REVERT: H 150 PHE cc_start: 0.8443 (t80) cc_final: 0.7966 (t80) REVERT: L 41 TRP cc_start: 0.8679 (m100) cc_final: 0.7831 (m100) REVERT: L 142 LEU cc_start: 0.9445 (tt) cc_final: 0.9075 (tt) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1892 time to fit residues: 38.9459 Evaluate side-chains 122 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 9 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 57 optimal weight: 0.3980 chunk 74 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9579 Z= 0.271 Angle : 0.694 8.671 13028 Z= 0.356 Chirality : 0.045 0.219 1466 Planarity : 0.005 0.062 1671 Dihedral : 5.765 55.466 1374 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.77 % Favored : 91.15 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % 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: -0.98 (0.24), residues: 1209 helix: -0.83 (0.41), residues: 147 sheet: 0.08 (0.25), residues: 423 loop : -1.09 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 47 HIS 0.007 0.001 HIS C 198 PHE 0.022 0.002 PHE C 118 TYR 0.023 0.001 TYR L 102 ARG 0.004 0.000 ARG A 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 THR cc_start: 0.8908 (p) cc_final: 0.8231 (p) REVERT: A 82 THR cc_start: 0.8923 (p) cc_final: 0.7975 (p) REVERT: A 85 HIS cc_start: 0.8804 (m90) cc_final: 0.8587 (m90) REVERT: A 94 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7449 (mm-30) REVERT: B 405 ASP cc_start: 0.8940 (m-30) cc_final: 0.8723 (m-30) REVERT: B 406 GLU cc_start: 0.8604 (mp0) cc_final: 0.8086 (mp0) REVERT: B 421 TYR cc_start: 0.8921 (m-80) cc_final: 0.8413 (m-80) REVERT: D 143 LYS cc_start: 0.6578 (pttt) cc_final: 0.6037 (tppt) REVERT: D 154 CYS cc_start: 0.5974 (m) cc_final: 0.5313 (m) REVERT: D 168 TRP cc_start: 0.8401 (m-10) cc_final: 0.8006 (m-10) REVERT: D 178 HIS cc_start: 0.8808 (m90) cc_final: 0.8194 (m90) REVERT: H 3 GLN cc_start: 0.8965 (mm110) cc_final: 0.8616 (mm-40) REVERT: H 144 CYS cc_start: 0.4531 (m) cc_final: 0.4102 (m) REVERT: H 149 TYR cc_start: 0.7640 (p90) cc_final: 0.7277 (p90) REVERT: H 150 PHE cc_start: 0.8491 (t80) cc_final: 0.7978 (t80) REVERT: L 41 TRP cc_start: 0.8729 (m100) cc_final: 0.7810 (m100) REVERT: L 142 LEU cc_start: 0.9460 (tt) cc_final: 0.9055 (tt) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.2036 time to fit residues: 41.5689 Evaluate side-chains 124 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 3.9990 chunk 13 optimal weight: 0.4980 chunk 26 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 68 optimal weight: 0.3980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.080031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.062109 restraints weight = 51986.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.064040 restraints weight = 27808.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.065500 restraints weight = 16244.701| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9579 Z= 0.205 Angle : 0.673 8.200 13028 Z= 0.342 Chirality : 0.045 0.211 1466 Planarity : 0.005 0.063 1671 Dihedral : 5.513 55.181 1374 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.53 % Favored : 92.39 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % 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: -0.84 (0.24), residues: 1209 helix: -0.79 (0.41), residues: 147 sheet: 0.23 (0.25), residues: 422 loop : -1.02 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 168 HIS 0.005 0.001 HIS A 52 PHE 0.020 0.002 PHE C 118 TYR 0.019 0.001 TYR L 102 ARG 0.002 0.000 ARG L 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2122.32 seconds wall clock time: 39 minutes 46.87 seconds (2386.87 seconds total)