Starting phenix.real_space_refine on Thu Mar 14 17:44:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dw2_27749/03_2024/8dw2_27749.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dw2_27749/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dw2_27749/03_2024/8dw2_27749.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dw2_27749/03_2024/8dw2_27749.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dw2_27749/03_2024/8dw2_27749.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dw2_27749/03_2024/8dw2_27749.pdb" } 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 Residue "A GLU 163": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "D TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 162": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.98, per 1000 atoms: 0.64 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 3.87 Conformation dependent library (CDL) restraints added in 2.0 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: 0.95 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: 2.75 Time building geometry restraints manager: 4.15 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: 98.57 - 105.71: 192 105.71 - 112.85: 5058 112.85 - 119.98: 3224 119.98 - 127.12: 4447 127.12 - 134.25: 107 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 2.440 nonbonded pdb=" OG SER B 514 " pdb=" OE2 GLU B 516 " model vdw 2.174 2.440 nonbonded pdb=" O SER H 192 " pdb=" OG SER H 192 " model vdw 2.199 2.440 nonbonded pdb=" OD2 ASP A 110 " pdb=" OH TYR B 489 " model vdw 2.201 2.440 nonbonded pdb=" OD1 ASP L 176 " pdb=" OG1 THR L 178 " model vdw 2.205 2.440 ... (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 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: 0.790 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: 4.010 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 28.760 Find NCS groups from input model: 0.470 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.940 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 5 poor density : 144 time to evaluate : 1.065 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: 0.1964 time to fit residues: 40.5741 Evaluate side-chains 135 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 131 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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: 2.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 48 optimal weight: 20.0000 chunk 93 optimal weight: 8.9990 chunk 36 optimal weight: 0.4980 chunk 56 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- 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 138 ASN D 65 GLN L 164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9579 Z= 0.269 Angle : 0.686 7.493 13028 Z= 0.352 Chirality : 0.045 0.206 1466 Planarity : 0.006 0.075 1671 Dihedral : 7.389 68.129 1374 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.35 % Favored : 91.56 % Rotamer: Outliers : 0.10 % Allowed : 4.55 % Favored : 95.36 % 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: -0.90 (0.24), residues: 1209 helix: -0.71 (0.40), residues: 148 sheet: 0.44 (0.26), residues: 409 loop : -1.27 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 50 HIS 0.006 0.001 HIS D 214 PHE 0.027 0.003 PHE B 464 TYR 0.027 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 187 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 186 time to evaluate : 1.155 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 82 THR cc_start: 0.8750 (p) cc_final: 0.7400 (p) REVERT: A 85 HIS cc_start: 0.8728 (m90) cc_final: 0.8276 (m90) REVERT: A 94 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7426 (mm-30) REVERT: B 366 SER cc_start: 0.9214 (p) cc_final: 0.9004 (p) REVERT: B 405 ASP cc_start: 0.8700 (m-30) cc_final: 0.8482 (m-30) REVERT: C 138 ASN cc_start: 0.9182 (m-40) cc_final: 0.8896 (m110) REVERT: D 152 LEU cc_start: 0.8686 (mt) cc_final: 0.8342 (pp) REVERT: D 178 HIS cc_start: 0.8897 (m90) cc_final: 0.8562 (m90) REVERT: H 3 GLN cc_start: 0.8874 (mm110) cc_final: 0.8616 (mm-40) REVERT: L 142 LEU cc_start: 0.9370 (tp) cc_final: 0.8967 (tt) REVERT: L 167 GLU cc_start: 0.8580 (tt0) cc_final: 0.8332 (tm-30) outliers start: 1 outliers final: 1 residues processed: 187 average time/residue: 0.2138 time to fit residues: 54.8579 Evaluate side-chains 132 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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: 2.9990 chunk 33 optimal weight: 7.9990 chunk 89 optimal weight: 30.0000 chunk 73 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 137 ASN H 39 GLN ** H 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9579 Z= 0.340 Angle : 0.714 8.691 13028 Z= 0.368 Chirality : 0.045 0.183 1466 Planarity : 0.006 0.071 1671 Dihedral : 6.739 57.062 1374 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 22.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.68 % Favored : 91.23 % Rotamer: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % 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: -0.97 (0.24), residues: 1209 helix: -0.66 (0.41), residues: 148 sheet: 0.28 (0.26), residues: 418 loop : -1.28 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP L 41 HIS 0.004 0.001 HIS D 214 PHE 0.016 0.002 PHE B 456 TYR 0.025 0.002 TYR L 102 ARG 0.008 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 144 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.089 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: 0.9115 (m90) cc_final: 0.8673 (m90) REVERT: A 94 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7475 (mm-30) REVERT: A 118 HIS cc_start: 0.8685 (t70) cc_final: 0.8422 (t-170) REVERT: B 405 ASP cc_start: 0.8739 (m-30) cc_final: 0.8525 (m-30) REVERT: B 421 TYR cc_start: 0.8930 (m-10) cc_final: 0.8658 (m-80) REVERT: D 178 HIS cc_start: 0.8910 (m90) cc_final: 0.8516 (m90) REVERT: H 3 GLN cc_start: 0.8922 (mm110) cc_final: 0.8608 (mm-40) REVERT: H 144 CYS cc_start: 0.4746 (m) cc_final: 0.4380 (m) REVERT: L 142 LEU cc_start: 0.9383 (tp) cc_final: 0.8938 (tp) REVERT: L 167 GLU cc_start: 0.8651 (tt0) cc_final: 0.8315 (tm-30) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2096 time to fit residues: 42.1651 Evaluate side-chains 115 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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: 1.9990 chunk 81 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 chunk 108 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 102 optimal weight: 0.5980 chunk 30 optimal weight: 9.9990 chunk 95 optimal weight: 0.1980 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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** D 214 HIS H 39 GLN ** H 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9579 Z= 0.199 Angle : 0.633 8.122 13028 Z= 0.323 Chirality : 0.044 0.161 1466 Planarity : 0.005 0.064 1671 Dihedral : 5.867 56.087 1374 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.61 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % 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: -0.45 (0.42), residues: 141 sheet: 0.45 (0.26), residues: 418 loop : -1.11 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 168 HIS 0.003 0.001 HIS C 92 PHE 0.025 0.002 PHE B 377 TYR 0.017 0.001 TYR D 100 ARG 0.005 0.001 ARG L 217 *********************** 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 161 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.107 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: 0.8689 (p) cc_final: 0.7715 (p) REVERT: A 52 HIS cc_start: 0.9076 (m90) cc_final: 0.8694 (m90) REVERT: A 61 GLU cc_start: 0.9061 (mp0) cc_final: 0.8831 (mm-30) REVERT: A 90 THR cc_start: 0.8200 (t) cc_final: 0.7943 (p) REVERT: A 94 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7440 (mm-30) REVERT: B 405 ASP cc_start: 0.8665 (m-30) cc_final: 0.8400 (m-30) REVERT: B 421 TYR cc_start: 0.8947 (m-10) cc_final: 0.8696 (m-80) REVERT: B 498 GLN cc_start: 0.8170 (mm110) cc_final: 0.7939 (mm110) REVERT: C 138 ASN cc_start: 0.9133 (m-40) cc_final: 0.8861 (m110) REVERT: D 70 MET cc_start: 0.6951 (mtt) cc_final: 0.6742 (mtt) REVERT: D 178 HIS cc_start: 0.8825 (m90) cc_final: 0.8442 (m90) REVERT: H 3 GLN cc_start: 0.8910 (mm110) cc_final: 0.8568 (mm-40) REVERT: H 144 CYS cc_start: 0.4588 (m) cc_final: 0.4152 (m) REVERT: L 41 TRP cc_start: 0.8556 (m100) cc_final: 0.7907 (m100) REVERT: L 142 LEU cc_start: 0.9382 (tp) cc_final: 0.9179 (tt) REVERT: L 167 GLU cc_start: 0.8671 (tt0) cc_final: 0.8343 (tm-30) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2132 time to fit residues: 47.5895 Evaluate side-chains 128 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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: 3.9990 chunk 1 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 58 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9579 Z= 0.322 Angle : 0.698 8.663 13028 Z= 0.358 Chirality : 0.045 0.163 1466 Planarity : 0.005 0.062 1671 Dihedral : 6.010 56.601 1374 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.18 % Favored : 90.74 % Rotamer: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % 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: -0.97 (0.25), residues: 1209 helix: -0.69 (0.42), residues: 148 sheet: 0.17 (0.26), residues: 430 loop : -1.20 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP H 47 HIS 0.005 0.001 HIS H 168 PHE 0.017 0.002 PHE D 114 TYR 0.042 0.002 TYR L 102 ARG 0.006 0.001 ARG A 31 *********************** 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 141 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 THR cc_start: 0.8775 (p) cc_final: 0.7783 (p) REVERT: A 52 HIS cc_start: 0.9118 (m90) cc_final: 0.8705 (m90) REVERT: A 61 GLU cc_start: 0.9124 (mp0) cc_final: 0.8850 (pm20) REVERT: A 62 ILE cc_start: 0.8718 (pt) cc_final: 0.8279 (pt) REVERT: A 90 THR cc_start: 0.8291 (t) cc_final: 0.8059 (p) REVERT: A 94 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7489 (mm-30) REVERT: A 118 HIS cc_start: 0.8691 (t70) cc_final: 0.8466 (t-170) REVERT: B 405 ASP cc_start: 0.8750 (m-30) cc_final: 0.8508 (m-30) REVERT: B 498 GLN cc_start: 0.8186 (mm110) cc_final: 0.7934 (mm110) REVERT: D 154 CYS cc_start: 0.6328 (m) cc_final: 0.5388 (m) REVERT: D 178 HIS cc_start: 0.8910 (m90) cc_final: 0.8480 (m90) REVERT: H 3 GLN cc_start: 0.8973 (mm110) cc_final: 0.8630 (mm-40) REVERT: H 144 CYS cc_start: 0.4743 (m) cc_final: 0.4073 (m) REVERT: L 41 TRP cc_start: 0.8644 (m100) cc_final: 0.8016 (m100) REVERT: L 142 LEU cc_start: 0.9381 (tp) cc_final: 0.8907 (tp) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.2018 time to fit residues: 40.4988 Evaluate side-chains 112 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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: 10.0000 chunk 22 optimal weight: 0.7980 chunk 67 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 111 optimal weight: 20.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9579 Z= 0.278 Angle : 0.662 7.681 13028 Z= 0.340 Chirality : 0.044 0.260 1466 Planarity : 0.005 0.062 1671 Dihedral : 5.849 56.039 1374 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.19 % Favored : 91.73 % Rotamer: Outliers : 0.10 % Allowed : 2.13 % Favored : 97.78 % 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: -0.95 (0.25), residues: 1209 helix: -0.64 (0.42), residues: 147 sheet: 0.24 (0.26), residues: 424 loop : -1.23 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP D 168 HIS 0.003 0.001 HIS H 168 PHE 0.020 0.002 PHE C 72 TYR 0.027 0.001 TYR L 102 ARG 0.006 0.001 ARG C 18 *********************** 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 148 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 HIS cc_start: 0.9121 (m90) cc_final: 0.8723 (m90) REVERT: A 61 GLU cc_start: 0.9106 (mp0) cc_final: 0.8848 (pm20) REVERT: A 62 ILE cc_start: 0.8737 (pt) cc_final: 0.8292 (pt) REVERT: A 90 THR cc_start: 0.8261 (t) cc_final: 0.8014 (p) REVERT: A 94 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7513 (mm-30) REVERT: A 118 HIS cc_start: 0.8684 (t70) cc_final: 0.8402 (t-170) REVERT: B 405 ASP cc_start: 0.8726 (m-30) cc_final: 0.8452 (m-30) REVERT: B 498 GLN cc_start: 0.8118 (mm110) cc_final: 0.7872 (mm110) REVERT: D 3 GLN cc_start: 0.8938 (mm110) cc_final: 0.8538 (mp10) REVERT: D 154 CYS cc_start: 0.6170 (m) cc_final: 0.5328 (m) REVERT: D 178 HIS cc_start: 0.8877 (m90) cc_final: 0.8411 (m90) REVERT: H 3 GLN cc_start: 0.8962 (mm110) cc_final: 0.8616 (mm-40) REVERT: H 144 CYS cc_start: 0.4725 (m) cc_final: 0.3700 (m) REVERT: H 150 PHE cc_start: 0.8421 (t80) cc_final: 0.8073 (t80) REVERT: H 175 GLN cc_start: 0.7784 (pp30) cc_final: 0.7568 (pp30) REVERT: L 41 TRP cc_start: 0.8656 (m100) cc_final: 0.8070 (m100) REVERT: L 142 LEU cc_start: 0.9379 (tp) cc_final: 0.8898 (tp) outliers start: 1 outliers final: 0 residues processed: 148 average time/residue: 0.1919 time to fit residues: 40.5368 Evaluate side-chains 117 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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: 3.9990 chunk 65 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 52 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 155 GLN ** H 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9579 Z= 0.221 Angle : 0.642 7.877 13028 Z= 0.328 Chirality : 0.044 0.235 1466 Planarity : 0.005 0.059 1671 Dihedral : 5.605 55.428 1374 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.86 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: -0.85 (0.25), residues: 1209 helix: -0.64 (0.42), residues: 147 sheet: 0.28 (0.25), residues: 424 loop : -1.13 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 168 HIS 0.003 0.001 HIS A 59 PHE 0.015 0.002 PHE C 72 TYR 0.023 0.001 TYR L 102 ARG 0.004 0.001 ARG B 355 *********************** 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 149 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 THR cc_start: 0.8719 (p) cc_final: 0.7809 (p) REVERT: A 52 HIS cc_start: 0.9071 (m90) cc_final: 0.8751 (m90) REVERT: A 90 THR cc_start: 0.8217 (t) cc_final: 0.7975 (p) REVERT: A 94 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7474 (mm-30) REVERT: A 118 HIS cc_start: 0.8639 (t70) cc_final: 0.8364 (t-170) REVERT: B 405 ASP cc_start: 0.8719 (m-30) cc_final: 0.8385 (m-30) REVERT: D 3 GLN cc_start: 0.8919 (mm110) cc_final: 0.8536 (mp10) REVERT: D 143 LYS cc_start: 0.6507 (pttt) cc_final: 0.6113 (tppt) REVERT: D 154 CYS cc_start: 0.6080 (m) cc_final: 0.5255 (m) REVERT: D 168 TRP cc_start: 0.8116 (m-10) cc_final: 0.7911 (m-10) REVERT: D 178 HIS cc_start: 0.8810 (m90) cc_final: 0.8341 (m90) REVERT: H 3 GLN cc_start: 0.8970 (mm110) cc_final: 0.8623 (mm-40) REVERT: H 144 CYS cc_start: 0.4617 (m) cc_final: 0.3942 (m) REVERT: H 149 TYR cc_start: 0.7676 (p90) cc_final: 0.7463 (p90) REVERT: H 150 PHE cc_start: 0.8387 (t80) cc_final: 0.7984 (t80) REVERT: L 41 TRP cc_start: 0.8675 (m100) cc_final: 0.8079 (m100) REVERT: L 142 LEU cc_start: 0.9361 (tp) cc_final: 0.8883 (tp) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1829 time to fit residues: 40.4886 Evaluate side-chains 119 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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: 20.0000 chunk 34 optimal weight: 0.5980 chunk 22 optimal weight: 0.4980 chunk 72 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 56 optimal weight: 0.0030 chunk 10 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 chunk 100 optimal weight: 6.9990 overall best weight: 2.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9579 Z= 0.224 Angle : 0.636 7.677 13028 Z= 0.325 Chirality : 0.044 0.210 1466 Planarity : 0.005 0.059 1671 Dihedral : 5.510 55.266 1374 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.44 % Favored : 91.48 % 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: -0.85 (0.25), residues: 1209 helix: -0.61 (0.42), residues: 148 sheet: 0.31 (0.26), residues: 414 loop : -1.14 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 168 HIS 0.003 0.001 HIS A 59 PHE 0.017 0.002 PHE C 118 TYR 0.020 0.001 TYR L 102 ARG 0.003 0.001 ARG A 31 *********************** 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 154 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 THR cc_start: 0.8713 (p) cc_final: 0.7809 (p) REVERT: A 52 HIS cc_start: 0.9063 (m90) cc_final: 0.8733 (m90) REVERT: A 90 THR cc_start: 0.8259 (t) cc_final: 0.7988 (p) REVERT: A 94 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7512 (mm-30) REVERT: A 118 HIS cc_start: 0.8555 (t70) cc_final: 0.8207 (t-170) REVERT: B 405 ASP cc_start: 0.8680 (m-30) cc_final: 0.8462 (m-30) REVERT: D 48 MET cc_start: 0.9096 (mmp) cc_final: 0.8865 (mmm) REVERT: D 143 LYS cc_start: 0.6483 (pttt) cc_final: 0.6164 (tppt) REVERT: D 154 CYS cc_start: 0.6044 (m) cc_final: 0.5302 (m) REVERT: D 168 TRP cc_start: 0.8267 (m-10) cc_final: 0.7986 (m-10) REVERT: D 178 HIS cc_start: 0.8807 (m90) cc_final: 0.8218 (m90) REVERT: H 3 GLN cc_start: 0.9009 (mm110) cc_final: 0.8656 (mm-40) REVERT: H 144 CYS cc_start: 0.4576 (m) cc_final: 0.3931 (m) REVERT: H 149 TYR cc_start: 0.7586 (p90) cc_final: 0.7293 (p90) REVERT: H 150 PHE cc_start: 0.8393 (t80) cc_final: 0.7982 (t80) REVERT: H 175 GLN cc_start: 0.7800 (pp30) cc_final: 0.7509 (pp30) REVERT: L 41 TRP cc_start: 0.8655 (m100) cc_final: 0.7980 (m100) REVERT: L 142 LEU cc_start: 0.9380 (tp) cc_final: 0.8869 (tp) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1954 time to fit residues: 42.8627 Evaluate side-chains 119 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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: 0.5980 chunk 109 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 46 optimal weight: 0.0670 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 113 optimal weight: 0.8980 chunk 68 optimal weight: 9.9990 overall best weight: 2.3122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3257 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= 0.211 Angle : 0.637 7.952 13028 Z= 0.326 Chirality : 0.044 0.212 1466 Planarity : 0.005 0.057 1671 Dihedral : 5.447 55.146 1374 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.94 % Favored : 91.98 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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: -0.81 (0.25), residues: 1209 helix: -0.58 (0.42), residues: 149 sheet: 0.23 (0.25), residues: 429 loop : -1.05 (0.26), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 168 HIS 0.003 0.001 HIS A 52 PHE 0.017 0.002 PHE C 118 TYR 0.017 0.001 TYR L 102 ARG 0.004 0.001 ARG B 355 *********************** 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 160 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.148 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: 0.8708 (p) cc_final: 0.7804 (p) REVERT: A 52 HIS cc_start: 0.9059 (m90) cc_final: 0.8744 (m90) REVERT: A 61 GLU cc_start: 0.9248 (mm-30) cc_final: 0.8610 (pm20) REVERT: A 90 THR cc_start: 0.8238 (t) cc_final: 0.7961 (p) REVERT: A 94 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7484 (mm-30) REVERT: A 118 HIS cc_start: 0.8517 (t70) cc_final: 0.8160 (t-170) REVERT: B 405 ASP cc_start: 0.8693 (m-30) cc_final: 0.8485 (m-30) REVERT: B 409 GLN cc_start: 0.8349 (mt0) cc_final: 0.7913 (mt0) REVERT: D 143 LYS cc_start: 0.6497 (pttt) cc_final: 0.6198 (tppt) REVERT: D 154 CYS cc_start: 0.6224 (m) cc_final: 0.5287 (m) REVERT: D 178 HIS cc_start: 0.8780 (m90) cc_final: 0.8200 (m90) REVERT: H 3 GLN cc_start: 0.9010 (mm110) cc_final: 0.8650 (mm-40) REVERT: H 144 CYS cc_start: 0.4354 (m) cc_final: 0.3517 (m) REVERT: H 149 TYR cc_start: 0.7578 (p90) cc_final: 0.7269 (p90) REVERT: H 150 PHE cc_start: 0.8377 (t80) cc_final: 0.7946 (t80) REVERT: H 175 GLN cc_start: 0.7742 (pp30) cc_final: 0.7455 (pp30) REVERT: L 41 TRP cc_start: 0.8644 (m100) cc_final: 0.8066 (m100) REVERT: L 142 LEU cc_start: 0.9378 (tp) cc_final: 0.8838 (tp) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1856 time to fit residues: 42.5598 Evaluate side-chains 128 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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: 30.0000 chunk 78 optimal weight: 4.9990 chunk 118 optimal weight: 7.9990 chunk 109 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9579 Z= 0.207 Angle : 0.637 7.530 13028 Z= 0.325 Chirality : 0.044 0.204 1466 Planarity : 0.005 0.058 1671 Dihedral : 5.384 55.046 1374 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.61 % Favored : 92.31 % 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: -0.79 (0.25), residues: 1209 helix: -0.48 (0.43), residues: 149 sheet: 0.23 (0.25), residues: 430 loop : -1.06 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP H 158 HIS 0.004 0.001 HIS H 168 PHE 0.018 0.002 PHE C 118 TYR 0.022 0.001 TYR H 52 ARG 0.002 0.000 ARG L 60 ********************** 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 162 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 0.830 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: 0.8753 (p) cc_final: 0.7862 (p) REVERT: A 52 HIS cc_start: 0.9055 (m90) cc_final: 0.8741 (m90) REVERT: A 61 GLU cc_start: 0.9239 (mm-30) cc_final: 0.8652 (pm20) REVERT: A 90 THR cc_start: 0.8256 (t) cc_final: 0.7948 (p) REVERT: A 94 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7470 (mm-30) REVERT: A 118 HIS cc_start: 0.8445 (t70) cc_final: 0.8119 (t-170) REVERT: D 143 LYS cc_start: 0.6506 (pttt) cc_final: 0.6231 (tppt) REVERT: D 154 CYS cc_start: 0.6021 (m) cc_final: 0.5168 (m) REVERT: D 168 TRP cc_start: 0.8270 (m-10) cc_final: 0.7823 (m-10) REVERT: D 178 HIS cc_start: 0.8685 (m90) cc_final: 0.8096 (m90) REVERT: H 3 GLN cc_start: 0.9021 (mm110) cc_final: 0.8651 (mm-40) REVERT: H 149 TYR cc_start: 0.7550 (p90) cc_final: 0.7216 (p90) REVERT: H 150 PHE cc_start: 0.8331 (t80) cc_final: 0.7851 (t80) REVERT: H 175 GLN cc_start: 0.7747 (pp30) cc_final: 0.7453 (pp30) REVERT: H 213 LYS cc_start: 0.5806 (tptm) cc_final: 0.5199 (tptp) REVERT: L 41 TRP cc_start: 0.8632 (m100) cc_final: 0.8131 (m100) REVERT: L 142 LEU cc_start: 0.9205 (tp) cc_final: 0.8622 (tp) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1863 time to fit residues: 42.8071 Evaluate side-chains 128 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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: 1.9990 chunk 13 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 97 optimal weight: 0.0170 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 20.0000 overall best weight: 2.0024 ------------------------------------------------------------------------------- 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 27 GLN ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.080648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.062118 restraints weight = 52503.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.064114 restraints weight = 27135.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.065413 restraints weight = 17475.695| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 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 = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9579 Z= 0.197 Angle : 0.639 7.554 13028 Z= 0.325 Chirality : 0.044 0.198 1466 Planarity : 0.005 0.059 1671 Dihedral : 5.321 54.998 1374 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.69 % Favored : 92.22 % 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: -0.77 (0.25), residues: 1209 helix: -0.51 (0.42), residues: 149 sheet: 0.27 (0.25), residues: 431 loop : -1.05 (0.26), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 168 HIS 0.003 0.001 HIS A 52 PHE 0.017 0.002 PHE C 118 TYR 0.021 0.001 TYR H 52 ARG 0.002 0.000 ARG L 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2092.45 seconds wall clock time: 38 minutes 47.86 seconds (2327.86 seconds total)