Starting phenix.real_space_refine on Wed Mar 4 20:28:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7njt_12422/03_2026/7njt_12422.cif Found real_map, /net/cci-nas-00/data/ceres_data/7njt_12422/03_2026/7njt_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/cci-nas-00/data/ceres_data/7njt_12422/03_2026/7njt_12422.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7njt_12422/03_2026/7njt_12422.map" model { file = "/net/cci-nas-00/data/ceres_data/7njt_12422/03_2026/7njt_12422.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7njt_12422/03_2026/7njt_12422.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 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. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.17, per 1000 atoms: 0.19 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 454.8 milliseconds 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: 0.30 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: 3.94 Time building geometry restraints manager: 1.66 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: 0.00 - 1.04: 28342 1.04 - 2.08: 1751 2.08 - 3.12: 57 3.12 - 4.16: 42 4.16 - 5.20: 10 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 2.450 nonbonded pdb=" OE2 GLU a 21 " pdb=" HG1 THR a 26 " model vdw 1.650 2.450 nonbonded pdb=" O VAL a 89 " pdb=" HG SER a 93 " model vdw 1.690 2.450 nonbonded pdb=" O PHE M 78 " pdb=" HG1 THR M 82 " model vdw 1.696 2.450 nonbonded pdb=" OE1 GLU M 48 " pdb=" H GLU M 48 " model vdw 1.721 2.450 ... (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 Time spend for trying shortcut: 0.00 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: 11.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.550 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.630 ------------------------------------------------------------------------------- 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= 0.153 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (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 ARG 0.006 0.000 ARG Q 52 TYR 0.012 0.001 TYR a 145 PHE 0.016 0.001 PHE L 69 TRP 0.011 0.001 TRP a 218 HIS 0.002 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8291) covalent geometry : angle 0.48161 (11265) hydrogen bonds : bond 0.12378 ( 797) hydrogen bonds : angle 6.33011 ( 2379) *********************** 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 to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.432 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: 1.4646 time to fit residues: 156.2564 Evaluate side-chains 62 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 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 = 0.3280 r_free = 0.3280 target = 0.082359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.068650 restraints weight = 43927.047| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.76 r_work: 0.2913 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1091 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= 0.189 Angle : 0.530 5.499 11265 Z= 0.289 Chirality : 0.039 0.122 1326 Planarity : 0.004 0.053 1449 Dihedral : 3.819 15.881 1153 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.29 % Allowed : 7.86 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.12 (0.26), residues: 1098 helix: 2.27 (0.17), residues: 933 sheet: None (None), residues: 0 loop : 0.98 (0.55), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG b 72 TYR 0.024 0.001 TYR a 145 PHE 0.015 0.002 PHE M 69 TRP 0.012 0.001 TRP a 218 HIS 0.002 0.001 HIS a 16 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 8291) covalent geometry : angle 0.52992 (11265) hydrogen bonds : bond 0.05275 ( 797) hydrogen bonds : angle 4.34381 ( 2379) *********************** 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 78 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: L 75 MET cc_start: 0.8708 (tmm) cc_final: 0.8488 (tmt) REVERT: P 65 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: Q 52 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7863 (tpt-90) REVERT: R 48 GLU cc_start: 0.7130 (pp20) cc_final: 0.6919 (pp20) REVERT: S 48 GLU cc_start: 0.7956 (pp20) cc_final: 0.7584 (pp20) REVERT: d 33 GLN cc_start: 0.7078 (OUTLIER) cc_final: 0.6869 (tt0) outliers start: 10 outliers final: 1 residues processed: 74 average time/residue: 1.5170 time to fit residues: 118.5337 Evaluate side-chains 64 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 99 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 7 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.081258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.067421 restraints weight = 44778.655| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.78 r_work: 0.2886 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8291 Z= 0.215 Angle : 0.523 5.361 11265 Z= 0.286 Chirality : 0.039 0.132 1326 Planarity : 0.004 0.052 1449 Dihedral : 3.901 15.821 1153 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.19 % Allowed : 9.79 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.38 (0.26), residues: 1098 helix: 2.48 (0.17), residues: 933 sheet: None (None), residues: 0 loop : 0.84 (0.55), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG b 72 TYR 0.021 0.001 TYR a 145 PHE 0.018 0.002 PHE N 74 TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS a 16 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 8291) covalent geometry : angle 0.52302 (11265) hydrogen bonds : bond 0.05234 ( 797) hydrogen bonds : angle 4.23765 ( 2379) *********************** 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 79 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: P 65 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7591 (mp0) REVERT: Q 52 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7896 (tpt-90) REVERT: d 33 GLN cc_start: 0.7085 (OUTLIER) cc_final: 0.6800 (tt0) REVERT: d 55 ASP cc_start: 0.8247 (m-30) cc_final: 0.7842 (m-30) REVERT: b 66 LYS cc_start: 0.8178 (tmmt) cc_final: 0.7840 (ttpp) outliers start: 17 outliers final: 5 residues processed: 73 average time/residue: 1.4864 time to fit residues: 114.6220 Evaluate side-chains 67 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain P residue 46 GLN Chi-restraints excluded: chain P residue 65 GLU 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 101 optimal weight: 1.9990 chunk 105 optimal weight: 0.0980 chunk 92 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 102 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 ** d 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.082102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.068452 restraints weight = 44098.953| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.76 r_work: 0.2914 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1448 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= 0.156 Angle : 0.495 5.248 11265 Z= 0.268 Chirality : 0.038 0.121 1326 Planarity : 0.004 0.055 1449 Dihedral : 3.822 15.535 1153 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.93 % Allowed : 10.57 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.69 (0.26), residues: 1098 helix: 2.71 (0.17), residues: 933 sheet: None (None), residues: 0 loop : 0.84 (0.55), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG b 72 TYR 0.021 0.001 TYR a 145 PHE 0.013 0.001 PHE a 142 TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8291) covalent geometry : angle 0.49476 (11265) hydrogen bonds : bond 0.04828 ( 797) hydrogen bonds : angle 4.08020 ( 2379) *********************** 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 80 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: M 46 GLN cc_start: 0.7871 (mp10) cc_final: 0.7344 (mp10) REVERT: Q 52 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7889 (tpt-90) REVERT: d 55 ASP cc_start: 0.8250 (m-30) cc_final: 0.7839 (m-30) REVERT: b 66 LYS cc_start: 0.8171 (tmmt) cc_final: 0.7850 (ttpp) outliers start: 15 outliers final: 6 residues processed: 73 average time/residue: 1.4613 time to fit residues: 112.9793 Evaluate side-chains 68 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 192 ASN Chi-restraints excluded: chain a residue 199 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 56 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 87 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 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 229 GLN ** d 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.081778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.068223 restraints weight = 43984.223| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.76 r_work: 0.2903 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1489 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= 0.178 Angle : 0.505 5.273 11265 Z= 0.274 Chirality : 0.038 0.126 1326 Planarity : 0.004 0.038 1449 Dihedral : 3.839 18.161 1153 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.55 % Allowed : 12.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.68 (0.26), residues: 1098 helix: 2.70 (0.17), residues: 933 sheet: None (None), residues: 0 loop : 0.87 (0.55), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 72 TYR 0.020 0.001 TYR a 145 PHE 0.027 0.001 PHE L 69 TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 8291) covalent geometry : angle 0.50470 (11265) hydrogen bonds : bond 0.04886 ( 797) hydrogen bonds : angle 4.06775 ( 2379) *********************** 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 75 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: Q 52 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7891 (tpt-90) REVERT: S 75 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8222 (tmm) REVERT: d 33 GLN cc_start: 0.7029 (OUTLIER) cc_final: 0.6752 (mt0) REVERT: b 66 LYS cc_start: 0.8189 (tmmt) cc_final: 0.7851 (ttpp) outliers start: 12 outliers final: 4 residues processed: 69 average time/residue: 1.5055 time to fit residues: 109.8809 Evaluate side-chains 67 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 40 optimal weight: 1.9990 chunk 69 optimal weight: 0.0770 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.6540 ------------------------------------------------------------------------------- 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 = 0.3271 r_free = 0.3271 target = 0.081849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.068316 restraints weight = 43975.275| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.75 r_work: 0.2908 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8291 Z= 0.167 Angle : 0.502 5.268 11265 Z= 0.270 Chirality : 0.038 0.124 1326 Planarity : 0.004 0.039 1449 Dihedral : 3.810 15.859 1153 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.68 % Allowed : 12.50 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.79 (0.26), residues: 1098 helix: 2.78 (0.17), residues: 933 sheet: None (None), residues: 0 loop : 0.86 (0.55), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 72 TYR 0.020 0.001 TYR a 145 PHE 0.014 0.001 PHE a 142 TRP 0.011 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8291) covalent geometry : angle 0.50205 (11265) hydrogen bonds : bond 0.04801 ( 797) hydrogen bonds : angle 4.03109 ( 2379) *********************** 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 78 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: M 46 GLN cc_start: 0.7873 (mp10) cc_final: 0.7520 (mp-120) REVERT: Q 52 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7905 (tpt-90) REVERT: d 33 GLN cc_start: 0.7037 (OUTLIER) cc_final: 0.6491 (tp40) REVERT: d 55 ASP cc_start: 0.8235 (m-30) cc_final: 0.7835 (m-30) REVERT: b 66 LYS cc_start: 0.8186 (tmmt) cc_final: 0.7846 (ttpp) outliers start: 13 outliers final: 3 residues processed: 69 average time/residue: 1.4492 time to fit residues: 105.7999 Evaluate side-chains 68 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 a residue 199 LEU Chi-restraints excluded: chain d residue 33 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 56 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 103 optimal weight: 0.1980 chunk 105 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3262 r_free = 0.3262 target = 0.081380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.067676 restraints weight = 44324.396| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.76 r_work: 0.2898 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1583 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= 0.186 Angle : 0.509 5.304 11265 Z= 0.275 Chirality : 0.038 0.129 1326 Planarity : 0.004 0.039 1449 Dihedral : 3.829 15.610 1153 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.80 % Allowed : 13.53 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.75 (0.26), residues: 1098 helix: 2.75 (0.17), residues: 933 sheet: None (None), residues: 0 loop : 0.86 (0.55), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG b 72 TYR 0.019 0.001 TYR a 145 PHE 0.015 0.001 PHE a 142 TRP 0.011 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 8291) covalent geometry : angle 0.50858 (11265) hydrogen bonds : bond 0.04882 ( 797) hydrogen bonds : angle 4.05256 ( 2379) *********************** 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 78 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: Q 52 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7918 (tpt-90) REVERT: d 33 GLN cc_start: 0.7078 (OUTLIER) cc_final: 0.6509 (tp40) REVERT: d 55 ASP cc_start: 0.8238 (m-30) cc_final: 0.7843 (m-30) REVERT: b 66 LYS cc_start: 0.8185 (tmmt) cc_final: 0.7861 (ttpp) outliers start: 14 outliers final: 5 residues processed: 69 average time/residue: 1.5039 time to fit residues: 109.7280 Evaluate side-chains 67 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 46 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.081195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.067651 restraints weight = 44506.459| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.75 r_work: 0.2889 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1635 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= 0.190 Angle : 0.516 5.297 11265 Z= 0.279 Chirality : 0.038 0.134 1326 Planarity : 0.004 0.039 1449 Dihedral : 3.849 15.566 1153 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.42 % Allowed : 13.92 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.71 (0.26), residues: 1098 helix: 2.72 (0.17), residues: 933 sheet: None (None), residues: 0 loop : 0.84 (0.54), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 72 TYR 0.019 0.001 TYR a 145 PHE 0.015 0.001 PHE a 142 TRP 0.011 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 8291) covalent geometry : angle 0.51635 (11265) hydrogen bonds : bond 0.04907 ( 797) hydrogen bonds : angle 4.06106 ( 2379) *********************** 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 73 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: M 46 GLN cc_start: 0.7950 (mp10) cc_final: 0.7608 (mp-120) REVERT: Q 52 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7903 (tpt-90) REVERT: d 33 GLN cc_start: 0.7105 (OUTLIER) cc_final: 0.6523 (tp40) REVERT: d 55 ASP cc_start: 0.8225 (m-30) cc_final: 0.7832 (m-30) REVERT: b 66 LYS cc_start: 0.8198 (tmmt) cc_final: 0.7871 (ttpp) outliers start: 11 outliers final: 6 residues processed: 66 average time/residue: 1.4281 time to fit residues: 99.6688 Evaluate side-chains 69 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 S 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 88 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 12 optimal weight: 0.3980 chunk 87 optimal weight: 0.7980 chunk 89 optimal weight: 0.2980 chunk 70 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 92 optimal weight: 0.3980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3284 r_free = 0.3284 target = 0.082644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.069130 restraints weight = 43922.045| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.75 r_work: 0.2921 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8291 Z= 0.141 Angle : 0.492 5.228 11265 Z= 0.263 Chirality : 0.038 0.130 1326 Planarity : 0.004 0.040 1449 Dihedral : 3.740 15.033 1153 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.29 % Allowed : 13.92 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.97 (0.26), residues: 1098 helix: 2.90 (0.17), residues: 933 sheet: None (None), residues: 0 loop : 0.90 (0.55), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG b 72 TYR 0.020 0.001 TYR a 145 PHE 0.012 0.001 PHE a 142 TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8291) covalent geometry : angle 0.49171 (11265) hydrogen bonds : bond 0.04579 ( 797) hydrogen bonds : angle 3.95143 ( 2379) *********************** 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 79 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: M 46 GLN cc_start: 0.7895 (mp10) cc_final: 0.7542 (mp-120) REVERT: O 45 ARG cc_start: 0.8253 (mmt-90) cc_final: 0.8040 (mmt90) REVERT: Q 52 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7849 (tpt-90) REVERT: d 33 GLN cc_start: 0.7048 (OUTLIER) cc_final: 0.6495 (tp40) REVERT: d 55 ASP cc_start: 0.8209 (m-30) cc_final: 0.7813 (m-30) REVERT: b 66 LYS cc_start: 0.8185 (tmmt) cc_final: 0.7857 (ttpp) outliers start: 10 outliers final: 4 residues processed: 74 average time/residue: 1.4216 time to fit residues: 111.1789 Evaluate side-chains 70 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 a residue 67 GLU Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain d residue 33 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 63 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 192 ASN ** d 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.081279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.067714 restraints weight = 44429.872| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.76 r_work: 0.2894 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8291 Z= 0.195 Angle : 0.527 5.567 11265 Z= 0.283 Chirality : 0.038 0.141 1326 Planarity : 0.004 0.040 1449 Dihedral : 3.809 15.489 1153 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.29 % Allowed : 13.66 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.79 (0.26), residues: 1098 helix: 2.78 (0.17), residues: 933 sheet: None (None), residues: 0 loop : 0.86 (0.55), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG b 72 TYR 0.018 0.001 TYR a 145 PHE 0.015 0.001 PHE a 142 TRP 0.011 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 8291) covalent geometry : angle 0.52661 (11265) hydrogen bonds : bond 0.04872 ( 797) hydrogen bonds : angle 4.02902 ( 2379) ********************** 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 to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: M 46 GLN cc_start: 0.7946 (mp10) cc_final: 0.7407 (mp10) REVERT: Q 52 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7873 (tpt-90) REVERT: S 75 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8451 (tmm) REVERT: d 33 GLN cc_start: 0.7077 (OUTLIER) cc_final: 0.6514 (tp40) REVERT: d 55 ASP cc_start: 0.8225 (m-30) cc_final: 0.7832 (m-30) REVERT: b 66 LYS cc_start: 0.8190 (tmmt) cc_final: 0.7856 (ttpp) outliers start: 10 outliers final: 4 residues processed: 68 average time/residue: 1.4706 time to fit residues: 105.8357 Evaluate side-chains 70 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 a residue 67 GLU Chi-restraints excluded: chain a residue 192 ASN Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain d residue 33 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 22 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 97 optimal weight: 0.1980 chunk 56 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 95 optimal weight: 0.1980 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 5 optimal weight: 0.0870 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3263 r_free = 0.3263 target = 0.081440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.067832 restraints weight = 44660.463| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.76 r_work: 0.2896 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.177 8291 Z= 0.219 Angle : 0.883 59.196 11265 Z= 0.536 Chirality : 0.038 0.134 1326 Planarity : 0.004 0.040 1449 Dihedral : 3.847 18.642 1153 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.90 % Allowed : 14.05 % Favored : 85.05 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.77 (0.26), residues: 1098 helix: 2.76 (0.17), residues: 933 sheet: None (None), residues: 0 loop : 0.86 (0.55), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG a 188 TYR 0.019 0.001 TYR a 145 PHE 0.015 0.001 PHE a 142 TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 8291) covalent geometry : angle 0.88270 (11265) hydrogen bonds : bond 0.04821 ( 797) hydrogen bonds : angle 4.03305 ( 2379) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4812.99 seconds wall clock time: 82 minutes 4.91 seconds (4924.91 seconds total)