Starting phenix.real_space_refine on Wed Feb 14 07:24:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upn_26673/02_2024/7upn_26673.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upn_26673/02_2024/7upn_26673.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upn_26673/02_2024/7upn_26673.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upn_26673/02_2024/7upn_26673.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upn_26673/02_2024/7upn_26673.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upn_26673/02_2024/7upn_26673.pdb" } resolution = 3.5 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= 0.003 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 58 5.16 5 C 5698 2.51 5 N 1526 2.21 5 O 1588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 102": "OE1" <-> "OE2" Residue "G GLU 102": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8872 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1248 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 6, 'TRANS': 156} Chain: "C" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1771 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 684 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain breaks: 1 Chain: "H" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 732 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1248 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 6, 'TRANS': 156} Chain: "F" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1771 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 684 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain breaks: 1 Chain: "I" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 732 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2218 SG CYS C 135 91.948 47.665 47.487 1.00 94.84 S ATOM 2230 SG CYS C 137 95.347 47.388 45.860 1.00 97.86 S ATOM 2412 SG CYS C 157 94.166 50.756 46.865 1.00 93.10 S ATOM 2433 SG CYS C 160 95.075 48.157 49.582 1.00 84.53 S ATOM 6653 SG CYS F 135 55.449 44.735 47.627 1.00 94.28 S ATOM 6665 SG CYS F 137 52.062 45.021 45.976 1.00100.38 S ATOM 6847 SG CYS F 157 53.228 41.650 46.990 1.00 93.43 S ATOM 6868 SG CYS F 160 52.307 44.252 49.701 1.00 84.59 S Time building chain proxies: 4.99, per 1000 atoms: 0.56 Number of scatterers: 8872 At special positions: 0 Unit cell: (148.5, 94.6, 106.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 58 16.00 O 1588 8.00 N 1526 7.00 C 5698 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.20 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 137 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 135 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 157 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 160 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 137 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 135 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 157 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 160 " Number of angles added : 12 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2028 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 10 sheets defined 26.2% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 29 through 42 removed outlier: 3.918A pdb=" N ALA A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 144 Processing helix chain 'C' and resid 41 through 52 Processing helix chain 'C' and resid 115 through 120 Processing helix chain 'C' and resid 123 through 135 removed outlier: 3.593A pdb=" N TRP C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE C 132 " --> pdb=" O PHE C 128 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N CYS C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 169 removed outlier: 3.516A pdb=" N GLN C 162 " --> pdb=" O LYS C 158 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY C 163 " --> pdb=" O SER C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 183 Processing helix chain 'C' and resid 218 through 223 Processing helix chain 'E' and resid 33 through 37 Processing helix chain 'E' and resid 39 through 48 Processing helix chain 'E' and resid 66 through 83 removed outlier: 3.698A pdb=" N MET E 75 " --> pdb=" O SER E 71 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR E 76 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE E 77 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR E 78 " --> pdb=" O CYS E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 111 removed outlier: 4.231A pdb=" N LEU E 101 " --> pdb=" O PRO E 97 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLU E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU E 104 " --> pdb=" O ALA E 100 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N MET E 105 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE E 109 " --> pdb=" O MET E 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 36 removed outlier: 4.233A pdb=" N LEU H 27 " --> pdb=" O THR H 23 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY H 33 " --> pdb=" O ARG H 29 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE H 34 " --> pdb=" O ILE H 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 42 removed outlier: 3.919A pdb=" N ALA B 33 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 144 Processing helix chain 'F' and resid 41 through 52 Processing helix chain 'F' and resid 115 through 120 Processing helix chain 'F' and resid 123 through 135 removed outlier: 3.592A pdb=" N TRP F 127 " --> pdb=" O GLU F 123 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE F 132 " --> pdb=" O PHE F 128 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS F 135 " --> pdb=" O ARG F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 169 removed outlier: 3.516A pdb=" N GLN F 162 " --> pdb=" O LYS F 158 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY F 163 " --> pdb=" O SER F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 183 Processing helix chain 'F' and resid 218 through 223 Processing helix chain 'G' and resid 33 through 37 Processing helix chain 'G' and resid 39 through 48 Processing helix chain 'G' and resid 66 through 83 removed outlier: 3.698A pdb=" N MET G 75 " --> pdb=" O SER G 71 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR G 76 " --> pdb=" O LYS G 72 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE G 77 " --> pdb=" O VAL G 73 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR G 78 " --> pdb=" O CYS G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 111 removed outlier: 4.231A pdb=" N LEU G 101 " --> pdb=" O PRO G 97 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLU G 102 " --> pdb=" O GLU G 98 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N MET G 105 " --> pdb=" O LEU G 101 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE G 109 " --> pdb=" O MET G 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 36 removed outlier: 4.233A pdb=" N LEU I 27 " --> pdb=" O THR I 23 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY I 33 " --> pdb=" O ARG I 29 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 57 removed outlier: 3.699A pdb=" N ARG A 55 " --> pdb=" O GLN A 63 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLN A 111 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N MET A 100 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N VAL A 128 " --> pdb=" O MET A 100 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER A 21 " --> pdb=" O LYS A 133 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL A 12 " --> pdb=" O PRO A 16 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY A 18 " --> pdb=" O ILE A 10 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N THR A 5 " --> pdb=" O GLN A 163 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLN A 163 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N PHE A 7 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N CYS A 161 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASP A 9 " --> pdb=" O ALA A 159 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 61 through 64 removed outlier: 4.263A pdb=" N GLU C 69 " --> pdb=" O VAL C 62 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 28 through 32 removed outlier: 8.382A pdb=" N VAL E 60 " --> pdb=" O TYR E 18 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LYS E 20 " --> pdb=" O VAL E 60 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 12 through 18 removed outlier: 3.867A pdb=" N ALA H 73 " --> pdb=" O PHE H 4 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 45 through 46 Processing sheet with id=AA6, first strand: chain 'B' and resid 55 through 57 removed outlier: 3.698A pdb=" N ARG B 55 " --> pdb=" O GLN B 63 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLN B 111 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N MET B 100 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N VAL B 128 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER B 21 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL B 12 " --> pdb=" O PRO B 16 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY B 18 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR B 5 " --> pdb=" O GLN B 163 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLN B 163 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N PHE B 7 " --> pdb=" O CYS B 161 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N CYS B 161 " --> pdb=" O PHE B 7 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASP B 9 " --> pdb=" O ALA B 159 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 61 through 64 removed outlier: 4.265A pdb=" N GLU F 69 " --> pdb=" O VAL F 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 28 through 32 removed outlier: 8.382A pdb=" N VAL G 60 " --> pdb=" O TYR G 18 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LYS G 20 " --> pdb=" O VAL G 60 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 12 through 18 removed outlier: 3.867A pdb=" N ALA I 73 " --> pdb=" O PHE I 4 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 45 through 46 248 hydrogen bonds defined for protein. 690 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: 2.13 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2515 1.33 - 1.45: 1621 1.45 - 1.57: 4878 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 9104 Sorted by residual: bond pdb=" CA GLU F 64 " pdb=" C GLU F 64 " ideal model delta sigma weight residual 1.533 1.507 0.026 9.60e-03 1.09e+04 7.50e+00 bond pdb=" CA ASN F 65 " pdb=" C ASN F 65 " ideal model delta sigma weight residual 1.522 1.497 0.025 1.18e-02 7.18e+03 4.49e+00 bond pdb=" CA ASN C 65 " pdb=" C ASN C 65 " ideal model delta sigma weight residual 1.521 1.500 0.022 1.17e-02 7.31e+03 3.48e+00 bond pdb=" C TYR C 68 " pdb=" O TYR C 68 " ideal model delta sigma weight residual 1.235 1.216 0.020 1.21e-02 6.83e+03 2.61e+00 bond pdb=" C LEU C 23 " pdb=" N PRO C 24 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.56e+00 ... (remaining 9099 not shown) Histogram of bond angle deviations from ideal: 99.69 - 106.57: 282 106.57 - 113.44: 4761 113.44 - 120.31: 3239 120.31 - 127.18: 3866 127.18 - 134.06: 136 Bond angle restraints: 12284 Sorted by residual: angle pdb=" C HIS I 10 " pdb=" CA HIS I 10 " pdb=" CB HIS I 10 " ideal model delta sigma weight residual 110.42 116.96 -6.54 1.99e+00 2.53e-01 1.08e+01 angle pdb=" C HIS H 10 " pdb=" CA HIS H 10 " pdb=" CB HIS H 10 " ideal model delta sigma weight residual 110.42 116.92 -6.50 1.99e+00 2.53e-01 1.07e+01 angle pdb=" CA PRO F 24 " pdb=" N PRO F 24 " pdb=" CD PRO F 24 " ideal model delta sigma weight residual 112.00 107.59 4.41 1.40e+00 5.10e-01 9.93e+00 angle pdb=" CA PRO C 24 " pdb=" N PRO C 24 " pdb=" CD PRO C 24 " ideal model delta sigma weight residual 112.00 107.66 4.34 1.40e+00 5.10e-01 9.62e+00 angle pdb=" N PRO C 24 " pdb=" CA PRO C 24 " pdb=" C PRO C 24 " ideal model delta sigma weight residual 112.47 118.61 -6.14 2.06e+00 2.36e-01 8.89e+00 ... (remaining 12279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 4765 17.61 - 35.22: 485 35.22 - 52.83: 78 52.83 - 70.44: 18 70.44 - 88.05: 12 Dihedral angle restraints: 5358 sinusoidal: 2214 harmonic: 3144 Sorted by residual: dihedral pdb=" CA LEU C 23 " pdb=" C LEU C 23 " pdb=" N PRO C 24 " pdb=" CA PRO C 24 " ideal model delta harmonic sigma weight residual -180.00 -156.42 -23.58 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA LEU F 23 " pdb=" C LEU F 23 " pdb=" N PRO F 24 " pdb=" CA PRO F 24 " ideal model delta harmonic sigma weight residual -180.00 -156.47 -23.53 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CB GLU E 59 " pdb=" CG GLU E 59 " pdb=" CD GLU E 59 " pdb=" OE1 GLU E 59 " ideal model delta sinusoidal sigma weight residual 0.00 -88.05 88.05 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 5355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 987 0.044 - 0.088: 231 0.088 - 0.132: 56 0.132 - 0.176: 6 0.176 - 0.220: 2 Chirality restraints: 1282 Sorted by residual: chirality pdb=" CA PRO C 24 " pdb=" N PRO C 24 " pdb=" C PRO C 24 " pdb=" CB PRO C 24 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA PRO F 24 " pdb=" N PRO F 24 " pdb=" C PRO F 24 " pdb=" CB PRO F 24 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA GLN C 66 " pdb=" N GLN C 66 " pdb=" C GLN C 66 " pdb=" CB GLN C 66 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.21e-01 ... (remaining 1279 not shown) Planarity restraints: 1562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 23 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO C 24 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO C 24 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 24 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 23 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO F 24 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO F 24 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO F 24 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 91 " 0.021 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO H 92 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO H 92 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO H 92 " 0.017 5.00e-02 4.00e+02 ... (remaining 1559 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2443 2.81 - 3.33: 7770 3.33 - 3.85: 13561 3.85 - 4.38: 14798 4.38 - 4.90: 26239 Nonbonded interactions: 64811 Sorted by model distance: nonbonded pdb=" O LYS G 80 " pdb=" OG1 THR G 84 " model vdw 2.284 2.440 nonbonded pdb=" O LYS E 80 " pdb=" OG1 THR E 84 " model vdw 2.285 2.440 nonbonded pdb=" O ASP F 87 " pdb=" N ARG F 95 " model vdw 2.329 2.520 nonbonded pdb=" O ASP C 87 " pdb=" N ARG C 95 " model vdw 2.329 2.520 nonbonded pdb=" OE2 GLU C 123 " pdb=" NE1 TRP C 127 " model vdw 2.347 2.520 ... (remaining 64806 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 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 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: 2.860 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 26.930 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 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 : 0.002 0.059 9104 Z= 0.162 Angle : 0.529 7.278 12284 Z= 0.282 Chirality : 0.041 0.220 1282 Planarity : 0.005 0.104 1562 Dihedral : 14.658 88.054 3330 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.37 % Favored : 92.26 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.25), residues: 1072 helix: 0.49 (0.32), residues: 270 sheet: 0.85 (0.66), residues: 72 loop : -1.66 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 28 HIS 0.005 0.001 HIS H 10 PHE 0.012 0.001 PHE B 113 TYR 0.006 0.001 TYR C 213 ARG 0.002 0.000 ARG E 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.7820 (ppp) cc_final: 0.7067 (ppp) REVERT: C 225 MET cc_start: 0.7755 (ttm) cc_final: 0.7341 (ttm) REVERT: E 70 LEU cc_start: 0.8979 (tp) cc_final: 0.8751 (tt) REVERT: E 76 TYR cc_start: 0.7799 (t80) cc_final: 0.7497 (t80) REVERT: E 99 ILE cc_start: 0.8069 (tp) cc_final: 0.7748 (tt) REVERT: H 52 ASP cc_start: 0.9406 (p0) cc_final: 0.9179 (p0) REVERT: H 55 LYS cc_start: 0.8768 (tmmt) cc_final: 0.8357 (ptmm) REVERT: B 61 MET cc_start: 0.7656 (ppp) cc_final: 0.7052 (ppp) REVERT: F 225 MET cc_start: 0.7752 (ttm) cc_final: 0.7343 (ttm) REVERT: I 55 LYS cc_start: 0.8866 (tmmt) cc_final: 0.8575 (ptmm) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1833 time to fit residues: 39.2365 Evaluate side-chains 116 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 54 optimal weight: 7.9990 chunk 42 optimal weight: 0.0040 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 0.0050 chunk 61 optimal weight: 7.9990 chunk 96 optimal weight: 0.0570 overall best weight: 0.3326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN C 220 GLN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN B 106 ASN F 220 GLN ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 65 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 9104 Z= 0.158 Angle : 0.506 7.510 12284 Z= 0.265 Chirality : 0.042 0.216 1282 Planarity : 0.005 0.104 1562 Dihedral : 3.740 23.895 1176 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.00 % Favored : 92.44 % Rotamer: Outliers : 0.74 % Allowed : 8.37 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.25), residues: 1072 helix: 0.74 (0.32), residues: 280 sheet: 0.42 (0.57), residues: 96 loop : -1.90 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 130 HIS 0.004 0.000 HIS H 10 PHE 0.011 0.001 PHE A 113 TYR 0.013 0.001 TYR G 76 ARG 0.004 0.000 ARG G 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 122 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.7954 (ppp) cc_final: 0.7278 (ppp) REVERT: C 191 MET cc_start: 0.9017 (ttt) cc_final: 0.8407 (ttt) REVERT: E 76 TYR cc_start: 0.7823 (t80) cc_final: 0.7522 (t80) REVERT: H 52 ASP cc_start: 0.9499 (p0) cc_final: 0.9249 (p0) REVERT: H 55 LYS cc_start: 0.8771 (tmmt) cc_final: 0.8273 (ptmm) REVERT: B 61 MET cc_start: 0.7799 (ppp) cc_final: 0.7174 (ppp) REVERT: F 225 MET cc_start: 0.7852 (ttm) cc_final: 0.7484 (ttm) REVERT: I 55 LYS cc_start: 0.8914 (tmmt) cc_final: 0.8574 (ptmm) outliers start: 7 outliers final: 2 residues processed: 123 average time/residue: 0.1829 time to fit residues: 33.1811 Evaluate side-chains 117 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain B residue 122 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 96 optimal weight: 0.0980 chunk 104 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 95 optimal weight: 0.0870 chunk 32 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 overall best weight: 1.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 220 GLN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN F 220 GLN ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9104 Z= 0.222 Angle : 0.538 11.578 12284 Z= 0.280 Chirality : 0.042 0.213 1282 Planarity : 0.005 0.108 1562 Dihedral : 3.960 23.636 1176 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.75 % Allowed : 8.02 % Favored : 91.23 % Rotamer: Outliers : 1.06 % Allowed : 10.81 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.25), residues: 1072 helix: 0.73 (0.32), residues: 284 sheet: 0.33 (0.48), residues: 124 loop : -1.94 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 78 HIS 0.003 0.001 HIS H 10 PHE 0.011 0.001 PHE B 113 TYR 0.020 0.001 TYR G 76 ARG 0.005 0.000 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 1.164 Fit side-chains REVERT: A 61 MET cc_start: 0.8159 (ppp) cc_final: 0.7398 (ppp) REVERT: C 60 MET cc_start: 0.8030 (ptm) cc_final: 0.7801 (ptt) REVERT: E 99 ILE cc_start: 0.8496 (tp) cc_final: 0.8060 (tt) REVERT: H 6 MET cc_start: 0.6005 (mmm) cc_final: 0.5796 (mtt) REVERT: H 52 ASP cc_start: 0.9518 (p0) cc_final: 0.9194 (p0) REVERT: H 55 LYS cc_start: 0.8789 (tmmt) cc_final: 0.8242 (ptmm) REVERT: B 61 MET cc_start: 0.8141 (ppp) cc_final: 0.7402 (ppp) REVERT: I 26 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8348 (pm20) REVERT: I 55 LYS cc_start: 0.8728 (tmmt) cc_final: 0.8330 (ptmm) outliers start: 10 outliers final: 3 residues processed: 123 average time/residue: 0.1788 time to fit residues: 32.3450 Evaluate side-chains 104 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain I residue 26 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.0040 chunk 72 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 overall best weight: 3.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 HIS C 186 HIS H 49 GLN H 65 GLN F 181 HIS F 186 HIS I 49 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 9104 Z= 0.432 Angle : 0.704 10.793 12284 Z= 0.376 Chirality : 0.049 0.232 1282 Planarity : 0.006 0.121 1562 Dihedral : 5.072 24.881 1176 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.75 % Allowed : 9.70 % Favored : 89.55 % Rotamer: Outliers : 2.22 % Allowed : 12.08 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.24), residues: 1072 helix: 0.14 (0.31), residues: 288 sheet: -0.30 (0.45), residues: 140 loop : -2.26 (0.21), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 78 HIS 0.006 0.002 HIS B 92 PHE 0.017 0.002 PHE A 8 TYR 0.012 0.002 TYR G 76 ARG 0.005 0.000 ARG G 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 100 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8437 (ppp) cc_final: 0.7718 (ppp) REVERT: A 136 MET cc_start: 0.8320 (tpt) cc_final: 0.8026 (tpt) REVERT: C 225 MET cc_start: 0.8045 (ttm) cc_final: 0.7565 (ttm) REVERT: E 75 MET cc_start: 0.8394 (mtp) cc_final: 0.7964 (mtm) REVERT: H 26 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8201 (mp0) REVERT: H 52 ASP cc_start: 0.9623 (p0) cc_final: 0.9113 (p0) REVERT: H 55 LYS cc_start: 0.8824 (tmmt) cc_final: 0.8548 (tttt) REVERT: B 61 MET cc_start: 0.8488 (ppp) cc_final: 0.7744 (ppp) REVERT: B 136 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7934 (tpt) REVERT: F 71 TRP cc_start: 0.6373 (p-90) cc_final: 0.5715 (p-90) REVERT: G 75 MET cc_start: 0.8345 (mtp) cc_final: 0.8138 (mtm) REVERT: I 15 PHE cc_start: 0.6202 (p90) cc_final: 0.5891 (p90) REVERT: I 52 ASP cc_start: 0.9469 (p0) cc_final: 0.8899 (p0) REVERT: I 55 LYS cc_start: 0.8712 (tmmt) cc_final: 0.8399 (tttt) outliers start: 21 outliers final: 4 residues processed: 113 average time/residue: 0.1815 time to fit residues: 30.2460 Evaluate side-chains 93 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 142 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 42 optimal weight: 0.0970 chunk 87 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 34 optimal weight: 0.0060 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 HIS C 186 HIS ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9104 Z= 0.173 Angle : 0.571 12.810 12284 Z= 0.289 Chirality : 0.043 0.196 1282 Planarity : 0.005 0.116 1562 Dihedral : 4.439 28.567 1176 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.46 % Favored : 91.79 % Rotamer: Outliers : 1.06 % Allowed : 14.62 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.24), residues: 1072 helix: 0.62 (0.32), residues: 288 sheet: -0.01 (0.47), residues: 128 loop : -2.20 (0.21), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 78 HIS 0.003 0.001 HIS H 10 PHE 0.012 0.001 PHE A 113 TYR 0.016 0.001 TYR G 76 ARG 0.004 0.000 ARG C 176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 1.152 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.8300 (ppp) cc_final: 0.7369 (ppp) REVERT: E 75 MET cc_start: 0.8317 (mtp) cc_final: 0.8039 (mtm) REVERT: E 105 MET cc_start: 0.9297 (mmm) cc_final: 0.9036 (mmm) REVERT: H 26 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8150 (mp0) REVERT: H 52 ASP cc_start: 0.9614 (p0) cc_final: 0.9065 (p0) REVERT: H 55 LYS cc_start: 0.8736 (tmmt) cc_final: 0.8485 (tttt) REVERT: B 61 MET cc_start: 0.8323 (ppp) cc_final: 0.7400 (ppp) REVERT: G 75 MET cc_start: 0.8247 (mtp) cc_final: 0.7983 (mtm) REVERT: I 52 ASP cc_start: 0.9345 (p0) cc_final: 0.8704 (p0) REVERT: I 55 LYS cc_start: 0.8778 (tmmt) cc_final: 0.8465 (tttt) outliers start: 10 outliers final: 4 residues processed: 115 average time/residue: 0.1824 time to fit residues: 30.7183 Evaluate side-chains 103 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain F residue 74 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 102 optimal weight: 20.0000 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN F 186 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9104 Z= 0.295 Angle : 0.608 11.525 12284 Z= 0.315 Chirality : 0.045 0.203 1282 Planarity : 0.006 0.120 1562 Dihedral : 4.491 26.916 1176 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.75 % Allowed : 9.33 % Favored : 89.93 % Rotamer: Outliers : 1.17 % Allowed : 16.10 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.24), residues: 1072 helix: 0.48 (0.32), residues: 286 sheet: -0.14 (0.46), residues: 128 loop : -2.24 (0.21), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 78 HIS 0.006 0.001 HIS B 126 PHE 0.013 0.002 PHE A 113 TYR 0.011 0.001 TYR G 79 ARG 0.005 0.000 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.8468 (ppp) cc_final: 0.7732 (ppp) REVERT: C 96 ASN cc_start: 0.7937 (OUTLIER) cc_final: 0.7635 (p0) REVERT: E 75 MET cc_start: 0.8380 (mtp) cc_final: 0.8159 (mtm) REVERT: H 26 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8228 (mp0) REVERT: H 52 ASP cc_start: 0.9607 (p0) cc_final: 0.9055 (p0) REVERT: H 55 LYS cc_start: 0.8855 (tmmt) cc_final: 0.8653 (tttt) REVERT: B 61 MET cc_start: 0.8495 (ppp) cc_final: 0.7085 (ppp) REVERT: G 63 ARG cc_start: 0.8570 (mmm160) cc_final: 0.8259 (mmm160) REVERT: G 75 MET cc_start: 0.8304 (mtp) cc_final: 0.8049 (mtm) REVERT: I 52 ASP cc_start: 0.9452 (p0) cc_final: 0.8809 (p0) REVERT: I 55 LYS cc_start: 0.8756 (tmmt) cc_final: 0.8437 (tttt) outliers start: 11 outliers final: 7 residues processed: 104 average time/residue: 0.1889 time to fit residues: 28.6514 Evaluate side-chains 99 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 185 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 102 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 HIS C 186 HIS ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 GLN B 111 GLN ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9104 Z= 0.310 Angle : 0.624 11.676 12284 Z= 0.323 Chirality : 0.045 0.218 1282 Planarity : 0.006 0.123 1562 Dihedral : 4.695 29.489 1176 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.75 % Allowed : 9.14 % Favored : 90.11 % Rotamer: Outliers : 2.54 % Allowed : 16.00 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.24), residues: 1072 helix: 0.35 (0.32), residues: 276 sheet: -0.27 (0.45), residues: 130 loop : -2.28 (0.21), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 78 HIS 0.006 0.001 HIS B 126 PHE 0.013 0.002 PHE A 113 TYR 0.010 0.001 TYR G 79 ARG 0.004 0.000 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 98 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8483 (ppp) cc_final: 0.7703 (ppp) REVERT: C 96 ASN cc_start: 0.7922 (OUTLIER) cc_final: 0.7654 (p0) REVERT: C 109 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7948 (mt) REVERT: E 75 MET cc_start: 0.8455 (mtp) cc_final: 0.8208 (mtm) REVERT: H 26 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8121 (mp0) REVERT: H 52 ASP cc_start: 0.9664 (p0) cc_final: 0.9065 (p0) REVERT: H 74 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8678 (t) REVERT: B 61 MET cc_start: 0.8498 (ppp) cc_final: 0.7695 (ppp) REVERT: F 96 ASN cc_start: 0.7951 (OUTLIER) cc_final: 0.7663 (p0) REVERT: G 75 MET cc_start: 0.8413 (mtp) cc_final: 0.8164 (mtm) REVERT: G 105 MET cc_start: 0.9166 (mmm) cc_final: 0.8918 (mmm) REVERT: I 26 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8058 (mp0) REVERT: I 52 ASP cc_start: 0.9534 (p0) cc_final: 0.8844 (p0) REVERT: I 55 LYS cc_start: 0.8770 (tmmt) cc_final: 0.8552 (tttt) outliers start: 24 outliers final: 9 residues processed: 116 average time/residue: 0.2427 time to fit residues: 40.6165 Evaluate side-chains 104 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 89 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain I residue 26 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 HIS ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 9104 Z= 0.387 Angle : 0.674 10.615 12284 Z= 0.351 Chirality : 0.047 0.235 1282 Planarity : 0.006 0.128 1562 Dihedral : 4.897 29.213 1176 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.75 % Allowed : 10.45 % Favored : 88.81 % Rotamer: Outliers : 2.22 % Allowed : 16.95 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.24), residues: 1072 helix: 0.18 (0.32), residues: 276 sheet: -0.40 (0.44), residues: 130 loop : -2.36 (0.21), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 78 HIS 0.008 0.002 HIS A 126 PHE 0.021 0.002 PHE I 15 TYR 0.011 0.002 TYR E 79 ARG 0.005 0.000 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 1.174 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.8512 (ppp) cc_final: 0.7435 (ppp) REVERT: A 136 MET cc_start: 0.8310 (tpt) cc_final: 0.7995 (tpt) REVERT: C 96 ASN cc_start: 0.8032 (OUTLIER) cc_final: 0.7722 (p0) REVERT: C 109 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8058 (mt) REVERT: C 225 MET cc_start: 0.8006 (ttm) cc_final: 0.7598 (ttm) REVERT: E 75 MET cc_start: 0.8481 (mtp) cc_final: 0.8256 (mtm) REVERT: H 26 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8146 (mp0) REVERT: H 52 ASP cc_start: 0.9579 (p0) cc_final: 0.9034 (p0) REVERT: B 61 MET cc_start: 0.8533 (ppp) cc_final: 0.7423 (ppp) REVERT: F 96 ASN cc_start: 0.8003 (OUTLIER) cc_final: 0.7731 (p0) REVERT: F 109 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7960 (mt) REVERT: I 26 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8085 (mp0) REVERT: I 52 ASP cc_start: 0.9522 (p0) cc_final: 0.8796 (p0) outliers start: 21 outliers final: 11 residues processed: 109 average time/residue: 0.1884 time to fit residues: 30.0249 Evaluate side-chains 106 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain I residue 26 GLU Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.2980 chunk 97 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 86 optimal weight: 0.0980 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 HIS ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9104 Z= 0.230 Angle : 0.615 10.990 12284 Z= 0.313 Chirality : 0.044 0.209 1282 Planarity : 0.006 0.126 1562 Dihedral : 4.731 31.030 1176 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.75 % Allowed : 8.68 % Favored : 90.58 % Rotamer: Outliers : 1.38 % Allowed : 18.64 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -1.95 (0.24), residues: 1072 helix: 0.10 (0.32), residues: 288 sheet: -0.33 (0.45), residues: 128 loop : -2.28 (0.21), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 78 HIS 0.004 0.001 HIS A 126 PHE 0.024 0.001 PHE I 15 TYR 0.011 0.001 TYR E 79 ARG 0.013 0.000 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8456 (ppp) cc_final: 0.7761 (ppp) REVERT: C 78 TRP cc_start: 0.7223 (m-10) cc_final: 0.6978 (m-10) REVERT: C 96 ASN cc_start: 0.7914 (OUTLIER) cc_final: 0.7697 (p0) REVERT: E 75 MET cc_start: 0.8448 (mtp) cc_final: 0.8224 (mtm) REVERT: H 26 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: H 52 ASP cc_start: 0.9572 (p0) cc_final: 0.9061 (p0) REVERT: B 61 MET cc_start: 0.8466 (ppp) cc_final: 0.7753 (ppp) REVERT: F 96 ASN cc_start: 0.7981 (OUTLIER) cc_final: 0.7704 (p0) REVERT: G 105 MET cc_start: 0.9154 (mmm) cc_final: 0.8803 (mmm) REVERT: I 26 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8092 (mp0) REVERT: I 52 ASP cc_start: 0.9486 (p0) cc_final: 0.8851 (p0) outliers start: 13 outliers final: 9 residues processed: 101 average time/residue: 0.1844 time to fit residues: 27.2712 Evaluate side-chains 105 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain I residue 26 GLU Chi-restraints excluded: chain I residue 51 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 105 optimal weight: 30.0000 chunk 97 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 89 optimal weight: 7.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 HIS ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9104 Z= 0.276 Angle : 0.641 10.725 12284 Z= 0.328 Chirality : 0.045 0.214 1282 Planarity : 0.006 0.127 1562 Dihedral : 4.740 29.923 1176 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.75 % Allowed : 9.98 % Favored : 89.27 % Rotamer: Outliers : 1.48 % Allowed : 18.64 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.24), residues: 1072 helix: 0.08 (0.32), residues: 288 sheet: -0.40 (0.45), residues: 128 loop : -2.29 (0.21), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 78 HIS 0.006 0.001 HIS A 126 PHE 0.029 0.002 PHE I 15 TYR 0.011 0.001 TYR G 79 ARG 0.004 0.000 ARG H 9 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.8477 (ppp) cc_final: 0.7703 (ppp) REVERT: C 96 ASN cc_start: 0.7973 (OUTLIER) cc_final: 0.7699 (p0) REVERT: H 26 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8043 (mp0) REVERT: H 52 ASP cc_start: 0.9589 (p0) cc_final: 0.9057 (p0) REVERT: B 61 MET cc_start: 0.8514 (ppp) cc_final: 0.7736 (ppp) REVERT: F 96 ASN cc_start: 0.7957 (OUTLIER) cc_final: 0.7697 (p0) REVERT: G 105 MET cc_start: 0.9134 (mmm) cc_final: 0.8783 (mmm) REVERT: I 26 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8134 (mp0) REVERT: I 52 ASP cc_start: 0.9484 (p0) cc_final: 0.8868 (p0) outliers start: 14 outliers final: 9 residues processed: 98 average time/residue: 0.1759 time to fit residues: 25.5874 Evaluate side-chains 100 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain I residue 26 GLU Chi-restraints excluded: chain I residue 51 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 HIS C 186 HIS ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.079347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.058703 restraints weight = 36334.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.060538 restraints weight = 18815.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.061695 restraints weight = 13044.932| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9104 Z= 0.230 Angle : 0.638 10.779 12284 Z= 0.320 Chirality : 0.045 0.209 1282 Planarity : 0.006 0.126 1562 Dihedral : 4.633 30.692 1176 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.75 % Allowed : 8.68 % Favored : 90.58 % Rotamer: Outliers : 1.48 % Allowed : 18.96 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -1.93 (0.24), residues: 1072 helix: 0.13 (0.32), residues: 288 sheet: -0.38 (0.44), residues: 128 loop : -2.27 (0.21), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP F 78 HIS 0.005 0.001 HIS A 126 PHE 0.034 0.001 PHE I 15 TYR 0.011 0.001 TYR G 79 ARG 0.003 0.000 ARG H 9 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1803.17 seconds wall clock time: 33 minutes 31.92 seconds (2011.92 seconds total)