Starting phenix.real_space_refine on Fri Feb 16 23:09:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkn_12444/02_2024/7nkn_12444.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkn_12444/02_2024/7nkn_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkn_12444/02_2024/7nkn_12444.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkn_12444/02_2024/7nkn_12444.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkn_12444/02_2024/7nkn_12444.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkn_12444/02_2024/7nkn_12444.pdb" } resolution = 2.71 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 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 Residue "G GLU 70": "OE1" <-> "OE2" Residue "G TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 250": "OE1" <-> "OE2" Residue "P PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ASP 32": "OD1" <-> "OD2" Residue "Q GLU 65": "OE1" <-> "OE2" Residue "S GLU 48": "OE1" <-> "OE2" Residue "C GLU 526": "OE1" <-> "OE2" Residue "C ASP 532": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: 8.78, per 1000 atoms: 0.52 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 - 3.50 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: 15.67 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.14 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: 6.32 Time building geometry restraints manager: 15.82 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: 99.98 - 106.82: 253 106.82 - 113.65: 20167 113.65 - 120.48: 6019 120.48 - 127.31: 4262 127.31 - 134.14: 59 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 1.850 nonbonded pdb=" OE1 GLU N 48 " pdb=" H GLU N 48 " model vdw 1.644 1.850 nonbonded pdb=" OE1 GLU O 48 " pdb=" H GLU O 48 " model vdw 1.648 1.850 nonbonded pdb=" OE1 GLU G 213 " pdb=" H GLU G 213 " model vdw 1.670 1.850 nonbonded pdb=" OE1 GLU G 148 " pdb="HH21 ARG G 151 " model vdw 1.671 1.850 ... (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 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: 8.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.300 Extract box with map and model: 26.450 Check model and map are aligned: 0.280 Set scattering table: 0.160 Process input model: 60.710 Find NCS groups from input model: 0.760 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:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.490 ------------------------------------------------------------------------------- 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= 0.185 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 (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: 1.75 (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 TRP 0.004 0.001 TRP H 109 HIS 0.003 0.001 HIS H 38 PHE 0.010 0.001 PHE R 69 TYR 0.010 0.001 TYR G 147 ARG 0.005 0.000 ARG Q 45 *********************** 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 fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.643 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: 3.1283 time to fit residues: 275.1856 Evaluate side-chains 56 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.473 ------------------------------------------------------------------------------- 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: 0.0270 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.2980 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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: 0.8464 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8531 Z= 0.265 Angle : 0.507 5.320 11567 Z= 0.275 Chirality : 0.041 0.203 1339 Planarity : 0.004 0.032 1531 Dihedral : 3.946 18.149 1214 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.50 % Allowed : 7.20 % Favored : 92.30 % 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: 2.98 (0.25), residues: 1130 helix: 2.58 (0.18), residues: 804 sheet: 0.18 (0.54), residues: 78 loop : 0.59 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP H 109 HIS 0.004 0.001 HIS H 38 PHE 0.015 0.002 PHE M 74 TYR 0.013 0.001 TYR G 147 ARG 0.003 0.000 ARG N 45 *********************** 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 71 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 1.386 Fit side-chains REVERT: O 85 LEU cc_start: 0.8155 (tp) cc_final: 0.7847 (tm) REVERT: Q 50 GLN cc_start: 0.8126 (tm-30) cc_final: 0.7730 (tm-30) REVERT: R 2 ASP cc_start: 0.6059 (t70) cc_final: 0.5670 (t70) outliers start: 4 outliers final: 1 residues processed: 71 average time/residue: 2.6813 time to fit residues: 203.7328 Evaluate side-chains 55 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 55 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.8476 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8531 Z= 0.293 Angle : 0.505 5.430 11567 Z= 0.274 Chirality : 0.041 0.208 1339 Planarity : 0.004 0.041 1531 Dihedral : 3.996 18.088 1214 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.87 % Allowed : 8.70 % Favored : 90.43 % 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: 3.32 (0.25), residues: 1130 helix: 2.90 (0.17), residues: 804 sheet: 0.03 (0.51), residues: 90 loop : 0.62 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP H 109 HIS 0.004 0.001 HIS H 38 PHE 0.014 0.002 PHE M 74 TYR 0.012 0.001 TYR G 147 ARG 0.003 0.000 ARG O 45 *********************** 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 71 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 1.414 Fit side-chains REVERT: M 65 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7418 (mm-30) REVERT: O 85 LEU cc_start: 0.8164 (tp) cc_final: 0.7862 (tm) REVERT: Q 50 GLN cc_start: 0.8143 (tm-30) cc_final: 0.7746 (tm-30) REVERT: R 2 ASP cc_start: 0.5955 (t70) cc_final: 0.5589 (t70) outliers start: 7 outliers final: 3 residues processed: 68 average time/residue: 2.6171 time to fit residues: 191.2874 Evaluate side-chains 62 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain Q residue 46 GLN 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 98 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 chunk 47 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 28 optimal weight: 0.0770 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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: 0.8473 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8531 Z= 0.260 Angle : 0.493 5.265 11567 Z= 0.266 Chirality : 0.040 0.198 1339 Planarity : 0.004 0.037 1531 Dihedral : 3.986 18.063 1214 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.87 % Allowed : 10.06 % 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 (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: 3.52 (0.25), residues: 1130 helix: 3.05 (0.17), residues: 804 sheet: 0.09 (0.51), residues: 90 loop : 0.65 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP H 109 HIS 0.004 0.001 HIS H 38 PHE 0.013 0.002 PHE S 74 TYR 0.012 0.001 TYR G 147 ARG 0.003 0.000 ARG O 45 *********************** 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 69 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 65 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7416 (mm-30) REVERT: O 85 LEU cc_start: 0.8167 (tp) cc_final: 0.7866 (tm) REVERT: Q 50 GLN cc_start: 0.8178 (tm-30) cc_final: 0.7781 (tm-30) REVERT: R 2 ASP cc_start: 0.5959 (t70) cc_final: 0.5586 (t70) outliers start: 7 outliers final: 3 residues processed: 65 average time/residue: 2.9142 time to fit residues: 201.4391 Evaluate side-chains 62 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 1.330 ------------------------------------------------------------------------------- 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 88 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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: 0.8493 moved from start: 0.1442 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= 0.359 Angle : 0.528 5.737 11567 Z= 0.287 Chirality : 0.041 0.222 1339 Planarity : 0.004 0.039 1531 Dihedral : 4.106 18.556 1214 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.87 % Allowed : 10.81 % Favored : 88.32 % 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: 1130 helix: 2.96 (0.17), residues: 804 sheet: 0.08 (0.51), residues: 90 loop : 0.62 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 109 HIS 0.004 0.001 HIS H 38 PHE 0.015 0.002 PHE Q 74 TYR 0.013 0.001 TYR G 147 ARG 0.003 0.000 ARG O 45 *********************** 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 71 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 1.423 Fit side-chains revert: symmetry clash REVERT: O 85 LEU cc_start: 0.8163 (tp) cc_final: 0.7854 (tm) REVERT: Q 50 GLN cc_start: 0.8127 (tm-30) cc_final: 0.7665 (tm-30) REVERT: R 2 ASP cc_start: 0.5993 (t70) cc_final: 0.5626 (t70) outliers start: 7 outliers final: 3 residues processed: 67 average time/residue: 2.7519 time to fit residues: 197.7853 Evaluate side-chains 61 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 1.351 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 0.2980 chunk 102 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.8477 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8531 Z= 0.252 Angle : 0.493 5.191 11567 Z= 0.266 Chirality : 0.040 0.196 1339 Planarity : 0.004 0.038 1531 Dihedral : 4.032 18.134 1214 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.75 % Allowed : 11.30 % Favored : 87.95 % 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: 3.57 (0.25), residues: 1130 helix: 3.10 (0.17), residues: 804 sheet: 0.02 (0.50), residues: 90 loop : 0.70 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 109 HIS 0.003 0.001 HIS H 38 PHE 0.013 0.001 PHE Q 74 TYR 0.012 0.001 TYR G 147 ARG 0.003 0.000 ARG O 45 *********************** 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 68 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 1.493 Fit side-chains revert: symmetry clash REVERT: G 41 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7503 (mp0) REVERT: O 85 LEU cc_start: 0.8165 (tp) cc_final: 0.7866 (tm) REVERT: Q 50 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7687 (tm-30) REVERT: R 2 ASP cc_start: 0.5930 (t70) cc_final: 0.5562 (t70) outliers start: 6 outliers final: 3 residues processed: 65 average time/residue: 2.9381 time to fit residues: 203.4703 Evaluate side-chains 61 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 1.285 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 42 optimal weight: 0.9990 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8531 Z= 0.319 Angle : 0.513 5.539 11567 Z= 0.278 Chirality : 0.041 0.212 1339 Planarity : 0.004 0.039 1531 Dihedral : 4.080 18.398 1214 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.75 % Allowed : 11.30 % Favored : 87.95 % 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 (0.25), residues: 1130 helix: 3.03 (0.17), residues: 804 sheet: 0.04 (0.50), residues: 90 loop : 0.66 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 109 HIS 0.004 0.001 HIS H 38 PHE 0.014 0.002 PHE Q 74 TYR 0.013 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) ************************************************ 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 fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 1.494 Fit side-chains revert: symmetry clash REVERT: O 85 LEU cc_start: 0.8169 (tp) cc_final: 0.7868 (tm) REVERT: P 50 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7412 (tm-30) REVERT: Q 50 GLN cc_start: 0.8127 (tm-30) cc_final: 0.7674 (tm-30) REVERT: R 2 ASP cc_start: 0.5926 (t70) cc_final: 0.5590 (t70) outliers start: 6 outliers final: 3 residues processed: 63 average time/residue: 2.8768 time to fit residues: 193.3509 Evaluate side-chains 64 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain P residue 50 GLN Chi-restraints excluded: chain S residue 75 MET 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 63 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 83 optimal weight: 0.2980 chunk 96 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.8482 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8531 Z= 0.278 Angle : 0.502 5.312 11567 Z= 0.271 Chirality : 0.041 0.202 1339 Planarity : 0.004 0.038 1531 Dihedral : 4.045 18.246 1214 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.75 % Allowed : 11.18 % 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 (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: 3.57 (0.25), residues: 1130 helix: 3.10 (0.17), residues: 804 sheet: 0.03 (0.50), residues: 90 loop : 0.67 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP H 109 HIS 0.003 0.001 HIS H 38 PHE 0.013 0.002 PHE Q 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) ************************************************ 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 fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 1.370 Fit side-chains revert: symmetry clash REVERT: G 41 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7492 (mp0) REVERT: O 85 LEU cc_start: 0.8169 (tp) cc_final: 0.7871 (tm) REVERT: P 50 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7399 (tm-30) REVERT: Q 50 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7687 (tm-30) REVERT: R 2 ASP cc_start: 0.6016 (t70) cc_final: 0.5689 (t70) outliers start: 6 outliers final: 3 residues processed: 63 average time/residue: 2.8476 time to fit residues: 191.6503 Evaluate side-chains 65 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain P residue 50 GLN Chi-restraints excluded: chain S residue 75 MET 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 98 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 104 optimal weight: 0.5980 chunk 63 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8531 Z= 0.300 Angle : 0.516 5.425 11567 Z= 0.278 Chirality : 0.041 0.208 1339 Planarity : 0.004 0.038 1531 Dihedral : 4.059 18.319 1214 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.82 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 (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: 3.53 (0.25), residues: 1130 helix: 3.07 (0.17), residues: 804 sheet: 0.02 (0.50), residues: 90 loop : 0.65 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP H 109 HIS 0.003 0.001 HIS H 38 PHE 0.013 0.002 PHE Q 74 TYR 0.012 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) ************************************************ 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 69 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 85 LEU cc_start: 0.8171 (tp) cc_final: 0.7873 (tm) REVERT: P 50 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7359 (tm-30) REVERT: Q 50 GLN cc_start: 0.8135 (tm-30) cc_final: 0.7686 (tm-30) REVERT: R 2 ASP cc_start: 0.6014 (t70) cc_final: 0.5688 (t70) outliers start: 7 outliers final: 4 residues processed: 63 average time/residue: 2.7151 time to fit residues: 184.3141 Evaluate side-chains 64 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain P residue 50 GLN Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain S residue 75 MET 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 49 optimal weight: 0.2980 chunk 72 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.8484 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8531 Z= 0.293 Angle : 0.516 5.387 11567 Z= 0.278 Chirality : 0.041 0.205 1339 Planarity : 0.004 0.039 1531 Dihedral : 4.056 18.298 1214 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.62 % Allowed : 12.05 % 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 (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: 3.53 (0.25), residues: 1130 helix: 3.07 (0.17), residues: 804 sheet: 0.02 (0.50), residues: 90 loop : 0.65 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP H 109 HIS 0.003 0.001 HIS H 38 PHE 0.013 0.002 PHE Q 74 TYR 0.012 0.001 TYR G 147 ARG 0.004 0.000 ARG O 45 ********************** 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 65 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 1.427 Fit side-chains revert: symmetry clash REVERT: O 85 LEU cc_start: 0.8171 (tp) cc_final: 0.7874 (tm) REVERT: P 50 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7358 (tm-30) REVERT: Q 50 GLN cc_start: 0.8131 (tm-30) cc_final: 0.7683 (tm-30) REVERT: R 2 ASP cc_start: 0.5969 (t70) cc_final: 0.5649 (t70) outliers start: 5 outliers final: 4 residues processed: 60 average time/residue: 2.6666 time to fit residues: 171.7225 Evaluate side-chains 63 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain P residue 50 GLN Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain S residue 75 MET 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 80 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 89 optimal weight: 0.0370 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.089486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.070211 restraints weight = 39795.881| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.00 r_work: 0.2823 rms_B_bonded: 2.31 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: 0.8685 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8531 Z= 0.265 Angle : 0.509 5.597 11567 Z= 0.273 Chirality : 0.040 0.198 1339 Planarity : 0.004 0.039 1531 Dihedral : 4.016 18.115 1214 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.62 % Allowed : 12.17 % 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 (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: 3.60 (0.25), residues: 1130 helix: 3.12 (0.18), residues: 804 sheet: 0.04 (0.50), residues: 90 loop : 0.68 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP H 109 HIS 0.003 0.001 HIS H 38 PHE 0.013 0.001 PHE Q 74 TYR 0.012 0.001 TYR G 147 ARG 0.004 0.000 ARG O 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5647.82 seconds wall clock time: 100 minutes 4.56 seconds (6004.56 seconds total)