Starting phenix.real_space_refine on Wed Jul 30 12:43:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cl0_16708/07_2025/8cl0_16708.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cl0_16708/07_2025/8cl0_16708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cl0_16708/07_2025/8cl0_16708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cl0_16708/07_2025/8cl0_16708.map" model { file = "/net/cci-nas-00/data/ceres_data/8cl0_16708/07_2025/8cl0_16708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cl0_16708/07_2025/8cl0_16708.cif" } resolution = 3.12 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= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2586 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 6567 2.51 5 N 1799 2.21 5 O 1949 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10387 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1644 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 199} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "G" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 76 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "B" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1650 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "H" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 84 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "C" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1652 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "I" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 84 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "D" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1645 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 199} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "J" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 84 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "E" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1649 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 199} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "K" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 84 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "F" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1651 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 199} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "L" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 84 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Time building chain proxies: 7.57, per 1000 atoms: 0.73 Number of scatterers: 10387 At special positions: 0 Unit cell: (113.46, 109.74, 75.33, 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 72 16.00 O 1949 8.00 N 1799 7.00 C 6567 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 1.2 seconds 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2530 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 6 sheets defined 69.2% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 59 removed outlier: 3.634A pdb=" N VAL A 59 " --> pdb=" O MET A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 119 Processing helix chain 'A' and resid 125 through 145 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 178 through 193 removed outlier: 4.396A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 removed outlier: 3.650A pdb=" N GLY A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'B' and resid 16 through 31 Processing helix chain 'B' and resid 35 through 44 Processing helix chain 'B' and resid 48 through 59 removed outlier: 3.666A pdb=" N VAL B 59 " --> pdb=" O MET B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 84 Processing helix chain 'B' and resid 100 through 105 Processing helix chain 'B' and resid 110 through 119 Processing helix chain 'B' and resid 125 through 145 removed outlier: 3.669A pdb=" N LYS B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 176 Processing helix chain 'B' and resid 178 through 193 removed outlier: 4.517A pdb=" N LEU B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 204 removed outlier: 4.224A pdb=" N THR B 200 " --> pdb=" O PRO B 196 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 Processing helix chain 'C' and resid 16 through 31 Processing helix chain 'C' and resid 35 through 45 Processing helix chain 'C' and resid 48 through 59 removed outlier: 3.627A pdb=" N VAL C 59 " --> pdb=" O MET C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 84 Processing helix chain 'C' and resid 100 through 105 Processing helix chain 'C' and resid 110 through 119 Processing helix chain 'C' and resid 125 through 145 removed outlier: 3.633A pdb=" N LYS C 140 " --> pdb=" O LEU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 160 through 176 Processing helix chain 'C' and resid 178 through 193 removed outlier: 4.145A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 205 removed outlier: 3.762A pdb=" N THR C 200 " --> pdb=" O PRO C 196 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 219 Processing helix chain 'D' and resid 16 through 31 Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 48 through 59 removed outlier: 3.586A pdb=" N VAL D 59 " --> pdb=" O MET D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 84 Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 110 through 120 Processing helix chain 'D' and resid 125 through 145 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 160 through 176 Processing helix chain 'D' and resid 178 through 193 removed outlier: 4.167A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN D 192 " --> pdb=" O THR D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 removed outlier: 3.997A pdb=" N THR D 200 " --> pdb=" O PRO D 196 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 219 Processing helix chain 'E' and resid 16 through 31 Processing helix chain 'E' and resid 35 through 44 Processing helix chain 'E' and resid 48 through 59 removed outlier: 3.657A pdb=" N VAL E 59 " --> pdb=" O MET E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 84 Processing helix chain 'E' and resid 100 through 105 Processing helix chain 'E' and resid 110 through 119 Processing helix chain 'E' and resid 125 through 145 removed outlier: 3.540A pdb=" N LYS E 140 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'E' and resid 160 through 176 Processing helix chain 'E' and resid 178 through 193 removed outlier: 4.452A pdb=" N LEU E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 205 removed outlier: 3.760A pdb=" N ILE E 201 " --> pdb=" O ASP E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 218 Processing helix chain 'F' and resid 16 through 31 Processing helix chain 'F' and resid 35 through 44 Processing helix chain 'F' and resid 48 through 59 removed outlier: 3.600A pdb=" N VAL F 59 " --> pdb=" O MET F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 84 Processing helix chain 'F' and resid 100 through 105 Processing helix chain 'F' and resid 110 through 120 Processing helix chain 'F' and resid 125 through 146 Processing helix chain 'F' and resid 149 through 153 Processing helix chain 'F' and resid 160 through 176 Processing helix chain 'F' and resid 178 through 193 removed outlier: 4.001A pdb=" N LEU F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 204 removed outlier: 3.716A pdb=" N THR F 200 " --> pdb=" O PRO F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 219 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'B' and resid 2 through 4 Processing sheet with id=AA3, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AA4, first strand: chain 'D' and resid 2 through 4 Processing sheet with id=AA5, first strand: chain 'E' and resid 2 through 4 Processing sheet with id=AA6, first strand: chain 'F' and resid 2 through 4 639 hydrogen bonds defined for protein. 1887 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: 2.71 Time building geometry restraints manager: 3.01 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: 3380 1.34 - 1.46: 1099 1.46 - 1.57: 5998 1.57 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 10609 Sorted by residual: bond pdb=" CB GLU D 35 " pdb=" CG GLU D 35 " ideal model delta sigma weight residual 1.520 1.445 0.075 3.00e-02 1.11e+03 6.27e+00 bond pdb=" N ASN L1409 " pdb=" CA ASN L1409 " ideal model delta sigma weight residual 1.458 1.504 -0.046 1.90e-02 2.77e+03 5.74e+00 bond pdb=" N ASN J1409 " pdb=" CA ASN J1409 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.90e-02 2.77e+03 4.63e+00 bond pdb=" CA ASN J1409 " pdb=" C ASN J1409 " ideal model delta sigma weight residual 1.525 1.569 -0.044 2.10e-02 2.27e+03 4.47e+00 bond pdb=" N ASN H1409 " pdb=" CA ASN H1409 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.90e-02 2.77e+03 4.26e+00 ... (remaining 10604 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 13515 1.63 - 3.27: 801 3.27 - 4.90: 84 4.90 - 6.53: 18 6.53 - 8.17: 3 Bond angle restraints: 14421 Sorted by residual: angle pdb=" CA VAL F 3 " pdb=" CB VAL F 3 " pdb=" CG1 VAL F 3 " ideal model delta sigma weight residual 110.40 118.57 -8.17 1.70e+00 3.46e-01 2.31e+01 angle pdb=" CA VAL F 3 " pdb=" CB VAL F 3 " pdb=" CG2 VAL F 3 " ideal model delta sigma weight residual 110.40 116.14 -5.74 1.70e+00 3.46e-01 1.14e+01 angle pdb=" CA GLU D 45 " pdb=" CB GLU D 45 " pdb=" CG GLU D 45 " ideal model delta sigma weight residual 114.10 107.40 6.70 2.00e+00 2.50e-01 1.12e+01 angle pdb=" N SER C 44 " pdb=" CA SER C 44 " pdb=" C SER C 44 " ideal model delta sigma weight residual 111.71 115.55 -3.84 1.15e+00 7.56e-01 1.12e+01 angle pdb=" CG1 VAL F 3 " pdb=" CB VAL F 3 " pdb=" CG2 VAL F 3 " ideal model delta sigma weight residual 110.80 117.88 -7.08 2.20e+00 2.07e-01 1.04e+01 ... (remaining 14416 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 6032 17.88 - 35.75: 319 35.75 - 53.63: 63 53.63 - 71.51: 16 71.51 - 89.39: 13 Dihedral angle restraints: 6443 sinusoidal: 2552 harmonic: 3891 Sorted by residual: dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N SER E 33 " pdb=" CA SER E 33 " ideal model delta harmonic sigma weight residual 180.00 150.40 29.60 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA PHE C 32 " pdb=" C PHE C 32 " pdb=" N SER C 33 " pdb=" CA SER C 33 " ideal model delta harmonic sigma weight residual 180.00 150.92 29.08 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA PHE B 32 " pdb=" C PHE B 32 " pdb=" N SER B 33 " pdb=" CA SER B 33 " ideal model delta harmonic sigma weight residual 180.00 151.48 28.52 0 5.00e+00 4.00e-02 3.25e+01 ... (remaining 6440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.222: 1634 0.222 - 0.444: 4 0.444 - 0.667: 0 0.667 - 0.889: 0 0.889 - 1.111: 1 Chirality restraints: 1639 Sorted by residual: chirality pdb=" CB VAL F 3 " pdb=" CA VAL F 3 " pdb=" CG1 VAL F 3 " pdb=" CG2 VAL F 3 " both_signs ideal model delta sigma weight residual False -2.63 -1.52 -1.11 2.00e-01 2.50e+01 3.09e+01 chirality pdb=" CA ASN H1409 " pdb=" N ASN H1409 " pdb=" C ASN H1409 " pdb=" CB ASN H1409 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA ASN K1409 " pdb=" N ASN K1409 " pdb=" C ASN K1409 " pdb=" CB ASN K1409 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 1636 not shown) Planarity restraints: 1867 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 97 " 0.318 9.50e-02 1.11e+02 1.43e-01 1.32e+01 pdb=" NE ARG C 97 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG C 97 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG C 97 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG C 97 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 97 " 0.303 9.50e-02 1.11e+02 1.36e-01 1.24e+01 pdb=" NE ARG B 97 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG B 97 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG B 97 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B 97 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 52 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.01e+00 pdb=" C LEU A 52 " -0.052 2.00e-02 2.50e+03 pdb=" O LEU A 52 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN A 53 " 0.018 2.00e-02 2.50e+03 ... (remaining 1864 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 66 2.65 - 3.21: 10322 3.21 - 3.78: 16474 3.78 - 4.34: 23328 4.34 - 4.90: 37545 Nonbonded interactions: 87735 Sorted by model distance: nonbonded pdb=" OG1 THR E 110 " pdb=" OE1 GLU E 113 " model vdw 2.091 3.040 nonbonded pdb=" NH1 ARG E 143 " pdb=" O ASN L1409 " model vdw 2.372 3.120 nonbonded pdb=" OG SER D 33 " pdb=" OE1 GLU D 35 " model vdw 2.437 3.040 nonbonded pdb=" OG SER C 33 " pdb=" OE1 GLU C 35 " model vdw 2.480 3.040 nonbonded pdb=" O THR A 54 " pdb=" OG1 THR A 58 " model vdw 2.481 3.040 ... (remaining 87730 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 'A' and (resid 1 through 87 or resid 96 through 151 or (resid 152 and (na \ me N or name CA or name C or name O or name CB )) or resid 153 through 157 or (r \ esid 158 and (name N or name CA or name C or name O or name CB )) or resid 159 t \ hrough 221)) selection = (chain 'B' and (resid 1 through 3 or (resid 4 through 7 and (name N or name CA o \ r name C or name O or name CB )) or resid 8 or (resid 9 through 10 and (name N o \ r name CA or name C or name O or name CB )) or resid 11 through 12 or (resid 13 \ through 14 and (name N or name CA or name C or name O or name CB )) or resid 15 \ through 151 or (resid 152 and (name N or name CA or name C or name O or name CB \ )) or resid 153 through 221)) selection = (chain 'C' and (resid 1 through 4 or (resid 5 through 7 and (name N or name CA o \ r name C or name O or name CB )) or resid 8 through 12 or (resid 13 through 14 a \ nd (name N or name CA or name C or name O or name CB )) or resid 15 through 87 o \ r resid 96 through 151 or (resid 152 and (name N or name CA or name C or name O \ or name CB )) or resid 153 through 221)) selection = (chain 'D' and (resid 1 through 3 or (resid 4 through 7 and (name N or name CA o \ r name C or name O or name CB )) or resid 8 through 12 or (resid 13 through 14 a \ nd (name N or name CA or name C or name O or name CB )) or resid 15 through 87 o \ r resid 96 through 221)) selection = (chain 'E' and (resid 1 through 8 or (resid 9 through 10 and (name N or name CA \ or name C or name O or name CB )) or resid 11 through 12 or (resid 13 through 14 \ and (name N or name CA or name C or name O or name CB )) or resid 15 through 87 \ or resid 96 through 157 or (resid 158 and (name N or name CA or name C or name \ O or name CB )) or resid 159 through 221)) selection = (chain 'F' and (resid 1 through 3 or (resid 4 through 7 and (name N or name CA o \ r name C or name O or name CB )) or resid 8 through 12 or (resid 13 through 14 a \ nd (name N or name CA or name C or name O or name CB )) or resid 15 through 87 o \ r resid 96 through 151 or (resid 152 and (name N or name CA or name C or name O \ or name CB )) or resid 153 through 221)) } ncs_group { reference = chain 'G' selection = (chain 'H' and resid 1410 through 1420) selection = (chain 'I' and resid 1410 through 1420) selection = (chain 'J' and resid 1410 through 1420) selection = (chain 'K' and resid 1410 through 1420) selection = (chain 'L' and resid 1410 through 1420) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 26.910 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 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 : 0.005 0.079 10609 Z= 0.264 Angle : 0.869 8.165 14421 Z= 0.525 Chirality : 0.059 1.111 1639 Planarity : 0.011 0.143 1867 Dihedral : 12.800 89.386 3913 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 0.18 % Allowed : 0.09 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.50 (0.20), residues: 1319 helix: -0.41 (0.15), residues: 881 sheet: -2.77 (0.43), residues: 45 loop : 0.72 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 117 HIS 0.014 0.003 HIS A 12 PHE 0.012 0.003 PHE H1417 TYR 0.027 0.006 TYR C 169 ARG 0.027 0.003 ARG B 154 Details of bonding type rmsd hydrogen bonds : bond 0.10258 ( 639) hydrogen bonds : angle 5.95054 ( 1887) covalent geometry : bond 0.00543 (10609) covalent geometry : angle 0.86933 (14421) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 224 time to evaluate : 1.193 Fit side-chains REVERT: B 76 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7638 (mm-30) REVERT: C 75 GLU cc_start: 0.7167 (tt0) cc_final: 0.6921 (tt0) REVERT: C 140 LYS cc_start: 0.8356 (mttt) cc_final: 0.8072 (mttp) REVERT: D 39 MET cc_start: 0.7727 (tpt) cc_final: 0.7526 (tpt) REVERT: D 219 GLN cc_start: 0.7029 (tt0) cc_final: 0.6815 (tt0) REVERT: E 68 MET cc_start: 0.8257 (mtm) cc_final: 0.7981 (mtt) REVERT: F 108 THR cc_start: 0.8562 (p) cc_final: 0.8273 (p) outliers start: 2 outliers final: 2 residues processed: 224 average time/residue: 0.2298 time to fit residues: 71.4827 Evaluate side-chains 172 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 170 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain E residue 96 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS ** B 192 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 = 0.3937 r_free = 0.3937 target = 0.172398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.144295 restraints weight = 10895.207| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.98 r_work: 0.3452 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10609 Z= 0.200 Angle : 0.579 6.339 14421 Z= 0.300 Chirality : 0.044 0.169 1639 Planarity : 0.005 0.035 1867 Dihedral : 5.131 54.135 1427 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 1.45 % Allowed : 3.99 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.22), residues: 1319 helix: 1.03 (0.17), residues: 878 sheet: -2.04 (0.54), residues: 45 loop : 1.03 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 117 HIS 0.003 0.001 HIS D 84 PHE 0.014 0.002 PHE E 32 TYR 0.020 0.002 TYR F 169 ARG 0.004 0.001 ARG D 173 Details of bonding type rmsd hydrogen bonds : bond 0.04247 ( 639) hydrogen bonds : angle 4.27576 ( 1887) covalent geometry : bond 0.00505 (10609) covalent geometry : angle 0.57868 (14421) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 1.254 Fit side-chains REVERT: B 159 GLU cc_start: 0.8001 (tt0) cc_final: 0.7746 (tt0) REVERT: B 187 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: C 29 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7718 (mm-30) REVERT: C 75 GLU cc_start: 0.7848 (tt0) cc_final: 0.7495 (tt0) REVERT: C 140 LYS cc_start: 0.8701 (mttt) cc_final: 0.8322 (mttp) REVERT: C 179 GLN cc_start: 0.8414 (tp40) cc_final: 0.8080 (tp-100) REVERT: C 199 LYS cc_start: 0.7837 (tttm) cc_final: 0.7616 (mtpp) REVERT: D 39 MET cc_start: 0.8374 (tpt) cc_final: 0.8101 (tpt) REVERT: E 103 ASP cc_start: 0.8093 (m-30) cc_final: 0.7784 (m-30) REVERT: E 113 GLU cc_start: 0.8256 (mp0) cc_final: 0.7449 (mp0) REVERT: F 143 ARG cc_start: 0.7939 (ttm170) cc_final: 0.7715 (ttp-170) REVERT: F 175 GLU cc_start: 0.8145 (tt0) cc_final: 0.7934 (mm-30) outliers start: 16 outliers final: 9 residues processed: 188 average time/residue: 0.2452 time to fit residues: 63.8586 Evaluate side-chains 180 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 170 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain F residue 35 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 47 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 30 optimal weight: 0.0170 chunk 38 optimal weight: 0.8980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN D 219 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.177554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.150617 restraints weight = 10832.805| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.89 r_work: 0.3460 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10609 Z= 0.138 Angle : 0.497 5.458 14421 Z= 0.254 Chirality : 0.041 0.151 1639 Planarity : 0.004 0.031 1867 Dihedral : 4.315 46.607 1424 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.54 % Allowed : 5.07 % Favored : 93.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.22), residues: 1319 helix: 1.49 (0.17), residues: 882 sheet: -0.93 (1.74), residues: 9 loop : 0.91 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 184 HIS 0.002 0.001 HIS D 84 PHE 0.014 0.002 PHE E 32 TYR 0.015 0.001 TYR F 169 ARG 0.003 0.000 ARG D 97 Details of bonding type rmsd hydrogen bonds : bond 0.03550 ( 639) hydrogen bonds : angle 3.85346 ( 1887) covalent geometry : bond 0.00348 (10609) covalent geometry : angle 0.49730 (14421) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 1.167 Fit side-chains REVERT: A 175 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7412 (mt-10) REVERT: B 159 GLU cc_start: 0.7869 (tt0) cc_final: 0.7667 (tt0) REVERT: B 187 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: C 29 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7775 (mm-30) REVERT: C 66 MET cc_start: 0.8765 (mmm) cc_final: 0.8367 (mmp) REVERT: C 75 GLU cc_start: 0.7931 (tt0) cc_final: 0.7598 (tt0) REVERT: C 140 LYS cc_start: 0.8728 (mttt) cc_final: 0.8515 (mtpp) REVERT: E 68 MET cc_start: 0.8606 (mtm) cc_final: 0.8379 (mtt) REVERT: E 103 ASP cc_start: 0.8034 (m-30) cc_final: 0.7754 (m-30) REVERT: E 113 GLU cc_start: 0.8217 (mp0) cc_final: 0.7635 (mp0) REVERT: E 180 GLU cc_start: 0.7377 (tm-30) cc_final: 0.6488 (mm-30) REVERT: F 96 MET cc_start: 0.7509 (mtm) cc_final: 0.7273 (mtm) REVERT: F 172 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8116 (tp) outliers start: 17 outliers final: 6 residues processed: 180 average time/residue: 0.2633 time to fit residues: 64.8343 Evaluate side-chains 166 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 158 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 61 optimal weight: 0.2980 chunk 36 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS D 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.173200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.145948 restraints weight = 10754.832| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.90 r_work: 0.3444 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10609 Z= 0.138 Angle : 0.489 5.558 14421 Z= 0.248 Chirality : 0.041 0.156 1639 Planarity : 0.004 0.036 1867 Dihedral : 3.928 19.825 1421 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.45 % Allowed : 5.89 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.23), residues: 1319 helix: 1.63 (0.17), residues: 882 sheet: -1.40 (0.63), residues: 45 loop : 1.02 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 184 HIS 0.003 0.001 HIS A 120 PHE 0.013 0.001 PHE E 32 TYR 0.015 0.001 TYR F 169 ARG 0.005 0.000 ARG F 143 Details of bonding type rmsd hydrogen bonds : bond 0.03488 ( 639) hydrogen bonds : angle 3.75889 ( 1887) covalent geometry : bond 0.00345 (10609) covalent geometry : angle 0.48933 (14421) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 1.101 Fit side-chains REVERT: A 175 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7448 (mt-10) REVERT: B 187 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7177 (mp0) REVERT: C 29 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7748 (mm-30) REVERT: C 66 MET cc_start: 0.8761 (mmm) cc_final: 0.8334 (mmp) REVERT: C 75 GLU cc_start: 0.7988 (tt0) cc_final: 0.7705 (tt0) REVERT: C 140 LYS cc_start: 0.8742 (mttt) cc_final: 0.8460 (mtpp) REVERT: D 39 MET cc_start: 0.8338 (tpt) cc_final: 0.8129 (tpt) REVERT: E 103 ASP cc_start: 0.8078 (m-30) cc_final: 0.7759 (m-30) REVERT: E 113 GLU cc_start: 0.8236 (mp0) cc_final: 0.7736 (mp0) REVERT: E 180 GLU cc_start: 0.7449 (tm-30) cc_final: 0.6593 (mm-30) REVERT: F 96 MET cc_start: 0.7520 (mtm) cc_final: 0.7303 (mtm) outliers start: 16 outliers final: 9 residues processed: 173 average time/residue: 0.2408 time to fit residues: 57.3751 Evaluate side-chains 162 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain F residue 35 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 15 optimal weight: 0.2980 chunk 52 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS B 219 GLN C 63 GLN D 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.170419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.141116 restraints weight = 10942.757| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.07 r_work: 0.3420 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10609 Z= 0.213 Angle : 0.543 5.958 14421 Z= 0.275 Chirality : 0.043 0.150 1639 Planarity : 0.005 0.037 1867 Dihedral : 4.131 21.134 1421 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.36 % Allowed : 6.79 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.23), residues: 1319 helix: 1.48 (0.18), residues: 878 sheet: -1.40 (0.62), residues: 45 loop : 1.08 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 80 HIS 0.003 0.001 HIS C 62 PHE 0.014 0.002 PHE F 32 TYR 0.017 0.002 TYR F 169 ARG 0.004 0.000 ARG F 143 Details of bonding type rmsd hydrogen bonds : bond 0.03863 ( 639) hydrogen bonds : angle 3.90150 ( 1887) covalent geometry : bond 0.00544 (10609) covalent geometry : angle 0.54259 (14421) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 1.132 Fit side-chains REVERT: A 167 ARG cc_start: 0.8322 (mtp180) cc_final: 0.8010 (mtp180) REVERT: A 175 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7422 (mt-10) REVERT: B 187 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: C 75 GLU cc_start: 0.7956 (tt0) cc_final: 0.7541 (tt0) REVERT: C 140 LYS cc_start: 0.8683 (mttt) cc_final: 0.8370 (mtpp) REVERT: D 39 MET cc_start: 0.8450 (tpt) cc_final: 0.8111 (tpt) REVERT: D 79 GLU cc_start: 0.7594 (mm-30) cc_final: 0.6998 (mt-10) REVERT: E 103 ASP cc_start: 0.8146 (m-30) cc_final: 0.7814 (m-30) REVERT: E 113 GLU cc_start: 0.8213 (mp0) cc_final: 0.7600 (mp0) REVERT: F 45 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7431 (mm-30) REVERT: F 172 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7999 (tp) outliers start: 15 outliers final: 11 residues processed: 183 average time/residue: 0.3226 time to fit residues: 80.6820 Evaluate side-chains 177 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 103 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 126 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 95 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS D 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.176906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.149727 restraints weight = 10852.294| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.88 r_work: 0.3456 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10609 Z= 0.131 Angle : 0.483 5.405 14421 Z= 0.245 Chirality : 0.041 0.142 1639 Planarity : 0.004 0.037 1867 Dihedral : 3.866 19.358 1421 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 1.36 % Allowed : 7.52 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.23), residues: 1319 helix: 1.62 (0.18), residues: 886 sheet: -1.32 (0.64), residues: 45 loop : 1.09 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 184 HIS 0.002 0.000 HIS D 84 PHE 0.013 0.001 PHE C 32 TYR 0.013 0.001 TYR F 169 ARG 0.006 0.000 ARG F 143 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 639) hydrogen bonds : angle 3.72004 ( 1887) covalent geometry : bond 0.00325 (10609) covalent geometry : angle 0.48317 (14421) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 1.242 Fit side-chains REVERT: A 175 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7463 (mt-10) REVERT: B 76 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7900 (mm-30) REVERT: B 187 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7160 (mp0) REVERT: C 75 GLU cc_start: 0.8070 (tt0) cc_final: 0.7700 (tt0) REVERT: C 140 LYS cc_start: 0.8728 (mttt) cc_final: 0.8428 (mtpp) REVERT: D 39 MET cc_start: 0.8445 (tpt) cc_final: 0.8193 (tpp) REVERT: E 103 ASP cc_start: 0.8054 (m-30) cc_final: 0.7750 (m-30) REVERT: E 113 GLU cc_start: 0.8205 (mp0) cc_final: 0.7667 (mp0) REVERT: F 45 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7489 (mm-30) REVERT: F 96 MET cc_start: 0.7395 (mtm) cc_final: 0.7166 (mtm) REVERT: F 154 ARG cc_start: 0.8051 (mtp-110) cc_final: 0.7633 (mtp180) REVERT: F 172 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8102 (tp) outliers start: 15 outliers final: 10 residues processed: 177 average time/residue: 0.2543 time to fit residues: 61.7199 Evaluate side-chains 168 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 5 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS D 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.175161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.147577 restraints weight = 11027.585| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.91 r_work: 0.3431 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10609 Z= 0.168 Angle : 0.516 7.592 14421 Z= 0.260 Chirality : 0.042 0.142 1639 Planarity : 0.004 0.038 1867 Dihedral : 3.916 20.086 1421 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.45 % Allowed : 7.52 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.23), residues: 1319 helix: 1.57 (0.17), residues: 886 sheet: -1.45 (0.57), residues: 54 loop : 1.12 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 80 HIS 0.003 0.001 HIS F 12 PHE 0.014 0.002 PHE C 32 TYR 0.015 0.001 TYR F 169 ARG 0.004 0.000 ARG F 143 Details of bonding type rmsd hydrogen bonds : bond 0.03630 ( 639) hydrogen bonds : angle 3.77142 ( 1887) covalent geometry : bond 0.00428 (10609) covalent geometry : angle 0.51576 (14421) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 1.253 Fit side-chains REVERT: A 167 ARG cc_start: 0.8403 (mtp180) cc_final: 0.8168 (mtp180) REVERT: A 175 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7491 (mt-10) REVERT: B 76 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7934 (mm-30) REVERT: B 187 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7156 (mp0) REVERT: C 75 GLU cc_start: 0.8088 (tt0) cc_final: 0.7749 (tt0) REVERT: C 140 LYS cc_start: 0.8754 (mttt) cc_final: 0.8431 (mtpp) REVERT: E 103 ASP cc_start: 0.8081 (m-30) cc_final: 0.7780 (m-30) REVERT: E 113 GLU cc_start: 0.8228 (mp0) cc_final: 0.7681 (mp0) REVERT: F 45 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7518 (mm-30) REVERT: F 96 MET cc_start: 0.7425 (mtm) cc_final: 0.7194 (mtm) REVERT: F 172 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8113 (tp) outliers start: 16 outliers final: 11 residues processed: 164 average time/residue: 0.2631 time to fit residues: 59.3103 Evaluate side-chains 170 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 189 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 45 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 25 optimal weight: 0.1980 chunk 23 optimal weight: 5.9990 chunk 31 optimal weight: 0.0570 chunk 61 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 36 optimal weight: 0.0870 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS D 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.178993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.151679 restraints weight = 10885.088| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.91 r_work: 0.3477 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10609 Z= 0.113 Angle : 0.471 5.940 14421 Z= 0.239 Chirality : 0.040 0.137 1639 Planarity : 0.004 0.038 1867 Dihedral : 3.685 18.147 1421 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 1.36 % Allowed : 8.15 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.12 (0.23), residues: 1319 helix: 1.78 (0.18), residues: 886 sheet: -1.18 (0.66), residues: 45 loop : 1.10 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 184 HIS 0.001 0.000 HIS D 84 PHE 0.012 0.001 PHE F 32 TYR 0.012 0.001 TYR F 169 ARG 0.006 0.000 ARG F 143 Details of bonding type rmsd hydrogen bonds : bond 0.03260 ( 639) hydrogen bonds : angle 3.63767 ( 1887) covalent geometry : bond 0.00277 (10609) covalent geometry : angle 0.47120 (14421) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 1.472 Fit side-chains revert: symmetry clash REVERT: A 175 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7408 (mt-10) REVERT: B 76 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7892 (mm-30) REVERT: B 175 GLU cc_start: 0.8292 (tt0) cc_final: 0.8091 (mt-10) REVERT: B 187 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: C 75 GLU cc_start: 0.8081 (tt0) cc_final: 0.7796 (tt0) REVERT: C 140 LYS cc_start: 0.8717 (mttt) cc_final: 0.8404 (mtpp) REVERT: D 39 MET cc_start: 0.8284 (tpt) cc_final: 0.7815 (tpt) REVERT: E 103 ASP cc_start: 0.8070 (m-30) cc_final: 0.7742 (m-30) REVERT: E 113 GLU cc_start: 0.8159 (mp0) cc_final: 0.7711 (mp0) REVERT: E 215 MET cc_start: 0.7392 (mtp) cc_final: 0.6941 (mtp) REVERT: F 96 MET cc_start: 0.7223 (mtm) cc_final: 0.7010 (mtm) REVERT: F 154 ARG cc_start: 0.8000 (mtp-110) cc_final: 0.7619 (mtp180) REVERT: F 195 ASN cc_start: 0.7499 (p0) cc_final: 0.7226 (p0) outliers start: 15 outliers final: 9 residues processed: 171 average time/residue: 0.3262 time to fit residues: 76.8356 Evaluate side-chains 170 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain F residue 35 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 100 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 127 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 35 optimal weight: 0.0980 chunk 126 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS D 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.175540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.146829 restraints weight = 10921.530| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.05 r_work: 0.3469 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10609 Z= 0.119 Angle : 0.480 5.437 14421 Z= 0.244 Chirality : 0.040 0.138 1639 Planarity : 0.004 0.039 1867 Dihedral : 3.654 17.879 1421 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.00 % Allowed : 8.79 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.13 (0.23), residues: 1319 helix: 1.80 (0.18), residues: 886 sheet: -1.31 (0.60), residues: 54 loop : 1.14 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 80 HIS 0.002 0.000 HIS D 84 PHE 0.012 0.001 PHE E 32 TYR 0.013 0.001 TYR F 169 ARG 0.006 0.000 ARG F 143 Details of bonding type rmsd hydrogen bonds : bond 0.03298 ( 639) hydrogen bonds : angle 3.65136 ( 1887) covalent geometry : bond 0.00293 (10609) covalent geometry : angle 0.48042 (14421) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 159 time to evaluate : 1.121 Fit side-chains REVERT: A 175 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7334 (mt-10) REVERT: B 76 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7857 (mm-30) REVERT: B 175 GLU cc_start: 0.8282 (tt0) cc_final: 0.7965 (mt-10) REVERT: B 187 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7061 (mp0) REVERT: C 29 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7568 (mm-30) REVERT: C 75 GLU cc_start: 0.8022 (tt0) cc_final: 0.7710 (tt0) REVERT: C 140 LYS cc_start: 0.8654 (mttt) cc_final: 0.8312 (mtpp) REVERT: D 39 MET cc_start: 0.8240 (tpt) cc_final: 0.7742 (tpt) REVERT: E 103 ASP cc_start: 0.8101 (m-30) cc_final: 0.7757 (m-30) REVERT: E 113 GLU cc_start: 0.8222 (mp0) cc_final: 0.7627 (mp0) REVERT: E 215 MET cc_start: 0.7486 (mtp) cc_final: 0.7058 (mtp) REVERT: F 96 MET cc_start: 0.7231 (mtm) cc_final: 0.7005 (mtm) REVERT: F 154 ARG cc_start: 0.7938 (mtp-110) cc_final: 0.7547 (mtp180) REVERT: F 195 ASN cc_start: 0.7417 (p0) cc_final: 0.7161 (p0) outliers start: 11 outliers final: 8 residues processed: 164 average time/residue: 0.2416 time to fit residues: 54.4401 Evaluate side-chains 163 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain F residue 35 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 102 optimal weight: 0.7980 chunk 101 optimal weight: 0.4980 chunk 95 optimal weight: 0.6980 chunk 36 optimal weight: 0.0570 chunk 2 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 99 optimal weight: 0.0010 overall best weight: 0.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS D 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.180643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.153914 restraints weight = 10874.094| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.87 r_work: 0.3505 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10609 Z= 0.109 Angle : 0.489 7.549 14421 Z= 0.246 Chirality : 0.040 0.137 1639 Planarity : 0.004 0.039 1867 Dihedral : 3.583 16.863 1421 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 1.09 % Allowed : 8.51 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.17 (0.23), residues: 1319 helix: 1.84 (0.18), residues: 888 sheet: -1.27 (0.60), residues: 54 loop : 1.12 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 80 HIS 0.001 0.000 HIS F 12 PHE 0.011 0.001 PHE E 32 TYR 0.013 0.001 TYR F 169 ARG 0.006 0.000 ARG F 143 Details of bonding type rmsd hydrogen bonds : bond 0.03225 ( 639) hydrogen bonds : angle 3.63223 ( 1887) covalent geometry : bond 0.00263 (10609) covalent geometry : angle 0.48929 (14421) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 1.254 Fit side-chains revert: symmetry clash REVERT: A 146 SER cc_start: 0.8090 (p) cc_final: 0.7878 (p) REVERT: A 175 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7407 (mt-10) REVERT: B 76 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7861 (mm-30) REVERT: B 175 GLU cc_start: 0.8279 (tt0) cc_final: 0.8074 (mt-10) REVERT: B 187 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7150 (mp0) REVERT: C 29 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7580 (mm-30) REVERT: C 75 GLU cc_start: 0.8095 (tt0) cc_final: 0.7808 (tt0) REVERT: C 140 LYS cc_start: 0.8679 (mttt) cc_final: 0.8387 (mtpp) REVERT: D 39 MET cc_start: 0.8198 (tpt) cc_final: 0.7710 (tpt) REVERT: E 103 ASP cc_start: 0.8033 (m-30) cc_final: 0.7731 (m-30) REVERT: E 215 MET cc_start: 0.7401 (mtp) cc_final: 0.7050 (mtp) REVERT: F 154 ARG cc_start: 0.7979 (mtp-110) cc_final: 0.7591 (mtp180) outliers start: 12 outliers final: 9 residues processed: 158 average time/residue: 0.2555 time to fit residues: 55.2297 Evaluate side-chains 159 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain F residue 35 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.6980 chunk 59 optimal weight: 0.0980 chunk 70 optimal weight: 0.0870 chunk 104 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 131 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 124 optimal weight: 0.0770 chunk 41 optimal weight: 2.9990 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN D 219 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.174365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.146170 restraints weight = 10857.921| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.98 r_work: 0.3495 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10609 Z= 0.106 Angle : 0.492 7.133 14421 Z= 0.244 Chirality : 0.040 0.137 1639 Planarity : 0.004 0.039 1867 Dihedral : 3.529 16.279 1421 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 1.18 % Allowed : 8.97 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.23 (0.23), residues: 1319 helix: 1.89 (0.18), residues: 888 sheet: -1.17 (0.61), residues: 54 loop : 1.13 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 80 HIS 0.001 0.000 HIS D 84 PHE 0.012 0.001 PHE E 32 TYR 0.012 0.001 TYR F 169 ARG 0.006 0.000 ARG F 143 Details of bonding type rmsd hydrogen bonds : bond 0.03141 ( 639) hydrogen bonds : angle 3.59060 ( 1887) covalent geometry : bond 0.00254 (10609) covalent geometry : angle 0.49244 (14421) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4788.09 seconds wall clock time: 84 minutes 1.24 seconds (5041.24 seconds total)