Starting phenix.real_space_refine on Fri Feb 16 20:17:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njt_12422/02_2024/7njt_12422.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njt_12422/02_2024/7njt_12422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njt_12422/02_2024/7njt_12422.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njt_12422/02_2024/7njt_12422.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njt_12422/02_2024/7njt_12422.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njt_12422/02_2024/7njt_12422.pdb" } resolution = 2.75 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 28 5.16 5 C 5363 2.51 5 N 1320 2.21 5 O 1412 1.98 5 H 8352 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L ASP 32": "OD1" <-> "OD2" Residue "N PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ASP 32": "OD1" <-> "OD2" Residue "a TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 246": "OE1" <-> "OE2" Residue "b GLU 61": "OE1" <-> "OE2" Residue "b ASP 70": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16475 Number of models: 1 Model: "" Number of chains: 12 Chain: "L" 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: "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: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "O" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "P" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "Q" 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: "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: "a" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3767 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 10, 'TRANS': 227} Chain: "d" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 952 Classifications: {'peptide': 61} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "b" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 968 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Time building chain proxies: 7.22, per 1000 atoms: 0.44 Number of scatterers: 16475 At special positions: 0 Unit cell: (92.96, 77.19, 121.18, 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 28 16.00 O 1412 8.00 N 1320 7.00 C 5363 6.00 H 8352 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: 13.52 Conformation dependent library (CDL) restraints added in 2.2 seconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1912 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 2 sheets defined 87.9% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'L' and resid 4 through 46 removed outlier: 3.612A pdb=" N ILE L 8 " --> pdb=" O ASP L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 51 removed outlier: 4.302A pdb=" N GLY L 51 " --> pdb=" O GLU L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 81 removed outlier: 4.241A pdb=" N ALA L 67 " --> pdb=" O LEU L 63 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR L 68 " --> pdb=" O VAL L 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 46 removed outlier: 3.548A pdb=" N ILE M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 80 removed outlier: 4.529A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) Proline residue: M 56 - end of helix removed outlier: 3.854A pdb=" N TYR M 68 " --> pdb=" O VAL M 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 46 removed outlier: 3.666A pdb=" N ILE N 8 " --> pdb=" O ASP N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 81 removed outlier: 4.449A pdb=" N THR N 55 " --> pdb=" O GLY N 51 " (cutoff:3.500A) Proline residue: N 56 - end of helix Processing helix chain 'O' and resid 4 through 46 Processing helix chain 'O' and resid 49 through 81 removed outlier: 5.057A pdb=" N THR O 55 " --> pdb=" O GLY O 51 " (cutoff:3.500A) Proline residue: O 56 - end of helix removed outlier: 3.858A pdb=" N ALA O 67 " --> pdb=" O LEU O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 46 removed outlier: 3.642A pdb=" N ILE P 8 " --> pdb=" O ASP P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 80 removed outlier: 3.660A pdb=" N PHE P 54 " --> pdb=" O GLN P 50 " (cutoff:3.500A) removed outlier: 4.568A 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 removed outlier: 3.687A pdb=" N ILE Q 8 " --> pdb=" O ASP Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 80 removed outlier: 3.739A pdb=" N PHE Q 54 " --> pdb=" O GLN Q 50 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR Q 55 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) Proline residue: Q 56 - end of helix Processing helix chain 'R' and resid 4 through 46 Processing helix chain 'R' and resid 49 through 81 removed outlier: 3.835A pdb=" N PHE R 54 " --> pdb=" O GLN R 50 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N THR R 55 " --> pdb=" O GLY R 51 " (cutoff:3.500A) Proline residue: R 56 - end of helix Processing helix chain 'S' and resid 4 through 46 Processing helix chain 'S' and resid 49 through 81 removed outlier: 4.552A pdb=" N THR S 55 " --> pdb=" O GLY S 51 " (cutoff:3.500A) Proline residue: S 56 - end of helix removed outlier: 4.038A pdb=" N ALA S 67 " --> pdb=" O LEU S 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 46 removed outlier: 3.683A pdb=" N ILE T 8 " --> pdb=" O ASP T 4 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 81 removed outlier: 3.964A pdb=" N THR T 55 " --> pdb=" O GLY T 51 " (cutoff:3.500A) Proline residue: T 56 - end of helix removed outlier: 4.201A pdb=" N ALA T 67 " --> pdb=" O LEU T 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 51 Processing helix chain 'a' and resid 60 through 81 Processing helix chain 'a' and resid 88 through 106 Processing helix chain 'a' and resid 107 through 109 No H-bonds generated for 'chain 'a' and resid 107 through 109' Processing helix chain 'a' and resid 126 through 129 Processing helix chain 'a' and resid 130 through 153 removed outlier: 3.557A pdb=" N VAL a 134 " --> pdb=" O ASP a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 153 through 165 removed outlier: 4.020A pdb=" N HIS a 158 " --> pdb=" O GLY a 154 " (cutoff:3.500A) Proline residue: a 159 - end of helix Processing helix chain 'a' and resid 167 through 169 No H-bonds generated for 'chain 'a' and resid 167 through 169' Processing helix chain 'a' and resid 170 through 204 Proline residue: a 182 - end of helix removed outlier: 3.823A pdb=" N LEU a 189 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY a 196 " --> pdb=" O ASN a 192 " (cutoff:3.500A) Processing helix chain 'a' and resid 207 through 245 removed outlier: 5.711A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix removed outlier: 3.902A pdb=" N PHE a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 22 Processing helix chain 'd' and resid 22 through 61 Processing helix chain 'b' and resid 29 through 49 removed outlier: 3.560A pdb=" N ALA b 33 " --> pdb=" O GLY b 29 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL b 49 " --> pdb=" O ILE b 45 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 84 removed outlier: 3.715A pdb=" N ALA b 79 " --> pdb=" O ALA b 75 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN b 82 " --> pdb=" O VAL b 78 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 20 through 22 Processing sheet with id=AA2, first strand: chain 'a' and resid 112 through 114 797 hydrogen bonds defined for protein. 2379 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: 6.33 Time building geometry restraints manager: 13.97 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: 8351 1.03 - 1.23: 2 1.23 - 1.42: 3375 1.42 - 1.61: 4860 1.61 - 1.80: 55 Bond restraints: 16643 Sorted by residual: bond pdb=" CB MET Q 21 " pdb=" CG MET Q 21 " ideal model delta sigma weight residual 1.520 1.499 0.021 3.00e-02 1.11e+03 5.08e-01 bond pdb=" C PHE N 58 " pdb=" O PHE N 58 " ideal model delta sigma weight residual 1.236 1.228 0.008 1.29e-02 6.01e+03 3.77e-01 bond pdb=" CB ASN L 71 " pdb=" CG ASN L 71 " ideal model delta sigma weight residual 1.516 1.501 0.015 2.50e-02 1.60e+03 3.72e-01 bond pdb=" C PHE R 58 " pdb=" O PHE R 58 " ideal model delta sigma weight residual 1.237 1.230 0.007 1.19e-02 7.06e+03 3.51e-01 bond pdb=" C VAL L 61 " pdb=" N GLY L 62 " ideal model delta sigma weight residual 1.334 1.327 0.007 1.23e-02 6.61e+03 3.45e-01 ... (remaining 16638 not shown) Histogram of bond angle deviations from ideal: 99.61 - 106.49: 234 106.49 - 113.37: 19714 113.37 - 120.24: 5746 120.24 - 127.12: 4436 127.12 - 133.99: 72 Bond angle restraints: 30202 Sorted by residual: angle pdb=" C ILE a 155 " pdb=" N VAL a 156 " pdb=" CA VAL a 156 " ideal model delta sigma weight residual 123.08 120.47 2.61 1.01e+00 9.80e-01 6.66e+00 angle pdb=" CA TYR a 145 " pdb=" CB TYR a 145 " pdb=" CG TYR a 145 " ideal model delta sigma weight residual 113.90 118.38 -4.48 1.80e+00 3.09e-01 6.19e+00 angle pdb=" C CYS a 144 " pdb=" N TYR a 145 " pdb=" CA TYR a 145 " ideal model delta sigma weight residual 120.68 116.87 3.81 1.70e+00 3.46e-01 5.02e+00 angle pdb=" CA VAL a 156 " pdb=" C VAL a 156 " pdb=" N GLY a 157 " ideal model delta sigma weight residual 117.23 119.36 -2.13 1.01e+00 9.80e-01 4.43e+00 angle pdb=" N VAL a 156 " pdb=" CA VAL a 156 " pdb=" C VAL a 156 " ideal model delta sigma weight residual 111.56 113.18 -1.62 8.60e-01 1.35e+00 3.54e+00 ... (remaining 30197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.29: 6659 16.29 - 32.57: 695 32.57 - 48.86: 160 48.86 - 65.15: 264 65.15 - 81.43: 5 Dihedral angle restraints: 7783 sinusoidal: 4162 harmonic: 3621 Sorted by residual: dihedral pdb=" CA ASP T 2 " pdb=" CB ASP T 2 " pdb=" CG ASP T 2 " pdb=" OD1 ASP T 2 " ideal model delta sinusoidal sigma weight residual -30.00 -88.07 58.07 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA PHE P 78 " pdb=" C PHE P 78 " pdb=" N VAL P 79 " pdb=" CA VAL P 79 " ideal model delta harmonic sigma weight residual -180.00 -164.78 -15.22 0 5.00e+00 4.00e-02 9.27e+00 dihedral pdb=" CA ASP a 130 " pdb=" CB ASP a 130 " pdb=" CG ASP a 130 " pdb=" OD1 ASP a 130 " ideal model delta sinusoidal sigma weight residual -30.00 -80.81 50.81 1 2.00e+01 2.50e-03 8.84e+00 ... (remaining 7780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 768 0.025 - 0.050: 292 0.050 - 0.075: 162 0.075 - 0.100: 94 0.100 - 0.125: 10 Chirality restraints: 1326 Sorted by residual: chirality pdb=" CA PRO L 47 " pdb=" N PRO L 47 " pdb=" C PRO L 47 " pdb=" CB PRO L 47 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.89e-01 chirality pdb=" CA ILE a 81 " pdb=" N ILE a 81 " pdb=" C ILE a 81 " pdb=" CB ILE a 81 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.45e-01 chirality pdb=" CA TYR a 145 " pdb=" N TYR a 145 " pdb=" C TYR a 145 " pdb=" CB TYR a 145 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.12 2.00e-01 2.50e+01 3.31e-01 ... (remaining 1323 not shown) Planarity restraints: 2508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG Q 52 " -0.154 9.50e-02 1.11e+02 5.17e-02 3.13e+00 pdb=" NE ARG Q 52 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG Q 52 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG Q 52 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG Q 52 " -0.003 2.00e-02 2.50e+03 pdb="HH11 ARG Q 52 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG Q 52 " 0.002 2.00e-02 2.50e+03 pdb="HH21 ARG Q 52 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG Q 52 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA a 86 " 0.028 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO a 87 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO a 87 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO a 87 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA Q 66 " 0.008 2.00e-02 2.50e+03 1.58e-02 2.48e+00 pdb=" C ALA Q 66 " -0.027 2.00e-02 2.50e+03 pdb=" O ALA Q 66 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA Q 67 " 0.009 2.00e-02 2.50e+03 ... (remaining 2505 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 1254 2.22 - 2.82: 36368 2.82 - 3.41: 49095 3.41 - 4.01: 65305 4.01 - 4.60: 101315 Nonbonded interactions: 253337 Sorted by model distance: nonbonded pdb=" OD1 ASN a 132 " pdb=" H ASN b 28 " model vdw 1.626 1.850 nonbonded pdb=" OE2 GLU a 21 " pdb=" HG1 THR a 26 " model vdw 1.650 1.850 nonbonded pdb=" O VAL a 89 " pdb=" HG SER a 93 " model vdw 1.690 1.850 nonbonded pdb=" O PHE M 78 " pdb=" HG1 THR M 82 " model vdw 1.696 1.850 nonbonded pdb=" OE1 GLU M 48 " pdb=" H GLU M 48 " model vdw 1.721 1.850 ... (remaining 253332 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' 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' 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 'O' selection = chain 'P' selection = chain 'Q' 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: 7.990 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: 0.250 Extract box with map and model: 25.160 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 55.100 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 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:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 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 0.025 8291 Z= 0.202 Angle : 0.482 5.200 11265 Z= 0.270 Chirality : 0.038 0.125 1326 Planarity : 0.005 0.070 1449 Dihedral : 13.469 81.433 2802 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.27), residues: 1098 helix: 1.64 (0.18), residues: 927 sheet: None (None), residues: 0 loop : 0.89 (0.53), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.002 0.001 HIS a 146 PHE 0.016 0.001 PHE L 69 TYR 0.012 0.001 TYR a 145 ARG 0.006 0.000 ARG Q 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 75 MET cc_start: 0.8232 (tmm) cc_final: 0.8021 (tmt) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 2.8184 time to fit residues: 302.2735 Evaluate side-chains 63 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8291 Z= 0.293 Angle : 0.530 5.404 11265 Z= 0.291 Chirality : 0.039 0.126 1326 Planarity : 0.004 0.049 1449 Dihedral : 3.838 15.902 1153 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.29 % Allowed : 8.25 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.06 (0.26), residues: 1098 helix: 2.23 (0.17), residues: 932 sheet: None (None), residues: 0 loop : 1.02 (0.55), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.002 0.001 HIS a 158 PHE 0.015 0.002 PHE M 69 TYR 0.023 0.001 TYR a 145 ARG 0.012 0.000 ARG b 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 1.117 Fit side-chains revert: symmetry clash REVERT: L 75 MET cc_start: 0.8345 (tmm) cc_final: 0.8121 (tmt) REVERT: P 65 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: Q 52 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7214 (tpt-90) REVERT: S 48 GLU cc_start: 0.7574 (pp20) cc_final: 0.7263 (pp20) REVERT: d 33 GLN cc_start: 0.6797 (OUTLIER) cc_final: 0.6458 (tt0) outliers start: 10 outliers final: 1 residues processed: 70 average time/residue: 3.0120 time to fit residues: 223.7130 Evaluate side-chains 63 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain Q residue 52 ARG Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain d residue 33 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 105 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8291 Z= 0.256 Angle : 0.507 5.260 11265 Z= 0.275 Chirality : 0.039 0.126 1326 Planarity : 0.004 0.055 1449 Dihedral : 3.864 15.550 1153 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.68 % Allowed : 9.41 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.52 (0.26), residues: 1098 helix: 2.56 (0.17), residues: 933 sheet: None (None), residues: 0 loop : 1.03 (0.55), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.002 0.001 HIS a 158 PHE 0.017 0.002 PHE N 74 TYR 0.022 0.001 TYR a 145 ARG 0.011 0.000 ARG b 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 62 time to evaluate : 1.385 Fit side-chains revert: symmetry clash REVERT: L 75 MET cc_start: 0.8401 (tmm) cc_final: 0.8121 (tmt) REVERT: Q 52 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7251 (tpt-90) REVERT: d 33 GLN cc_start: 0.6698 (OUTLIER) cc_final: 0.6365 (tt0) REVERT: d 55 ASP cc_start: 0.8089 (m-30) cc_final: 0.7705 (m-30) REVERT: b 66 LYS cc_start: 0.7911 (tmmt) cc_final: 0.7587 (ttpp) outliers start: 13 outliers final: 3 residues processed: 71 average time/residue: 2.8174 time to fit residues: 213.3374 Evaluate side-chains 65 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 52 ARG Chi-restraints excluded: chain S residue 75 MET Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain d residue 33 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 97 optimal weight: 0.4980 chunk 103 optimal weight: 0.3980 chunk 51 optimal weight: 0.8980 chunk 92 optimal weight: 0.0980 chunk 27 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 7 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8291 Z= 0.209 Angle : 0.487 5.298 11265 Z= 0.262 Chirality : 0.038 0.122 1326 Planarity : 0.004 0.039 1449 Dihedral : 3.779 15.277 1153 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.42 % Allowed : 10.70 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.82 (0.26), residues: 1098 helix: 2.78 (0.17), residues: 933 sheet: None (None), residues: 0 loop : 1.03 (0.55), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.002 0.001 HIS a 158 PHE 0.013 0.001 PHE a 142 TYR 0.021 0.001 TYR a 145 ARG 0.008 0.000 ARG b 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 46 GLN cc_start: 0.7597 (mp10) cc_final: 0.7138 (mp10) REVERT: Q 52 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7266 (tpt-90) REVERT: d 33 GLN cc_start: 0.6693 (OUTLIER) cc_final: 0.6480 (tt0) REVERT: d 55 ASP cc_start: 0.8076 (m-30) cc_final: 0.7692 (m-30) REVERT: b 66 LYS cc_start: 0.7913 (tmmt) cc_final: 0.7589 (ttpp) outliers start: 11 outliers final: 6 residues processed: 70 average time/residue: 2.8346 time to fit residues: 211.8243 Evaluate side-chains 68 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain Q residue 52 ARG Chi-restraints excluded: chain S residue 75 MET Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain d residue 7 GLN Chi-restraints excluded: chain d residue 33 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8291 Z= 0.287 Angle : 0.508 5.339 11265 Z= 0.275 Chirality : 0.038 0.129 1326 Planarity : 0.004 0.040 1449 Dihedral : 3.854 15.588 1153 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.93 % Allowed : 10.95 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.70 (0.26), residues: 1098 helix: 2.70 (0.17), residues: 933 sheet: None (None), residues: 0 loop : 0.97 (0.54), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 PHE 0.017 0.001 PHE S 74 TYR 0.019 0.001 TYR a 145 ARG 0.002 0.000 ARG b 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 61 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 52 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7260 (tpt-90) REVERT: S 75 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7819 (tmm) REVERT: d 33 GLN cc_start: 0.6694 (OUTLIER) cc_final: 0.6428 (tt0) REVERT: b 66 LYS cc_start: 0.7921 (tmmt) cc_final: 0.7591 (ttpp) outliers start: 15 outliers final: 6 residues processed: 70 average time/residue: 2.9404 time to fit residues: 218.5019 Evaluate side-chains 69 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 71 ASN Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain Q residue 52 ARG Chi-restraints excluded: chain S residue 75 MET Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain d residue 7 GLN Chi-restraints excluded: chain d residue 33 GLN Chi-restraints excluded: chain b residue 76 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 7 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8291 Z= 0.249 Angle : 0.501 5.310 11265 Z= 0.270 Chirality : 0.038 0.125 1326 Planarity : 0.004 0.040 1449 Dihedral : 3.835 15.548 1153 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.80 % Allowed : 11.98 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.78 (0.26), residues: 1098 helix: 2.75 (0.17), residues: 933 sheet: None (None), residues: 0 loop : 0.96 (0.54), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 PHE 0.015 0.001 PHE S 74 TYR 0.020 0.001 TYR a 145 ARG 0.003 0.000 ARG b 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 1.282 Fit side-chains revert: symmetry clash REVERT: M 46 GLN cc_start: 0.7682 (mp10) cc_final: 0.7236 (mp10) REVERT: Q 52 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7274 (tpt-90) REVERT: S 75 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7801 (tmm) REVERT: d 33 GLN cc_start: 0.6694 (OUTLIER) cc_final: 0.6459 (tt0) REVERT: d 55 ASP cc_start: 0.8086 (m-30) cc_final: 0.7704 (m-30) REVERT: b 66 LYS cc_start: 0.7912 (tmmt) cc_final: 0.7596 (ttpp) outliers start: 14 outliers final: 7 residues processed: 69 average time/residue: 2.9114 time to fit residues: 213.6444 Evaluate side-chains 71 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 71 ASN Chi-restraints excluded: chain O residue 21 MET Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain Q residue 52 ARG Chi-restraints excluded: chain R residue 48 GLU Chi-restraints excluded: chain S residue 75 MET Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain d residue 33 GLN Chi-restraints excluded: chain b residue 76 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 103 optimal weight: 0.1980 chunk 64 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 63 optimal weight: 0.1980 chunk 41 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 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 : 0.004 0.034 8291 Z= 0.229 Angle : 0.496 5.280 11265 Z= 0.267 Chirality : 0.038 0.132 1326 Planarity : 0.004 0.040 1449 Dihedral : 3.804 15.444 1153 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.68 % Allowed : 12.63 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.83 (0.26), residues: 1098 helix: 2.79 (0.17), residues: 933 sheet: None (None), residues: 0 loop : 1.00 (0.54), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 PHE 0.015 0.001 PHE S 74 TYR 0.020 0.001 TYR a 145 ARG 0.004 0.000 ARG b 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 1.220 Fit side-chains revert: symmetry clash REVERT: M 46 GLN cc_start: 0.7664 (mp10) cc_final: 0.7168 (mp10) REVERT: Q 52 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7227 (tpt-90) REVERT: S 75 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7803 (tmm) REVERT: d 33 GLN cc_start: 0.6674 (OUTLIER) cc_final: 0.6445 (tt0) REVERT: b 66 LYS cc_start: 0.7909 (tmmt) cc_final: 0.7596 (ttpp) outliers start: 13 outliers final: 6 residues processed: 69 average time/residue: 2.9351 time to fit residues: 215.1204 Evaluate side-chains 71 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 71 ASN Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain Q residue 52 ARG Chi-restraints excluded: chain S residue 75 MET Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain a residue 67 GLU Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain d residue 33 GLN Chi-restraints excluded: chain b residue 76 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8291 Z= 0.267 Angle : 0.509 5.306 11265 Z= 0.275 Chirality : 0.038 0.133 1326 Planarity : 0.004 0.058 1449 Dihedral : 3.842 15.657 1153 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.42 % Allowed : 12.89 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.78 (0.26), residues: 1098 helix: 2.75 (0.17), residues: 933 sheet: None (None), residues: 0 loop : 0.98 (0.55), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 PHE 0.015 0.001 PHE S 74 TYR 0.019 0.001 TYR a 145 ARG 0.007 0.000 ARG O 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 1.358 Fit side-chains revert: symmetry clash REVERT: M 46 GLN cc_start: 0.7664 (mp10) cc_final: 0.7160 (mp10) REVERT: Q 52 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7227 (tpt-90) REVERT: S 75 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7796 (tmm) REVERT: d 33 GLN cc_start: 0.6690 (OUTLIER) cc_final: 0.6450 (tt0) REVERT: d 55 ASP cc_start: 0.8089 (m-30) cc_final: 0.7733 (m-30) REVERT: b 66 LYS cc_start: 0.7906 (tmmt) cc_final: 0.7588 (ttpp) outliers start: 11 outliers final: 6 residues processed: 68 average time/residue: 2.9015 time to fit residues: 209.7519 Evaluate side-chains 70 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 71 ASN Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain Q residue 46 GLN Chi-restraints excluded: chain Q residue 52 ARG Chi-restraints excluded: chain S residue 75 MET Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain d residue 33 GLN Chi-restraints excluded: chain b residue 76 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.9990 chunk 96 optimal weight: 0.0980 chunk 98 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8291 Z= 0.237 Angle : 0.501 5.276 11265 Z= 0.270 Chirality : 0.038 0.124 1326 Planarity : 0.004 0.054 1449 Dihedral : 3.819 15.480 1153 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.29 % Allowed : 13.14 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.84 (0.26), residues: 1098 helix: 2.79 (0.17), residues: 933 sheet: None (None), residues: 0 loop : 1.01 (0.55), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 PHE 0.015 0.001 PHE S 74 TYR 0.019 0.001 TYR a 145 ARG 0.007 0.000 ARG O 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 1.361 Fit side-chains revert: symmetry clash REVERT: M 46 GLN cc_start: 0.7666 (mp10) cc_final: 0.7160 (mp10) REVERT: Q 52 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7220 (tpt-90) REVERT: S 75 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.8035 (tmm) REVERT: d 33 GLN cc_start: 0.6665 (OUTLIER) cc_final: 0.6396 (tt0) REVERT: d 55 ASP cc_start: 0.8087 (m-30) cc_final: 0.7729 (m-30) REVERT: b 66 LYS cc_start: 0.7901 (tmmt) cc_final: 0.7581 (ttpp) outliers start: 10 outliers final: 6 residues processed: 67 average time/residue: 3.0356 time to fit residues: 216.0808 Evaluate side-chains 70 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 71 ASN Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain Q residue 46 GLN Chi-restraints excluded: chain Q residue 52 ARG Chi-restraints excluded: chain S residue 75 MET Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain d residue 33 GLN Chi-restraints excluded: chain b residue 76 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 90 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8291 Z= 0.227 Angle : 0.503 5.487 11265 Z= 0.270 Chirality : 0.038 0.138 1326 Planarity : 0.004 0.057 1449 Dihedral : 3.791 15.417 1153 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.16 % Allowed : 13.40 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.89 (0.26), residues: 1098 helix: 2.82 (0.17), residues: 933 sheet: None (None), residues: 0 loop : 1.05 (0.55), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 PHE 0.015 0.001 PHE S 74 TYR 0.019 0.001 TYR a 145 ARG 0.007 0.000 ARG O 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 1.215 Fit side-chains revert: symmetry clash REVERT: M 46 GLN cc_start: 0.7656 (mp10) cc_final: 0.7158 (mp10) REVERT: Q 52 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7212 (tpt-90) REVERT: S 75 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.8054 (tmm) REVERT: d 33 GLN cc_start: 0.6649 (OUTLIER) cc_final: 0.6384 (tt0) REVERT: d 55 ASP cc_start: 0.8086 (m-30) cc_final: 0.7730 (m-30) REVERT: b 66 LYS cc_start: 0.7904 (tmmt) cc_final: 0.7580 (ttpp) outliers start: 9 outliers final: 6 residues processed: 69 average time/residue: 2.9783 time to fit residues: 218.3409 Evaluate side-chains 71 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 71 ASN Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain Q residue 46 GLN Chi-restraints excluded: chain Q residue 52 ARG Chi-restraints excluded: chain S residue 75 MET Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain d residue 33 GLN Chi-restraints excluded: chain b residue 76 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 0.2980 chunk 85 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 7 GLN ** 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 = 0.3265 r_free = 0.3265 target = 0.081671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.068085 restraints weight = 44329.127| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.76 r_work: 0.2900 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8291 Z= 0.246 Angle : 0.509 5.276 11265 Z= 0.273 Chirality : 0.038 0.130 1326 Planarity : 0.004 0.055 1449 Dihedral : 3.806 15.412 1153 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.16 % Allowed : 13.40 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.86 (0.26), residues: 1098 helix: 2.81 (0.17), residues: 933 sheet: None (None), residues: 0 loop : 1.03 (0.55), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 PHE 0.015 0.001 PHE S 74 TYR 0.019 0.001 TYR a 145 ARG 0.007 0.000 ARG O 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5449.11 seconds wall clock time: 96 minutes 38.88 seconds (5798.88 seconds total)