Starting phenix.real_space_refine on Wed Mar 4 21:25:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nkn_12444/03_2026/7nkn_12444.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nkn_12444/03_2026/7nkn_12444.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nkn_12444/03_2026/7nkn_12444.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nkn_12444/03_2026/7nkn_12444.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nkn_12444/03_2026/7nkn_12444.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nkn_12444/03_2026/7nkn_12444.map" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 5401 2.51 5 N 1408 2.21 5 O 1555 1.98 5 H 8457 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16846 Number of models: 1 Model: "" Number of chains: 12 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: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} 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: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} 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: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} 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: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "C" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 355 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 3, 'TRANS': 19} Time building chain proxies: 2.55, per 1000 atoms: 0.15 Number of scatterers: 16846 At special positions: 0 Unit cell: (70.55, 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 1555 8.00 N 1408 7.00 C 5401 6.00 H 8457 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 521.6 milliseconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1978 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 3 sheets defined 73.8% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'G' and resid 18 through 61 Proline residue: G 45 - end of helix Processing helix chain 'G' and resid 65 through 69 removed outlier: 3.537A pdb=" N VAL G 69 " --> pdb=" O PRO G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 111 Processing helix chain 'G' and resid 120 through 131 removed outlier: 3.590A 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: 3.782A 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 118 Processing helix chain 'L' and resid 4 through 46 Processing helix chain 'L' and resid 49 through 80 removed outlier: 3.609A pdb=" N PHE L 54 " --> pdb=" O GLN L 50 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N THR L 55 " --> pdb=" O GLY L 51 " (cutoff:3.500A) Proline residue: L 56 - end of helix removed outlier: 4.442A pdb=" N ALA L 67 " --> pdb=" O LEU L 63 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR L 68 " --> pdb=" O VAL L 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 46 Processing helix chain 'M' and resid 49 through 80 removed outlier: 4.505A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) Proline residue: M 56 - end of helix removed outlier: 3.730A pdb=" N TYR M 68 " --> pdb=" O VAL M 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 46 removed outlier: 3.517A pdb=" N ILE N 8 " --> pdb=" O ASP N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 81 removed outlier: 4.683A pdb=" N THR N 55 " --> pdb=" O GLY N 51 " (cutoff:3.500A) Proline residue: N 56 - end of helix removed outlier: 3.544A pdb=" N LEU N 77 " --> pdb=" O ALA N 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 46 Processing helix chain 'O' and resid 49 through 80 removed outlier: 4.670A pdb=" N THR O 55 " --> pdb=" O GLY O 51 " (cutoff:3.500A) Proline residue: O 56 - end of helix removed outlier: 3.510A pdb=" N ALA O 67 " --> pdb=" O LEU O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 46 removed outlier: 3.519A pdb=" N ILE P 8 " --> pdb=" O ASP P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 80 removed outlier: 3.754A pdb=" N PHE P 54 " --> pdb=" O GLN P 50 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR P 55 " --> pdb=" O GLY P 51 " (cutoff:3.500A) Proline residue: P 56 - end of helix Processing helix chain 'Q' and resid 4 through 46 Processing helix chain 'Q' and resid 47 through 50 Processing helix chain 'Q' and resid 53 through 81 Processing helix chain 'R' and resid 4 through 46 Processing helix chain 'R' and resid 49 through 80 removed outlier: 3.987A 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 removed outlier: 3.788A pdb=" N ILE S 8 " --> pdb=" O ASP S 4 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 80 removed outlier: 4.694A pdb=" N THR S 55 " --> pdb=" O GLY S 51 " (cutoff:3.500A) Proline residue: S 56 - end of helix removed outlier: 3.520A pdb=" N ASN S 71 " --> pdb=" O ALA S 67 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 46 removed outlier: 3.509A pdb=" N ILE T 8 " --> pdb=" O ASP T 4 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 81 removed outlier: 3.730A pdb=" N THR T 55 " --> pdb=" O GLY T 51 " (cutoff:3.500A) Proline residue: T 56 - end of helix removed outlier: 3.969A pdb=" N ALA T 67 " --> pdb=" O LEU T 63 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 134 through 138 removed outlier: 10.316A pdb=" N GLU G 136 " --> pdb=" O PRO G 114 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU G 116 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N TRP G 138 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL G 118 " --> pdb=" O TRP G 138 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ALA G 77 " --> pdb=" O VAL G 115 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N TYR G 117 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL G 79 " --> pdb=" O TYR G 117 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL G 119 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL G 81 " --> pdb=" O VAL G 119 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N HIS G 184 " --> pdb=" O ARG G 76 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLY G 78 " --> pdb=" O HIS G 184 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N VAL G 186 " --> pdb=" O GLY G 78 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU G 80 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N THR G 188 " --> pdb=" O LEU G 80 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N VAL G 82 " --> pdb=" O THR G 188 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU G 183 " --> pdb=" O ALA G 203 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLU C 534 " --> pdb=" O ARG G 201 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ALA G 203 " --> pdb=" O GLU C 534 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N GLU C 536 " --> pdb=" O ALA G 203 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N VAL C 538 " --> pdb=" O PRO G 205 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU G 207 " --> pdb=" O VAL C 538 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL C 540 " --> pdb=" O GLU G 207 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLU G 209 " --> pdb=" O VAL C 540 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 223 through 225 removed outlier: 6.122A pdb=" N SER G 223 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N GLN H 44 " --> pdb=" O SER G 223 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N GLU G 225 " --> pdb=" O GLN H 44 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLY H 68 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL H 81 " --> pdb=" O GLY H 68 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU H 70 " --> pdb=" O ILE H 79 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE H 79 " --> pdb=" O LEU H 70 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL H 72 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL H 77 " --> pdb=" O VAL H 72 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ALA H 10 " --> pdb=" O GLU H 14 " (cutoff:3.500A) removed outlier: 4.584A 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: 6.122A pdb=" N SER G 223 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N GLN H 44 " --> pdb=" O SER G 223 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N GLU G 225 " --> pdb=" O GLN H 44 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N MET H 50 " --> pdb=" O ARG H 26 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARG H 26 " --> pdb=" O MET H 50 " (cutoff:3.500A) 732 hydrogen bonds defined for protein. 2169 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: 3.87 Time building geometry restraints manager: 2.22 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: 8456 1.03 - 1.23: 1 1.23 - 1.42: 3477 1.42 - 1.61: 5005 1.61 - 1.81: 49 Bond restraints: 16988 Sorted by residual: bond pdb=" N SER H 71 " pdb=" CA SER H 71 " ideal model delta sigma weight residual 1.464 1.451 0.013 1.25e-02 6.40e+03 1.06e+00 bond pdb=" CG1 ILE M 20 " pdb=" CD1 ILE M 20 " ideal model delta sigma weight residual 1.513 1.476 0.037 3.90e-02 6.57e+02 8.87e-01 bond pdb=" C GLY G 120 " pdb=" O GLY G 120 " ideal model delta sigma weight residual 1.239 1.229 0.009 1.16e-02 7.43e+03 6.65e-01 bond pdb=" C VAL G 81 " pdb=" O VAL G 81 " ideal model delta sigma weight residual 1.237 1.229 0.008 1.10e-02 8.26e+03 5.26e-01 bond pdb=" CA VAL G 81 " pdb=" CB VAL G 81 " ideal model delta sigma weight residual 1.537 1.529 0.008 1.17e-02 7.31e+03 4.89e-01 ... (remaining 16983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 28998 1.02 - 2.05: 1654 2.05 - 3.07: 56 3.07 - 4.10: 44 4.10 - 5.12: 8 Bond angle restraints: 30760 Sorted by residual: angle pdb=" N PRO H 36 " pdb=" CA PRO H 36 " pdb=" C PRO H 36 " ideal model delta sigma weight residual 112.47 117.59 -5.12 2.06e+00 2.36e-01 6.19e+00 angle pdb=" N GLY H 68 " pdb=" CA GLY H 68 " pdb=" C GLY H 68 " ideal model delta sigma weight residual 111.12 115.11 -3.99 1.89e+00 2.80e-01 4.47e+00 angle pdb=" C GLY H 67 " pdb=" N GLY H 68 " pdb=" CA GLY H 68 " ideal model delta sigma weight residual 122.66 121.04 1.62 9.80e-01 1.04e+00 2.74e+00 angle pdb=" N VAL S 79 " pdb=" CA VAL S 79 " pdb=" C VAL S 79 " ideal model delta sigma weight residual 109.34 112.72 -3.38 2.08e+00 2.31e-01 2.64e+00 angle pdb=" N LEU G 116 " pdb=" CA LEU G 116 " pdb=" C LEU G 116 " ideal model delta sigma weight residual 109.24 111.80 -2.56 1.63e+00 3.76e-01 2.47e+00 ... (remaining 30755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 6873 16.71 - 33.41: 644 33.41 - 50.12: 195 50.12 - 66.83: 227 66.83 - 83.54: 4 Dihedral angle restraints: 7943 sinusoidal: 4325 harmonic: 3618 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 -162.90 -17.10 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ASP G 175 " pdb=" C ASP G 175 " pdb=" N GLY G 176 " pdb=" CA GLY G 176 " ideal model delta harmonic sigma weight residual 180.00 -164.09 -15.91 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CG ARG H 37 " pdb=" CD ARG H 37 " pdb=" NE ARG H 37 " pdb=" CZ ARG H 37 " ideal model delta sinusoidal sigma weight residual 180.00 137.66 42.34 2 1.50e+01 4.44e-03 9.68e+00 ... (remaining 7940 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 994 0.038 - 0.077: 227 0.077 - 0.115: 109 0.115 - 0.153: 8 0.153 - 0.192: 1 Chirality restraints: 1339 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 2.53 0.19 2.00e-01 2.50e+01 9.17e-01 chirality pdb=" CA ILE G 177 " pdb=" N ILE G 177 " pdb=" C ILE G 177 " pdb=" CB ILE G 177 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA ILE H 8 " pdb=" N ILE H 8 " pdb=" C ILE H 8 " pdb=" CB ILE H 8 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 1336 not shown) Planarity restraints: 2622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA R 66 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" C ALA R 66 " -0.025 2.00e-02 2.50e+03 pdb=" O ALA R 66 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA R 67 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Q 66 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.92e+00 pdb=" C ALA Q 66 " -0.024 2.00e-02 2.50e+03 pdb=" O ALA Q 66 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA Q 67 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY L 62 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" C GLY L 62 " -0.024 2.00e-02 2.50e+03 pdb=" O GLY L 62 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU L 63 " 0.008 2.00e-02 2.50e+03 ... (remaining 2619 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 1401 2.22 - 2.82: 37687 2.82 - 3.41: 49564 3.41 - 4.01: 67367 4.01 - 4.60: 104041 Nonbonded interactions: 260060 Sorted by model distance: nonbonded pdb=" O ALA G 47 " pdb=" HG1 THR G 51 " model vdw 1.631 2.450 nonbonded pdb=" OE1 GLU N 48 " pdb=" H GLU N 48 " model vdw 1.644 2.450 nonbonded pdb=" OE1 GLU O 48 " pdb=" H GLU O 48 " model vdw 1.648 2.450 nonbonded pdb=" OE1 GLU G 213 " pdb=" H GLU G 213 " model vdw 1.670 2.450 nonbonded pdb=" OE1 GLU G 148 " pdb="HH21 ARG G 151 " model vdw 1.671 2.450 ... (remaining 260055 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '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' 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 'N' selection = (chain 'O' 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 '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' 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 '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' 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)) } 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: 12.020 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.050 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 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:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8531 Z= 0.141 Angle : 0.472 5.125 11567 Z= 0.260 Chirality : 0.040 0.192 1339 Planarity : 0.004 0.027 1531 Dihedral : 13.516 83.537 2979 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.26), residues: 1130 helix: 1.42 (0.19), residues: 834 sheet: -0.29 (0.52), residues: 90 loop : 1.18 (0.46), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 45 TYR 0.010 0.001 TYR G 147 PHE 0.010 0.001 PHE R 69 TRP 0.004 0.001 TRP H 109 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8531) covalent geometry : angle 0.47179 (11567) hydrogen bonds : bond 0.13677 ( 728) hydrogen bonds : angle 6.84628 ( 2169) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.422 Fit side-chains REVERT: O 85 LEU cc_start: 0.8164 (tp) cc_final: 0.7863 (tm) REVERT: Q 50 GLN cc_start: 0.8161 (tm-30) cc_final: 0.7773 (tm-30) REVERT: R 2 ASP cc_start: 0.6038 (t70) cc_final: 0.5674 (t70) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 1.5196 time to fit residues: 132.8126 Evaluate side-chains 56 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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** R 6 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.088963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.069793 restraints weight = 40203.140| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.01 r_work: 0.2822 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8531 Z= 0.238 Angle : 0.545 5.751 11567 Z= 0.298 Chirality : 0.042 0.224 1339 Planarity : 0.004 0.037 1531 Dihedral : 4.057 18.484 1214 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.87 % Allowed : 7.20 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.25), residues: 1130 helix: 2.42 (0.18), residues: 804 sheet: -0.33 (0.50), residues: 90 loop : 0.63 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 45 TYR 0.014 0.002 TYR G 147 PHE 0.015 0.002 PHE M 74 TRP 0.008 0.002 TRP H 109 HIS 0.004 0.002 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00526 ( 8531) covalent geometry : angle 0.54540 (11567) hydrogen bonds : bond 0.05443 ( 728) hydrogen bonds : angle 4.49136 ( 2169) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: O 85 LEU cc_start: 0.8190 (tp) cc_final: 0.7791 (tm) REVERT: P 45 ARG cc_start: 0.7864 (mtp85) cc_final: 0.7630 (ttp-110) REVERT: Q 50 GLN cc_start: 0.8242 (tm-30) cc_final: 0.7813 (tm-30) REVERT: R 2 ASP cc_start: 0.6039 (t70) cc_final: 0.5614 (t70) outliers start: 7 outliers final: 2 residues processed: 75 average time/residue: 1.1996 time to fit residues: 95.8908 Evaluate side-chains 58 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 36 PRO Chi-restraints excluded: chain Q residue 46 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 30 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 77 optimal weight: 0.3980 chunk 47 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** R 6 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.089250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.070004 restraints weight = 40157.304| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.01 r_work: 0.2823 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8531 Z= 0.209 Angle : 0.515 5.415 11567 Z= 0.280 Chirality : 0.041 0.208 1339 Planarity : 0.004 0.040 1531 Dihedral : 4.047 18.521 1214 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.99 % Allowed : 8.82 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.13 (0.25), residues: 1130 helix: 2.79 (0.17), residues: 804 sheet: -0.36 (0.49), residues: 90 loop : 0.56 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 45 TYR 0.011 0.001 TYR G 147 PHE 0.014 0.002 PHE M 74 TRP 0.007 0.002 TRP H 109 HIS 0.004 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 8531) covalent geometry : angle 0.51499 (11567) hydrogen bonds : bond 0.05220 ( 728) hydrogen bonds : angle 4.26478 ( 2169) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: M 65 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7849 (mm-30) REVERT: O 85 LEU cc_start: 0.8149 (tp) cc_final: 0.7758 (tm) REVERT: P 45 ARG cc_start: 0.7842 (mtp85) cc_final: 0.7614 (ttp-110) REVERT: Q 50 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7851 (tm-30) REVERT: R 2 ASP cc_start: 0.6028 (t70) cc_final: 0.5594 (t70) outliers start: 8 outliers final: 2 residues processed: 70 average time/residue: 1.2399 time to fit residues: 92.5307 Evaluate side-chains 60 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain S residue 75 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 31 optimal weight: 0.1980 chunk 99 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 44 optimal weight: 0.4980 chunk 59 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** R 6 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.090002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.070849 restraints weight = 39989.006| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.01 r_work: 0.2838 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8531 Z= 0.167 Angle : 0.495 5.141 11567 Z= 0.266 Chirality : 0.040 0.192 1339 Planarity : 0.004 0.039 1531 Dihedral : 3.987 18.373 1214 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.75 % Allowed : 10.19 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.44 (0.25), residues: 1130 helix: 3.04 (0.18), residues: 804 sheet: -0.18 (0.51), residues: 78 loop : 0.49 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 52 TYR 0.011 0.001 TYR G 147 PHE 0.013 0.001 PHE M 74 TRP 0.005 0.001 TRP H 109 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 8531) covalent geometry : angle 0.49538 (11567) hydrogen bonds : bond 0.04874 ( 728) hydrogen bonds : angle 4.11892 ( 2169) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: O 85 LEU cc_start: 0.8177 (tp) cc_final: 0.7802 (tm) REVERT: P 45 ARG cc_start: 0.7862 (mtp85) cc_final: 0.7569 (ttp-110) REVERT: Q 50 GLN cc_start: 0.8293 (tm-30) cc_final: 0.7833 (tm-30) REVERT: R 2 ASP cc_start: 0.5935 (t70) cc_final: 0.5504 (t70) outliers start: 6 outliers final: 3 residues processed: 65 average time/residue: 1.2526 time to fit residues: 86.6542 Evaluate side-chains 59 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain S residue 75 MET Chi-restraints excluded: chain T residue 75 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 7 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** R 6 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.089032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.069721 restraints weight = 39786.031| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.01 r_work: 0.2823 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8531 Z= 0.221 Angle : 0.521 5.586 11567 Z= 0.283 Chirality : 0.041 0.214 1339 Planarity : 0.004 0.044 1531 Dihedral : 4.065 18.759 1214 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.24 % Allowed : 10.68 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.37 (0.25), residues: 1130 helix: 2.98 (0.17), residues: 804 sheet: -0.33 (0.50), residues: 90 loop : 0.63 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 45 TYR 0.012 0.001 TYR G 147 PHE 0.014 0.002 PHE Q 74 TRP 0.008 0.002 TRP H 109 HIS 0.005 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 8531) covalent geometry : angle 0.52053 (11567) hydrogen bonds : bond 0.05124 ( 728) hydrogen bonds : angle 4.15852 ( 2169) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: O 85 LEU cc_start: 0.8177 (tp) cc_final: 0.7794 (tm) REVERT: P 45 ARG cc_start: 0.7824 (mtp85) cc_final: 0.7541 (ttp-110) REVERT: Q 50 GLN cc_start: 0.8266 (tm-30) cc_final: 0.7796 (tm-30) REVERT: R 2 ASP cc_start: 0.6014 (t70) cc_final: 0.5570 (t70) outliers start: 10 outliers final: 4 residues processed: 68 average time/residue: 1.2403 time to fit residues: 89.8309 Evaluate side-chains 62 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain S residue 75 MET Chi-restraints excluded: chain T residue 48 GLU Chi-restraints excluded: chain T residue 75 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 89 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 0.0980 chunk 84 optimal weight: 0.7980 chunk 58 optimal weight: 0.3980 chunk 18 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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** R 6 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.089916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.070676 restraints weight = 39817.722| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.01 r_work: 0.2842 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8531 Z= 0.162 Angle : 0.491 5.037 11567 Z= 0.264 Chirality : 0.040 0.187 1339 Planarity : 0.004 0.041 1531 Dihedral : 3.985 18.434 1214 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.75 % Allowed : 11.68 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.56 (0.25), residues: 1130 helix: 3.14 (0.17), residues: 804 sheet: -0.21 (0.51), residues: 78 loop : 0.54 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 45 TYR 0.011 0.001 TYR G 147 PHE 0.012 0.001 PHE M 74 TRP 0.005 0.001 TRP H 109 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8531) covalent geometry : angle 0.49110 (11567) hydrogen bonds : bond 0.04798 ( 728) hydrogen bonds : angle 4.05066 ( 2169) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.430 Fit side-chains REVERT: O 85 LEU cc_start: 0.8166 (tp) cc_final: 0.7788 (tm) REVERT: P 45 ARG cc_start: 0.7844 (mtp85) cc_final: 0.7519 (ttp-110) REVERT: Q 48 GLU cc_start: 0.8006 (pm20) cc_final: 0.7789 (pm20) REVERT: Q 50 GLN cc_start: 0.8261 (tm-30) cc_final: 0.7800 (tm-30) REVERT: R 2 ASP cc_start: 0.6019 (t70) cc_final: 0.5578 (t70) outliers start: 6 outliers final: 4 residues processed: 63 average time/residue: 1.2749 time to fit residues: 85.5865 Evaluate side-chains 62 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain S residue 75 MET Chi-restraints excluded: chain T residue 48 GLU Chi-restraints excluded: chain T residue 75 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 60 optimal weight: 0.2980 chunk 96 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** R 6 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.089121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.069872 restraints weight = 39892.074| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.01 r_work: 0.2823 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8531 Z= 0.202 Angle : 0.513 5.363 11567 Z= 0.277 Chirality : 0.041 0.205 1339 Planarity : 0.004 0.043 1531 Dihedral : 4.025 18.617 1214 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.99 % Allowed : 11.68 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.49 (0.25), residues: 1130 helix: 3.08 (0.17), residues: 804 sheet: -0.35 (0.49), residues: 90 loop : 0.68 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 45 TYR 0.012 0.001 TYR G 147 PHE 0.013 0.002 PHE Q 74 TRP 0.007 0.002 TRP H 109 HIS 0.004 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 8531) covalent geometry : angle 0.51291 (11567) hydrogen bonds : bond 0.04974 ( 728) hydrogen bonds : angle 4.09449 ( 2169) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.427 Fit side-chains REVERT: O 85 LEU cc_start: 0.8163 (tp) cc_final: 0.7783 (tm) REVERT: Q 48 GLU cc_start: 0.8051 (pm20) cc_final: 0.7833 (pm20) REVERT: Q 50 GLN cc_start: 0.8247 (tm-30) cc_final: 0.7780 (tm-30) REVERT: R 2 ASP cc_start: 0.6032 (t70) cc_final: 0.5621 (t70) outliers start: 8 outliers final: 4 residues processed: 64 average time/residue: 1.4040 time to fit residues: 95.1613 Evaluate side-chains 64 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain S residue 75 MET Chi-restraints excluded: chain T residue 48 GLU Chi-restraints excluded: chain T residue 75 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 0 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 7 optimal weight: 0.1980 chunk 104 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 79 optimal weight: 0.3980 chunk 65 optimal weight: 0.0870 chunk 45 optimal weight: 0.9980 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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** R 6 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.090082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.070867 restraints weight = 40139.759| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.01 r_work: 0.2838 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8531 Z= 0.154 Angle : 0.490 4.932 11567 Z= 0.262 Chirality : 0.040 0.183 1339 Planarity : 0.004 0.049 1531 Dihedral : 3.949 18.207 1214 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.75 % Allowed : 12.17 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.66 (0.25), residues: 1130 helix: 3.21 (0.17), residues: 804 sheet: -0.21 (0.51), residues: 78 loop : 0.58 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 45 TYR 0.011 0.001 TYR G 147 PHE 0.012 0.001 PHE M 74 TRP 0.005 0.001 TRP H 109 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8531) covalent geometry : angle 0.48986 (11567) hydrogen bonds : bond 0.04702 ( 728) hydrogen bonds : angle 4.00391 ( 2169) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: H 60 ASP cc_start: 0.8747 (p0) cc_final: 0.8539 (p0) REVERT: O 85 LEU cc_start: 0.8151 (tp) cc_final: 0.7773 (tm) REVERT: Q 50 GLN cc_start: 0.8226 (tm-30) cc_final: 0.7629 (tm-30) REVERT: R 2 ASP cc_start: 0.6037 (t70) cc_final: 0.5606 (t70) outliers start: 6 outliers final: 4 residues processed: 66 average time/residue: 1.2810 time to fit residues: 90.1659 Evaluate side-chains 63 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain S residue 75 MET Chi-restraints excluded: chain T residue 48 GLU Chi-restraints excluded: chain T residue 75 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** R 6 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.088831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.069537 restraints weight = 40031.060| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.02 r_work: 0.2818 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8531 Z= 0.217 Angle : 0.535 6.005 11567 Z= 0.288 Chirality : 0.041 0.211 1339 Planarity : 0.004 0.060 1531 Dihedral : 4.040 18.631 1214 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.87 % Allowed : 11.93 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.49 (0.25), residues: 1130 helix: 3.07 (0.17), residues: 804 sheet: -0.34 (0.50), residues: 90 loop : 0.66 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG P 45 TYR 0.012 0.001 TYR G 147 PHE 0.013 0.002 PHE Q 74 TRP 0.008 0.002 TRP H 109 HIS 0.005 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 8531) covalent geometry : angle 0.53463 (11567) hydrogen bonds : bond 0.05020 ( 728) hydrogen bonds : angle 4.10333 ( 2169) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.417 Fit side-chains REVERT: O 85 LEU cc_start: 0.8172 (tp) cc_final: 0.7792 (tm) REVERT: P 45 ARG cc_start: 0.8086 (ttm-80) cc_final: 0.7828 (mtp85) REVERT: Q 50 GLN cc_start: 0.8201 (tm-30) cc_final: 0.7650 (tm-30) REVERT: R 2 ASP cc_start: 0.6117 (t70) cc_final: 0.5723 (t70) outliers start: 7 outliers final: 5 residues processed: 63 average time/residue: 1.2550 time to fit residues: 84.4306 Evaluate side-chains 62 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain S residue 75 MET Chi-restraints excluded: chain T residue 48 GLU Chi-restraints excluded: chain T residue 75 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 48 optimal weight: 0.0980 chunk 11 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 15 optimal weight: 0.0970 chunk 7 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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** R 6 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.089962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.070757 restraints weight = 39839.786| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.00 r_work: 0.2843 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8531 Z= 0.161 Angle : 0.510 6.592 11567 Z= 0.272 Chirality : 0.040 0.186 1339 Planarity : 0.004 0.047 1531 Dihedral : 3.959 18.266 1214 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.99 % Allowed : 11.80 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.65 (0.25), residues: 1130 helix: 3.20 (0.18), residues: 804 sheet: -0.22 (0.51), residues: 78 loop : 0.59 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 45 TYR 0.011 0.001 TYR G 147 PHE 0.012 0.001 PHE M 74 TRP 0.005 0.001 TRP H 109 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8531) covalent geometry : angle 0.50988 (11567) hydrogen bonds : bond 0.04733 ( 728) hydrogen bonds : angle 4.01394 ( 2169) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: O 85 LEU cc_start: 0.8151 (tp) cc_final: 0.7775 (tm) REVERT: P 45 ARG cc_start: 0.8073 (ttm-80) cc_final: 0.7789 (mtp85) REVERT: Q 50 GLN cc_start: 0.8222 (tm-30) cc_final: 0.7821 (tm-30) REVERT: R 2 ASP cc_start: 0.6108 (t70) cc_final: 0.5712 (t70) outliers start: 8 outliers final: 6 residues processed: 62 average time/residue: 1.2058 time to fit residues: 79.6541 Evaluate side-chains 67 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain Q residue 45 ARG Chi-restraints excluded: chain S residue 75 MET Chi-restraints excluded: chain T residue 48 GLU Chi-restraints excluded: chain T residue 75 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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** R 6 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.088672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.069318 restraints weight = 40264.085| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.02 r_work: 0.2806 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8531 Z= 0.234 Angle : 0.546 6.092 11567 Z= 0.294 Chirality : 0.041 0.216 1339 Planarity : 0.004 0.045 1531 Dihedral : 4.063 18.825 1214 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.99 % Allowed : 11.68 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.43 (0.25), residues: 1130 helix: 3.03 (0.17), residues: 804 sheet: -0.34 (0.49), residues: 90 loop : 0.65 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 45 TYR 0.012 0.001 TYR G 147 PHE 0.013 0.002 PHE Q 74 TRP 0.008 0.002 TRP H 109 HIS 0.004 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00520 ( 8531) covalent geometry : angle 0.54608 (11567) hydrogen bonds : bond 0.05090 ( 728) hydrogen bonds : angle 4.12910 ( 2169) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4910.03 seconds wall clock time: 83 minutes 41.41 seconds (5021.41 seconds total)