Starting phenix.real_space_refine on Fri Feb 16 22:29:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkb_12436/02_2024/7nkb_12436.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkb_12436/02_2024/7nkb_12436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkb_12436/02_2024/7nkb_12436.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkb_12436/02_2024/7nkb_12436.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkb_12436/02_2024/7nkb_12436.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkb_12436/02_2024/7nkb_12436.pdb" } resolution = 2.9 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= 0.000 sd= 0.001 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 S 25 5.16 5 C 5376 2.51 5 N 1401 2.21 5 O 1538 1.98 5 H 8429 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Q GLU 65": "OE1" <-> "OE2" Residue "R GLU 65": "OE1" <-> "OE2" Residue "T GLU 65": "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: 16769 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 326 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 3, 'TRANS': 17} Chain: "G" Number of atoms: 3865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 3865 Classifications: {'peptide': 251} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 240} Chain breaks: 1 Chain: "H" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1802 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "M" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "N" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "O" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "P" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "Q" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "R" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "S" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "T" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Time building chain proxies: 7.56, per 1000 atoms: 0.45 Number of scatterers: 16769 At special positions: 0 Unit cell: (78.02, 70.55, 150.23, 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) S 25 16.00 O 1538 8.00 N 1401 7.00 C 5376 6.00 H 8429 1.00 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: 15.33 Conformation dependent library (CDL) restraints added in 1.9 seconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1966 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 3 sheets defined 74.2% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'C' and resid 529 through 533 removed outlier: 3.569A pdb=" N LEU C 533 " --> pdb=" O PRO C 530 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 43 Processing helix chain 'G' and resid 43 through 60 Processing helix chain 'G' and resid 91 through 110 Processing helix chain 'G' and resid 120 through 130 removed outlier: 3.609A pdb=" N LEU G 124 " --> pdb=" O GLY G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 164 Processing helix chain 'G' and resid 172 through 176 removed outlier: 3.679A pdb=" N ASP G 175 " --> pdb=" O ALA G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 270 Proline residue: G 237 - end of helix Processing helix chain 'H' and resid 91 through 99 Processing helix chain 'H' and resid 103 through 117 Processing helix chain 'L' and resid 4 through 46 Processing helix chain 'L' and resid 49 through 80 removed outlier: 4.392A pdb=" N THR L 55 " --> pdb=" O GLY L 51 " (cutoff:3.500A) Proline residue: L 56 - end of helix removed outlier: 3.681A pdb=" N ALA L 66 " --> pdb=" O GLY L 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 46 removed outlier: 3.519A pdb=" N ILE M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 80 removed outlier: 4.307A pdb=" N ARG M 52 " --> pdb=" O GLU M 48 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE M 54 " --> pdb=" O GLN M 50 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) Proline residue: M 56 - end of helix removed outlier: 3.760A pdb=" N LEU M 63 " --> pdb=" O ILE M 59 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA M 67 " --> pdb=" O LEU M 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 46 removed outlier: 3.574A pdb=" N ILE N 8 " --> pdb=" O ASP N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 52 removed outlier: 4.160A pdb=" N GLY N 51 " --> pdb=" O GLU N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 81 removed outlier: 3.977A pdb=" N PHE N 57 " --> pdb=" O LEU N 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 46 removed outlier: 3.506A pdb=" N ILE O 8 " --> pdb=" O ASP O 4 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 81 removed outlier: 3.717A pdb=" N PHE O 54 " --> pdb=" O GLN O 50 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR O 55 " --> pdb=" O GLY O 51 " (cutoff:3.500A) Proline residue: O 56 - end of helix removed outlier: 3.652A pdb=" N ILE O 70 " --> pdb=" O ALA O 66 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 46 removed outlier: 3.761A pdb=" N ILE P 8 " --> pdb=" O ASP P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 80 removed outlier: 4.325A pdb=" N THR P 55 " --> pdb=" O GLY P 51 " (cutoff:3.500A) Proline residue: P 56 - end of helix removed outlier: 3.565A pdb=" N ILE P 59 " --> pdb=" O THR P 55 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA P 67 " --> pdb=" O LEU P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 46 Processing helix chain 'Q' and resid 49 through 80 removed outlier: 4.369A pdb=" N THR Q 55 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) Proline residue: Q 56 - end of helix Processing helix chain 'R' and resid 4 through 46 removed outlier: 3.963A pdb=" N ILE R 8 " --> pdb=" O ASP R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 80 removed outlier: 4.557A pdb=" N THR R 55 " --> pdb=" O GLY R 51 " (cutoff:3.500A) Proline residue: R 56 - end of helix Processing helix chain 'S' and resid 4 through 46 Processing helix chain 'S' and resid 47 through 51 Processing helix chain 'S' and resid 53 through 81 Processing helix chain 'T' and resid 4 through 46 removed outlier: 3.771A pdb=" N ILE T 8 " --> pdb=" O ASP T 4 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 80 removed outlier: 3.751A pdb=" N THR T 55 " --> pdb=" O GLY T 51 " (cutoff:3.500A) Proline residue: T 56 - end of helix removed outlier: 3.618A pdb=" N LEU T 63 " --> pdb=" O ILE T 59 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA T 67 " --> pdb=" O LEU T 63 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN T 71 " --> pdb=" O ALA T 67 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 534 through 540 removed outlier: 6.860A pdb=" N GLU C 534 " --> pdb=" O ARG G 202 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ALA G 204 " --> pdb=" O GLU C 534 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N GLU C 536 " --> pdb=" O ALA G 204 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N MET G 206 " --> pdb=" O GLU C 536 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL C 538 " --> pdb=" O MET G 206 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N VAL G 208 " --> pdb=" O VAL C 538 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL C 540 " --> pdb=" O VAL G 208 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N TYR G 210 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ALA G 198 " --> pdb=" O GLU G 189 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLU G 189 " --> pdb=" O ALA G 198 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ALA G 200 " --> pdb=" O PHE G 187 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N PHE G 187 " --> pdb=" O ALA G 200 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ARG G 202 " --> pdb=" O ILE G 185 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE G 185 " --> pdb=" O ARG G 202 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N THR G 188 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ALA G 77 " --> pdb=" O VAL G 115 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N TYR G 117 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL G 79 " --> pdb=" O TYR G 117 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL G 119 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL G 81 " --> pdb=" O VAL G 119 " (cutoff:3.500A) removed outlier: 10.238A pdb=" N GLU G 136 " --> pdb=" O PRO G 114 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LEU G 116 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N TRP G 138 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL G 118 " --> pdb=" O TRP G 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 223 through 225 removed outlier: 6.335A pdb=" N SER G 223 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N GLN H 44 " --> pdb=" O SER G 223 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N GLU G 225 " --> pdb=" O GLN H 44 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE H 63 " --> pdb=" O PHE H 86 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N PHE H 86 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL H 65 " --> pdb=" O ALA H 84 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA H 84 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY H 67 " --> pdb=" O GLU H 82 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASN H 5 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ILE H 79 " --> pdb=" O ASN H 5 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLU H 7 " --> pdb=" O ILE H 79 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL H 81 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL H 9 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN H 83 " --> pdb=" O VAL H 9 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ALA H 10 " --> pdb=" O GLU H 14 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU H 14 " --> pdb=" O ALA H 10 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 223 through 225 removed outlier: 6.335A pdb=" N SER G 223 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N GLN H 44 " --> pdb=" O SER G 223 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N GLU G 225 " --> pdb=" O GLN H 44 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N MET H 50 " --> pdb=" O ARG H 26 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG H 26 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE H 22 " --> pdb=" O GLU H 54 " (cutoff:3.500A) 723 hydrogen bonds defined for protein. 2133 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: 6.60 Time building geometry restraints manager: 15.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8428 1.03 - 1.23: 19 1.23 - 1.42: 3435 1.42 - 1.62: 4980 1.62 - 1.81: 49 Bond restraints: 16911 Sorted by residual: bond pdb=" CB MET R 21 " pdb=" CG MET R 21 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.20e+00 bond pdb=" CG LEU T 63 " pdb=" CD2 LEU T 63 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.18e+00 bond pdb=" CB PRO G 205 " pdb=" CG PRO G 205 " ideal model delta sigma weight residual 1.506 1.470 0.036 3.90e-02 6.57e+02 8.48e-01 bond pdb=" CG1 ILE S 43 " pdb=" CD1 ILE S 43 " ideal model delta sigma weight residual 1.513 1.477 0.036 3.90e-02 6.57e+02 8.45e-01 bond pdb=" CB VAL L 61 " pdb=" CG1 VAL L 61 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.36e-01 ... (remaining 16906 not shown) Histogram of bond angle deviations from ideal: 99.89 - 106.72: 243 106.72 - 113.55: 20036 113.55 - 120.37: 5931 120.37 - 127.20: 4356 127.20 - 134.03: 59 Bond angle restraints: 30625 Sorted by residual: angle pdb=" CB ARG R 52 " pdb=" CG ARG R 52 " pdb=" CD ARG R 52 " ideal model delta sigma weight residual 111.30 116.94 -5.64 2.30e+00 1.89e-01 6.02e+00 angle pdb=" N GLY L 62 " pdb=" CA GLY L 62 " pdb=" C GLY L 62 " ideal model delta sigma weight residual 113.99 110.98 3.01 1.28e+00 6.10e-01 5.53e+00 angle pdb=" N PRO H 36 " pdb=" CA PRO H 36 " pdb=" C PRO H 36 " ideal model delta sigma weight residual 113.75 116.47 -2.72 1.49e+00 4.50e-01 3.33e+00 angle pdb=" C LEU H 35 " pdb=" CA LEU H 35 " pdb=" CB LEU H 35 " ideal model delta sigma weight residual 109.48 112.05 -2.57 1.46e+00 4.69e-01 3.10e+00 angle pdb=" N LEU H 35 " pdb=" CA LEU H 35 " pdb=" C LEU H 35 " ideal model delta sigma weight residual 110.58 107.96 2.62 1.56e+00 4.11e-01 2.83e+00 ... (remaining 30620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 6923 17.58 - 35.16: 593 35.16 - 52.74: 265 52.74 - 70.32: 118 70.32 - 87.90: 6 Dihedral angle restraints: 7905 sinusoidal: 4305 harmonic: 3600 Sorted by residual: dihedral pdb=" CA VAL G 115 " pdb=" C VAL G 115 " pdb=" N LEU G 116 " pdb=" CA LEU G 116 " ideal model delta harmonic sigma weight residual -180.00 -161.44 -18.56 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA LEU H 35 " pdb=" C LEU H 35 " pdb=" N PRO H 36 " pdb=" CA PRO H 36 " ideal model delta harmonic sigma weight residual -180.00 -163.22 -16.78 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA LEU C 528 " pdb=" C LEU C 528 " pdb=" N ASP C 529 " pdb=" CA ASP C 529 " ideal model delta harmonic sigma weight residual 180.00 163.78 16.22 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 7902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 889 0.034 - 0.069: 290 0.069 - 0.103: 133 0.103 - 0.137: 19 0.137 - 0.171: 2 Chirality restraints: 1333 Sorted by residual: chirality pdb=" CA PRO H 36 " pdb=" N PRO H 36 " pdb=" C PRO H 36 " pdb=" CB PRO H 36 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.33e-01 chirality pdb=" CA PRO L 47 " pdb=" N PRO L 47 " pdb=" C PRO L 47 " pdb=" CB PRO L 47 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA ILE H 63 " pdb=" N ILE H 63 " pdb=" C ILE H 63 " pdb=" CB ILE H 63 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 ... (remaining 1330 not shown) Planarity restraints: 2604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 35 " 0.032 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO H 36 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO H 36 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 36 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY M 62 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.77e+00 pdb=" C GLY M 62 " -0.023 2.00e-02 2.50e+03 pdb=" O GLY M 62 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU M 63 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA L 66 " 0.007 2.00e-02 2.50e+03 1.32e-02 1.75e+00 pdb=" C ALA L 66 " -0.023 2.00e-02 2.50e+03 pdb=" O ALA L 66 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA L 67 " 0.008 2.00e-02 2.50e+03 ... (remaining 2601 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 711 2.18 - 2.78: 34221 2.78 - 3.39: 51341 3.39 - 3.99: 66895 3.99 - 4.60: 104733 Nonbonded interactions: 257901 Sorted by model distance: nonbonded pdb="HH21 ARG R 52 " pdb=" O ILE S 43 " model vdw 1.572 1.850 nonbonded pdb="HH12 ARG G 39 " pdb=" O PRO G 145 " model vdw 1.618 1.850 nonbonded pdb=" OD2 ASP G 167 " pdb=" H GLY G 179 " model vdw 1.642 1.850 nonbonded pdb="HD21 ASN T 6 " pdb=" O GLN T 86 " model vdw 1.643 1.850 nonbonded pdb=" OE1 GLU Q 48 " pdb=" H GLU Q 48 " model vdw 1.651 1.850 ... (remaining 257896 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 'L' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 4 through 86)) selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = (chain 'P' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 4 through 86)) selection = (chain 'Q' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 4 through 86)) selection = chain 'R' selection = (chain 'S' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 4 through 86)) selection = chain 'T' } 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: 9.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.260 Extract box with map and model: 26.140 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 58.790 Find NCS groups from input model: 0.730 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:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 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 : 0.004 0.036 8482 Z= 0.280 Angle : 0.501 5.642 11500 Z= 0.278 Chirality : 0.040 0.171 1333 Planarity : 0.004 0.048 1519 Dihedral : 13.118 87.900 2960 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.81 (0.26), residues: 1124 helix: 1.65 (0.19), residues: 811 sheet: -1.24 (0.53), residues: 89 loop : 0.88 (0.45), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 109 HIS 0.002 0.001 HIS H 38 PHE 0.017 0.002 PHE M 78 TYR 0.010 0.001 TYR G 147 ARG 0.012 0.001 ARG R 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.308 Fit side-chains REVERT: P 75 MET cc_start: 0.8181 (tmm) cc_final: 0.7942 (tmm) REVERT: R 21 MET cc_start: 0.8568 (mmm) cc_final: 0.8311 (mmm) REVERT: R 50 GLN cc_start: 0.8339 (tt0) cc_final: 0.7929 (tm130) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 2.5148 time to fit residues: 248.3786 Evaluate side-chains 60 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 GLN N 71 ASN Q 86 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8482 Z= 0.344 Angle : 0.544 4.841 11500 Z= 0.298 Chirality : 0.042 0.182 1333 Planarity : 0.004 0.048 1519 Dihedral : 4.145 19.574 1208 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.50 % Allowed : 7.26 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 2.62 (0.25), residues: 1124 helix: 2.31 (0.18), residues: 813 sheet: -1.19 (0.53), residues: 83 loop : 0.92 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 109 HIS 0.003 0.001 HIS H 38 PHE 0.015 0.002 PHE M 78 TYR 0.012 0.001 TYR G 147 ARG 0.004 0.000 ARG R 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 1.455 Fit side-chains REVERT: L 63 LEU cc_start: 0.7849 (tt) cc_final: 0.7590 (tt) REVERT: M 32 ASP cc_start: 0.8009 (m-30) cc_final: 0.7534 (m-30) REVERT: M 65 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.6945 (mp0) REVERT: P 75 MET cc_start: 0.8440 (tmm) cc_final: 0.8131 (tmm) REVERT: R 21 MET cc_start: 0.8599 (mmm) cc_final: 0.8352 (mmm) REVERT: R 50 GLN cc_start: 0.7949 (tt0) cc_final: 0.7571 (tm-30) REVERT: S 75 MET cc_start: 0.8666 (tmm) cc_final: 0.8449 (ttp) outliers start: 12 outliers final: 5 residues processed: 71 average time/residue: 2.4868 time to fit residues: 189.7912 Evaluate side-chains 67 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain M residue 65 GLU Chi-restraints excluded: chain O residue 65 GLU Chi-restraints excluded: chain Q residue 86 GLN Chi-restraints excluded: chain S residue 3 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 99 optimal weight: 0.1980 chunk 34 optimal weight: 0.3980 chunk 80 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 GLN Q 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8482 Z= 0.245 Angle : 0.503 4.761 11500 Z= 0.270 Chirality : 0.040 0.163 1333 Planarity : 0.004 0.042 1519 Dihedral : 4.094 19.203 1208 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.63 % Allowed : 8.51 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 3.10 (0.26), residues: 1124 helix: 2.70 (0.18), residues: 813 sheet: -1.05 (0.55), residues: 79 loop : 0.93 (0.44), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 109 HIS 0.002 0.001 HIS H 38 PHE 0.016 0.001 PHE R 74 TYR 0.010 0.001 TYR G 147 ARG 0.003 0.000 ARG N 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 62 time to evaluate : 1.300 Fit side-chains REVERT: M 65 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: P 75 MET cc_start: 0.8499 (tmm) cc_final: 0.8110 (tmm) REVERT: R 21 MET cc_start: 0.8585 (mmm) cc_final: 0.8337 (mmm) REVERT: R 50 GLN cc_start: 0.7906 (tt0) cc_final: 0.7523 (tm-30) outliers start: 13 outliers final: 5 residues processed: 67 average time/residue: 2.4223 time to fit residues: 174.9165 Evaluate side-chains 64 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain M residue 65 GLU Chi-restraints excluded: chain O residue 65 GLU Chi-restraints excluded: chain S residue 3 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8482 Z= 0.326 Angle : 0.521 5.815 11500 Z= 0.283 Chirality : 0.041 0.183 1333 Planarity : 0.004 0.043 1519 Dihedral : 4.121 19.611 1208 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.13 % Allowed : 9.14 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 3.10 (0.26), residues: 1124 helix: 2.72 (0.18), residues: 813 sheet: -1.21 (0.53), residues: 83 loop : 0.98 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 109 HIS 0.003 0.001 HIS H 38 PHE 0.016 0.002 PHE R 74 TYR 0.011 0.001 TYR G 147 ARG 0.004 0.000 ARG N 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 63 time to evaluate : 1.602 Fit side-chains REVERT: M 65 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: P 75 MET cc_start: 0.8574 (tmm) cc_final: 0.8242 (tmm) REVERT: Q 86 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.6315 (pm20) REVERT: R 21 MET cc_start: 0.8608 (mmm) cc_final: 0.8292 (mmm) REVERT: R 50 GLN cc_start: 0.7918 (tt0) cc_final: 0.7550 (tm-30) outliers start: 17 outliers final: 7 residues processed: 72 average time/residue: 2.5928 time to fit residues: 200.4543 Evaluate side-chains 67 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain M residue 65 GLU Chi-restraints excluded: chain O residue 65 GLU Chi-restraints excluded: chain Q residue 86 GLN Chi-restraints excluded: chain S residue 3 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8482 Z= 0.323 Angle : 0.521 5.013 11500 Z= 0.283 Chirality : 0.041 0.181 1333 Planarity : 0.004 0.042 1519 Dihedral : 4.149 19.812 1208 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.50 % Allowed : 9.51 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 3.13 (0.26), residues: 1124 helix: 2.75 (0.18), residues: 813 sheet: -1.29 (0.52), residues: 83 loop : 0.94 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 109 HIS 0.003 0.001 HIS H 38 PHE 0.017 0.002 PHE R 74 TYR 0.011 0.001 TYR G 147 ARG 0.003 0.000 ARG N 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 56 time to evaluate : 1.374 Fit side-chains revert: symmetry clash REVERT: M 65 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: P 75 MET cc_start: 0.8620 (tmm) cc_final: 0.8269 (tmm) REVERT: R 21 MET cc_start: 0.8595 (mmm) cc_final: 0.8277 (mmm) outliers start: 20 outliers final: 8 residues processed: 68 average time/residue: 2.2638 time to fit residues: 167.1938 Evaluate side-chains 64 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain M residue 65 GLU Chi-restraints excluded: chain O residue 65 GLU Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain S residue 3 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 GLN N 71 ASN O 71 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8482 Z= 0.338 Angle : 0.526 5.604 11500 Z= 0.285 Chirality : 0.041 0.185 1333 Planarity : 0.004 0.042 1519 Dihedral : 4.155 19.828 1208 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.38 % Allowed : 9.39 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 3.12 (0.26), residues: 1124 helix: 2.76 (0.18), residues: 813 sheet: -1.34 (0.52), residues: 83 loop : 0.93 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 109 HIS 0.004 0.001 HIS H 38 PHE 0.015 0.002 PHE R 74 TYR 0.011 0.001 TYR G 147 ARG 0.004 0.000 ARG O 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 59 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 65 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7052 (mp0) REVERT: R 21 MET cc_start: 0.8586 (mmm) cc_final: 0.8295 (mmm) outliers start: 19 outliers final: 9 residues processed: 69 average time/residue: 2.3731 time to fit residues: 177.2656 Evaluate side-chains 64 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain M residue 65 GLU Chi-restraints excluded: chain O residue 65 GLU Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain S residue 3 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 59 optimal weight: 0.0980 chunk 106 optimal weight: 0.8980 chunk 66 optimal weight: 0.0570 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 65 optimal weight: 0.0970 chunk 42 optimal weight: 0.9990 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8482 Z= 0.157 Angle : 0.474 6.427 11500 Z= 0.250 Chirality : 0.040 0.139 1333 Planarity : 0.003 0.032 1519 Dihedral : 3.936 18.533 1208 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.88 % Allowed : 10.26 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 3.71 (0.26), residues: 1124 helix: 3.22 (0.18), residues: 803 sheet: -1.15 (0.58), residues: 71 loop : 0.98 (0.43), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 109 HIS 0.001 0.000 HIS H 38 PHE 0.013 0.001 PHE R 74 TYR 0.009 0.001 TYR G 147 ARG 0.004 0.000 ARG O 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 56 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 264 LYS cc_start: 0.8333 (tptm) cc_final: 0.8115 (tptp) REVERT: M 65 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: O 75 MET cc_start: 0.9123 (tmm) cc_final: 0.8791 (tmm) REVERT: P 75 MET cc_start: 0.8716 (tmt) cc_final: 0.8360 (tmm) REVERT: R 21 MET cc_start: 0.8503 (mmm) cc_final: 0.8252 (mmm) outliers start: 15 outliers final: 8 residues processed: 64 average time/residue: 2.4089 time to fit residues: 166.3298 Evaluate side-chains 61 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 52 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain M residue 65 GLU Chi-restraints excluded: chain O residue 65 GLU Chi-restraints excluded: chain O residue 71 ASN Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain S residue 3 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8482 Z= 0.313 Angle : 0.519 7.716 11500 Z= 0.279 Chirality : 0.041 0.186 1333 Planarity : 0.004 0.036 1519 Dihedral : 4.037 19.036 1208 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.75 % Allowed : 11.14 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 3.49 (0.26), residues: 1124 helix: 3.06 (0.18), residues: 803 sheet: -1.32 (0.52), residues: 84 loop : 1.07 (0.43), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 109 HIS 0.004 0.001 HIS H 38 PHE 0.014 0.001 PHE R 74 TYR 0.012 0.001 TYR G 147 ARG 0.004 0.000 ARG O 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 1.240 Fit side-chains revert: symmetry clash REVERT: M 65 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: O 75 MET cc_start: 0.9104 (tmm) cc_final: 0.8753 (tmm) REVERT: R 21 MET cc_start: 0.8553 (mmm) cc_final: 0.8303 (mmm) REVERT: T 65 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.6630 (mp0) outliers start: 14 outliers final: 9 residues processed: 63 average time/residue: 2.3357 time to fit residues: 159.1785 Evaluate side-chains 67 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain M residue 65 GLU Chi-restraints excluded: chain O residue 65 GLU Chi-restraints excluded: chain O residue 71 ASN Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain S residue 3 LEU Chi-restraints excluded: chain T residue 65 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 chunk 43 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8482 Z= 0.230 Angle : 0.501 8.107 11500 Z= 0.265 Chirality : 0.040 0.162 1333 Planarity : 0.003 0.033 1519 Dihedral : 3.991 18.765 1208 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.13 % Allowed : 11.76 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 3.62 (0.26), residues: 1124 helix: 3.17 (0.18), residues: 803 sheet: -1.30 (0.53), residues: 84 loop : 1.11 (0.43), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 109 HIS 0.002 0.001 HIS H 38 PHE 0.013 0.001 PHE R 74 TYR 0.010 0.001 TYR G 147 ARG 0.004 0.000 ARG O 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 56 time to evaluate : 1.200 Fit side-chains revert: symmetry clash REVERT: M 65 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7073 (mp0) REVERT: O 75 MET cc_start: 0.9112 (tmm) cc_final: 0.8778 (tmm) REVERT: R 21 MET cc_start: 0.8527 (mmm) cc_final: 0.8290 (mmm) REVERT: T 65 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.6626 (mp0) outliers start: 17 outliers final: 10 residues processed: 66 average time/residue: 2.3669 time to fit residues: 168.3157 Evaluate side-chains 66 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 54 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain M residue 65 GLU Chi-restraints excluded: chain O residue 65 GLU Chi-restraints excluded: chain O residue 71 ASN Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain S residue 3 LEU Chi-restraints excluded: chain T residue 65 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8482 Z= 0.337 Angle : 0.533 8.293 11500 Z= 0.286 Chirality : 0.041 0.189 1333 Planarity : 0.004 0.033 1519 Dihedral : 4.091 19.367 1208 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.63 % Allowed : 12.27 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 3.41 (0.25), residues: 1124 helix: 3.01 (0.18), residues: 803 sheet: -1.29 (0.52), residues: 84 loop : 0.98 (0.43), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 109 HIS 0.004 0.001 HIS H 38 PHE 0.014 0.002 PHE R 74 TYR 0.011 0.001 TYR G 147 ARG 0.005 0.000 ARG O 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 55 time to evaluate : 1.506 Fit side-chains revert: symmetry clash REVERT: M 65 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7047 (mp0) REVERT: O 75 MET cc_start: 0.9114 (tmm) cc_final: 0.8757 (tmm) REVERT: T 65 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.6720 (mp0) outliers start: 13 outliers final: 9 residues processed: 62 average time/residue: 2.3851 time to fit residues: 160.1638 Evaluate side-chains 66 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain M residue 65 GLU Chi-restraints excluded: chain O residue 65 GLU Chi-restraints excluded: chain O residue 71 ASN Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain S residue 3 LEU Chi-restraints excluded: chain T residue 65 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 ASN ** O 71 ASN ** 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 = 0.3302 r_free = 0.3302 target = 0.085312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.065152 restraints weight = 45121.818| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.12 r_work: 0.2785 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8482 Z= 0.330 Angle : 0.534 7.972 11500 Z= 0.287 Chirality : 0.041 0.187 1333 Planarity : 0.004 0.031 1519 Dihedral : 4.120 19.645 1208 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.75 % Allowed : 12.27 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 3.37 (0.25), residues: 1124 helix: 2.99 (0.18), residues: 803 sheet: -1.31 (0.52), residues: 84 loop : 0.93 (0.42), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 109 HIS 0.003 0.001 HIS H 38 PHE 0.014 0.001 PHE R 74 TYR 0.011 0.001 TYR G 147 ARG 0.005 0.000 ARG O 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5552.34 seconds wall clock time: 98 minutes 10.90 seconds (5890.90 seconds total)