Starting phenix.real_space_refine on Wed Mar 4 20:18:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nju_12423/03_2026/7nju_12423.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nju_12423/03_2026/7nju_12423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nju_12423/03_2026/7nju_12423.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nju_12423/03_2026/7nju_12423.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nju_12423/03_2026/7nju_12423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nju_12423/03_2026/7nju_12423.map" } resolution = 3.74 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 5350 2.51 5 N 1317 2.21 5 O 1402 1.98 5 H 8341 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 16438 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: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "N" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "O" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "P" Number of atoms: 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: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "S" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} 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: "b" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 979 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} 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} Time building chain proxies: 2.89, per 1000 atoms: 0.18 Number of scatterers: 16438 At special positions: 0 Unit cell: (92.96, 78.02, 120.35, 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 1402 8.00 N 1317 7.00 C 5350 6.00 H 8341 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: 1.39 Conformation dependent library (CDL) restraints added in 432.0 milliseconds 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1906 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 2 sheets defined 87.5% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'L' and resid 4 through 46 removed outlier: 3.574A pdb=" N ILE L 8 " --> pdb=" O ASP L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 81 removed outlier: 4.323A pdb=" N THR L 55 " --> pdb=" O GLY L 51 " (cutoff:3.500A) Proline residue: L 56 - end of helix removed outlier: 4.177A pdb=" N ALA L 67 " --> pdb=" O LEU L 63 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR L 68 " --> pdb=" O VAL L 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 46 removed outlier: 3.631A pdb=" N ILE M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 80 removed outlier: 3.669A pdb=" N PHE M 54 " --> pdb=" O GLN M 50 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) Proline residue: M 56 - end of helix removed outlier: 3.568A pdb=" N ILE M 59 " --> pdb=" O THR M 55 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR M 68 " --> pdb=" O VAL M 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 46 removed outlier: 3.911A pdb=" N ILE N 8 " --> pdb=" O ASP N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 80 removed outlier: 3.903A pdb=" N PHE N 54 " --> pdb=" O GLN N 50 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR N 55 " --> pdb=" O GLY N 51 " (cutoff:3.500A) Proline residue: N 56 - end of helix removed outlier: 3.637A pdb=" N ILE N 59 " --> pdb=" O THR N 55 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU N 63 " --> pdb=" O ILE N 59 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA N 67 " --> pdb=" O LEU N 63 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR N 68 " --> pdb=" O VAL N 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 46 removed outlier: 3.646A pdb=" N ILE O 8 " --> pdb=" O ASP O 4 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 80 removed outlier: 4.555A pdb=" N THR O 55 " --> pdb=" O GLY O 51 " (cutoff:3.500A) Proline residue: O 56 - end of helix removed outlier: 3.530A pdb=" N ILE O 59 " --> pdb=" O THR O 55 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA O 67 " --> pdb=" O LEU O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 46 removed outlier: 3.695A pdb=" N ILE P 8 " --> pdb=" O ASP P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 80 removed outlier: 3.802A pdb=" N PHE P 54 " --> pdb=" O GLN P 50 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N THR P 55 " --> pdb=" O GLY P 51 " (cutoff:3.500A) Proline residue: P 56 - end of helix removed outlier: 3.555A pdb=" N LEU P 63 " --> pdb=" O ILE P 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 46 removed outlier: 3.640A pdb=" N ILE Q 8 " --> pdb=" O ASP Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 80 removed outlier: 3.865A pdb=" N THR Q 55 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) Proline residue: Q 56 - end of helix removed outlier: 3.661A pdb=" N LEU Q 63 " --> pdb=" O ILE Q 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 46 removed outlier: 3.785A pdb=" N ILE R 8 " --> pdb=" O ASP R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 80 removed outlier: 4.973A pdb=" N THR R 55 " --> pdb=" O GLY R 51 " (cutoff:3.500A) Proline residue: R 56 - end of helix removed outlier: 3.771A pdb=" N ILE R 59 " --> pdb=" O THR R 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 46 Processing helix chain 'S' and resid 49 through 80 removed outlier: 4.699A pdb=" N THR S 55 " --> pdb=" O GLY S 51 " (cutoff:3.500A) Proline residue: S 56 - end of helix removed outlier: 3.629A pdb=" N ILE S 59 " --> pdb=" O THR S 55 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA S 66 " --> pdb=" O GLY S 62 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ALA S 67 " --> pdb=" O LEU S 63 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA S 73 " --> pdb=" O PHE S 69 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 46 removed outlier: 3.680A pdb=" N ILE T 8 " --> pdb=" O ASP T 4 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 81 removed outlier: 3.880A pdb=" N THR T 55 " --> pdb=" O GLY T 51 " (cutoff:3.500A) Proline residue: T 56 - end of helix removed outlier: 3.602A pdb=" N ALA T 66 " --> pdb=" O GLY T 62 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA T 67 " --> pdb=" O LEU T 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 52 Processing helix chain 'a' and resid 60 through 81 Processing helix chain 'a' and resid 88 through 106 removed outlier: 3.770A pdb=" N LEU a 92 " --> pdb=" O PHE a 88 " (cutoff:3.500A) 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 154 removed outlier: 3.804A pdb=" N VAL a 134 " --> pdb=" O ASP a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 156 through 165 removed outlier: 3.513A pdb=" N ILE a 160 " --> pdb=" O VAL a 156 " (cutoff:3.500A) 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: 3.763A pdb=" N ARG a 188 " --> pdb=" O SER a 184 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU a 189 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY a 196 " --> pdb=" O ASN a 192 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA a 201 " --> pdb=" O GLY a 197 " (cutoff:3.500A) Processing helix chain 'a' and resid 207 through 245 removed outlier: 3.963A pdb=" N TRP a 212 " --> pdb=" O TRP a 208 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix Processing helix chain 'b' and resid 29 through 48 removed outlier: 3.754A pdb=" N ALA b 33 " --> pdb=" O GLY b 29 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 84 Processing helix chain 'd' and resid 2 through 22 Processing helix chain 'd' and resid 22 through 61 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 114 778 hydrogen bonds defined for protein. 2325 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: 3.77 Time building geometry restraints manager: 1.96 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: 8340 1.03 - 1.23: 8 1.23 - 1.42: 3356 1.42 - 1.62: 4847 1.62 - 1.81: 55 Bond restraints: 16606 Sorted by residual: bond pdb=" N ILE a 96 " pdb=" CA ILE a 96 " ideal model delta sigma weight residual 1.463 1.454 0.009 1.14e-02 7.69e+03 6.55e-01 bond pdb=" C THR a 220 " pdb=" O THR a 220 " ideal model delta sigma weight residual 1.236 1.245 -0.008 1.15e-02 7.56e+03 5.06e-01 bond pdb=" CG LEU L 19 " pdb=" CD1 LEU L 19 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 4.99e-01 bond pdb=" CG LEU M 19 " pdb=" CD2 LEU M 19 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 4.90e-01 bond pdb=" N PRO R 47 " pdb=" CA PRO R 47 " ideal model delta sigma weight residual 1.469 1.477 -0.009 1.28e-02 6.10e+03 4.72e-01 ... (remaining 16601 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 29148 1.23 - 2.47: 909 2.47 - 3.70: 54 3.70 - 4.94: 23 4.94 - 6.17: 3 Bond angle restraints: 30137 Sorted by residual: angle pdb=" C CYS a 144 " pdb=" N TYR a 145 " pdb=" CA TYR a 145 " ideal model delta sigma weight residual 120.68 116.24 4.44 1.70e+00 3.46e-01 6.81e+00 angle pdb=" N TYR a 145 " pdb=" CA TYR a 145 " pdb=" CB TYR a 145 " ideal model delta sigma weight residual 110.30 113.78 -3.48 1.54e+00 4.22e-01 5.12e+00 angle pdb=" CA TYR a 145 " pdb=" CB TYR a 145 " pdb=" CG TYR a 145 " ideal model delta sigma weight residual 113.90 117.89 -3.99 1.80e+00 3.09e-01 4.91e+00 angle pdb=" N ILE a 96 " pdb=" CA ILE a 96 " pdb=" C ILE a 96 " ideal model delta sigma weight residual 110.23 107.93 2.30 1.04e+00 9.25e-01 4.89e+00 angle pdb=" CB MET N 21 " pdb=" CG MET N 21 " pdb=" SD MET N 21 " ideal model delta sigma weight residual 112.70 118.72 -6.02 3.00e+00 1.11e-01 4.03e+00 ... (remaining 30132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 6650 17.08 - 34.16: 670 34.16 - 51.24: 216 51.24 - 68.32: 220 68.32 - 85.40: 9 Dihedral angle restraints: 7765 sinusoidal: 4153 harmonic: 3612 Sorted by residual: dihedral pdb=" CA GLN R 46 " pdb=" C GLN R 46 " pdb=" N PRO R 47 " pdb=" CA PRO R 47 " ideal model delta harmonic sigma weight residual -180.00 -163.79 -16.21 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CB GLU R 65 " pdb=" CG GLU R 65 " pdb=" CD GLU R 65 " pdb=" OE1 GLU R 65 " ideal model delta sinusoidal sigma weight residual 0.00 -85.40 85.40 1 3.00e+01 1.11e-03 9.81e+00 dihedral pdb=" CB MET a 25 " pdb=" CG MET a 25 " pdb=" SD MET a 25 " pdb=" CE MET a 25 " ideal model delta sinusoidal sigma weight residual 180.00 128.16 51.84 3 1.50e+01 4.44e-03 9.06e+00 ... (remaining 7762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 854 0.029 - 0.057: 248 0.057 - 0.086: 171 0.086 - 0.114: 45 0.114 - 0.143: 5 Chirality restraints: 1323 Sorted by residual: chirality pdb=" CA ILE b 26 " pdb=" N ILE b 26 " pdb=" C ILE b 26 " pdb=" CB ILE b 26 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA PRO R 47 " pdb=" N PRO R 47 " pdb=" C PRO R 47 " pdb=" CB PRO R 47 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA VAL a 58 " pdb=" N VAL a 58 " pdb=" C VAL a 58 " pdb=" CB VAL a 58 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 1320 not shown) Planarity restraints: 2498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE a 99 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.19e+00 pdb=" C PHE a 99 " -0.031 2.00e-02 2.50e+03 pdb=" O PHE a 99 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE a 100 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE a 97 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" C PHE a 97 " -0.026 2.00e-02 2.50e+03 pdb=" O PHE a 97 " 0.010 2.00e-02 2.50e+03 pdb=" N VAL a 98 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY a 191 " -0.007 2.00e-02 2.50e+03 1.41e-02 1.98e+00 pdb=" C GLY a 191 " 0.024 2.00e-02 2.50e+03 pdb=" O GLY a 191 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN a 192 " -0.008 2.00e-02 2.50e+03 ... (remaining 2495 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1638 2.23 - 2.83: 37492 2.83 - 3.42: 47377 3.42 - 4.01: 62369 4.01 - 4.60: 97235 Nonbonded interactions: 246111 Sorted by model distance: nonbonded pdb=" O PHE M 78 " pdb=" HG1 THR M 82 " model vdw 1.643 2.450 nonbonded pdb=" O PHE Q 78 " pdb=" HG1 THR Q 82 " model vdw 1.658 2.450 nonbonded pdb=" O PHE T 78 " pdb=" HG1 THR T 82 " model vdw 1.695 2.450 nonbonded pdb=" OD1 ASN a 132 " pdb=" H ASN b 28 " model vdw 1.695 2.450 nonbonded pdb=" O PHE S 78 " pdb=" HG1 THR S 82 " model vdw 1.700 2.450 ... (remaining 246106 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' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.740 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: 0.100 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 15.720 Find NCS groups from input model: 0.160 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 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 0.023 8265 Z= 0.141 Angle : 0.468 6.173 11229 Z= 0.255 Chirality : 0.038 0.143 1323 Planarity : 0.004 0.031 1442 Dihedral : 14.405 85.401 2792 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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: 2.44 (0.27), residues: 1095 helix: 1.71 (0.18), residues: 894 sheet: None (None), residues: 0 loop : 1.54 (0.52), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 45 TYR 0.009 0.001 TYR a 145 PHE 0.013 0.001 PHE L 69 TRP 0.009 0.001 TRP a 218 HIS 0.004 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8265) covalent geometry : angle 0.46823 (11229) hydrogen bonds : bond 0.13661 ( 778) hydrogen bonds : angle 6.58348 ( 2325) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 75 MET cc_start: 0.7370 (tmm) cc_final: 0.7166 (tmm) REVERT: b 63 MET cc_start: 0.7562 (ttp) cc_final: 0.7248 (tmm) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1630 time to fit residues: 16.8678 Evaluate side-chains 58 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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: 2.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.080769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.073735 restraints weight = 75856.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.075721 restraints weight = 28462.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.076910 restraints weight = 14050.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.077432 restraints weight = 8785.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.078040 restraints weight = 6972.998| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8265 Z= 0.200 Angle : 0.522 5.431 11229 Z= 0.286 Chirality : 0.039 0.145 1323 Planarity : 0.004 0.041 1442 Dihedral : 3.486 14.600 1150 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.39 % Allowed : 5.69 % Favored : 93.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.50 (0.26), residues: 1095 helix: 2.49 (0.17), residues: 904 sheet: None (None), residues: 0 loop : 1.64 (0.53), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 52 TYR 0.025 0.001 TYR a 145 PHE 0.016 0.001 PHE O 74 TRP 0.009 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 8265) covalent geometry : angle 0.52206 (11229) hydrogen bonds : bond 0.05256 ( 778) hydrogen bonds : angle 4.25000 ( 2325) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 75 MET cc_start: 0.7561 (tmm) cc_final: 0.7252 (tmm) REVERT: b 63 MET cc_start: 0.7670 (ttp) cc_final: 0.7334 (tmm) outliers start: 3 outliers final: 2 residues processed: 58 average time/residue: 0.1641 time to fit residues: 14.4284 Evaluate side-chains 56 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain S residue 63 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.081679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.074410 restraints weight = 76713.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.076464 restraints weight = 28535.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.077737 restraints weight = 14127.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.078356 restraints weight = 8622.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.078470 restraints weight = 6644.589| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8265 Z= 0.161 Angle : 0.482 5.107 11229 Z= 0.261 Chirality : 0.038 0.141 1323 Planarity : 0.004 0.042 1442 Dihedral : 3.475 12.738 1150 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.39 % Allowed : 7.76 % Favored : 91.85 % 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: 4.08 (0.25), residues: 1095 helix: 2.91 (0.17), residues: 906 sheet: None (None), residues: 0 loop : 1.69 (0.54), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 52 TYR 0.022 0.001 TYR a 145 PHE 0.019 0.001 PHE a 194 TRP 0.010 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 8265) covalent geometry : angle 0.48240 (11229) hydrogen bonds : bond 0.04690 ( 778) hydrogen bonds : angle 3.78472 ( 2325) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 75 MET cc_start: 0.7565 (tmm) cc_final: 0.7226 (tmm) REVERT: T 75 MET cc_start: 0.8463 (tmm) cc_final: 0.8254 (tmm) REVERT: a 205 MET cc_start: 0.7347 (mtm) cc_final: 0.6814 (ptt) REVERT: b 63 MET cc_start: 0.7677 (ttp) cc_final: 0.7334 (tmm) outliers start: 3 outliers final: 2 residues processed: 64 average time/residue: 0.1539 time to fit residues: 14.8744 Evaluate side-chains 58 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain R residue 55 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 98 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.080847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.073638 restraints weight = 74753.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.075633 restraints weight = 28273.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.076782 restraints weight = 14071.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.077681 restraints weight = 9032.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.077881 restraints weight = 6339.174| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8265 Z= 0.179 Angle : 0.490 5.138 11229 Z= 0.267 Chirality : 0.038 0.140 1323 Planarity : 0.004 0.040 1442 Dihedral : 3.512 13.264 1150 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.52 % Allowed : 8.80 % Favored : 90.69 % 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: 4.10 (0.25), residues: 1095 helix: 2.94 (0.16), residues: 906 sheet: None (None), residues: 0 loop : 1.57 (0.53), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 52 TYR 0.020 0.001 TYR a 145 PHE 0.017 0.001 PHE a 194 TRP 0.010 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 8265) covalent geometry : angle 0.48959 (11229) hydrogen bonds : bond 0.04645 ( 778) hydrogen bonds : angle 3.73657 ( 2325) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 205 MET cc_start: 0.7333 (mtm) cc_final: 0.6845 (ptt) REVERT: b 63 MET cc_start: 0.7684 (ttp) cc_final: 0.7341 (tmm) outliers start: 4 outliers final: 4 residues processed: 59 average time/residue: 0.1587 time to fit residues: 13.9563 Evaluate side-chains 61 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain S residue 63 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 29 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.080332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.073190 restraints weight = 75355.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.075175 restraints weight = 28364.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.076294 restraints weight = 14133.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.076740 restraints weight = 8987.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.077463 restraints weight = 7407.522| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8265 Z= 0.196 Angle : 0.500 5.120 11229 Z= 0.274 Chirality : 0.038 0.139 1323 Planarity : 0.004 0.038 1442 Dihedral : 3.564 12.800 1150 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.65 % Allowed : 10.48 % Favored : 88.87 % 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: 4.00 (0.25), residues: 1095 helix: 2.87 (0.16), residues: 908 sheet: None (None), residues: 0 loop : 1.54 (0.53), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 52 TYR 0.018 0.001 TYR a 145 PHE 0.017 0.001 PHE a 194 TRP 0.010 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 8265) covalent geometry : angle 0.50035 (11229) hydrogen bonds : bond 0.04657 ( 778) hydrogen bonds : angle 3.73465 ( 2325) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 75 MET cc_start: 0.7683 (tmm) cc_final: 0.7414 (tmm) REVERT: a 205 MET cc_start: 0.7257 (mtp) cc_final: 0.6905 (ptt) outliers start: 5 outliers final: 4 residues processed: 62 average time/residue: 0.1666 time to fit residues: 15.5269 Evaluate side-chains 62 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain S residue 63 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 82 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.080919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.073693 restraints weight = 75445.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.075735 restraints weight = 28283.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.076886 restraints weight = 13952.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.077639 restraints weight = 8818.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.078121 restraints weight = 6514.420| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8265 Z= 0.169 Angle : 0.485 5.038 11229 Z= 0.263 Chirality : 0.038 0.141 1323 Planarity : 0.004 0.035 1442 Dihedral : 3.546 13.093 1150 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.65 % Allowed : 11.64 % Favored : 87.71 % 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: 4.13 (0.25), residues: 1095 helix: 2.96 (0.16), residues: 908 sheet: None (None), residues: 0 loop : 1.58 (0.53), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 52 TYR 0.018 0.001 TYR a 145 PHE 0.016 0.001 PHE a 194 TRP 0.011 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8265) covalent geometry : angle 0.48452 (11229) hydrogen bonds : bond 0.04542 ( 778) hydrogen bonds : angle 3.65095 ( 2325) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 75 MET cc_start: 0.7640 (tmm) cc_final: 0.7332 (tmm) REVERT: b 63 MET cc_start: 0.7642 (tmm) cc_final: 0.7298 (tmm) outliers start: 5 outliers final: 3 residues processed: 62 average time/residue: 0.1564 time to fit residues: 14.8535 Evaluate side-chains 61 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain S residue 63 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 29 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 61 optimal weight: 0.2980 chunk 52 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 103 optimal weight: 0.0040 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.082088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.074800 restraints weight = 74807.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.076885 restraints weight = 27743.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.078163 restraints weight = 13654.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.078858 restraints weight = 8333.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.079442 restraints weight = 6265.191| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8265 Z= 0.121 Angle : 0.457 4.880 11229 Z= 0.242 Chirality : 0.038 0.145 1323 Planarity : 0.004 0.033 1442 Dihedral : 3.445 13.351 1150 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.26 % Allowed : 12.42 % Favored : 87.32 % 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: 4.57 (0.25), residues: 1095 helix: 3.26 (0.17), residues: 906 sheet: None (None), residues: 0 loop : 1.76 (0.53), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 52 TYR 0.020 0.001 TYR a 145 PHE 0.014 0.001 PHE a 194 TRP 0.010 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 8265) covalent geometry : angle 0.45693 (11229) hydrogen bonds : bond 0.04265 ( 778) hydrogen bonds : angle 3.50006 ( 2325) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 75 MET cc_start: 0.7568 (tmm) cc_final: 0.7259 (tmm) REVERT: R 65 GLU cc_start: 0.7020 (pt0) cc_final: 0.6766 (pt0) REVERT: b 63 MET cc_start: 0.7612 (tmm) cc_final: 0.7314 (tmm) outliers start: 2 outliers final: 2 residues processed: 68 average time/residue: 0.1565 time to fit residues: 16.2008 Evaluate side-chains 64 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain S residue 63 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 6 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 8 optimal weight: 0.0030 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.081811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.074436 restraints weight = 75059.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.076544 restraints weight = 27946.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.077716 restraints weight = 13720.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.078310 restraints weight = 8688.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.078954 restraints weight = 6872.941| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8265 Z= 0.143 Angle : 0.469 4.995 11229 Z= 0.250 Chirality : 0.038 0.142 1323 Planarity : 0.004 0.032 1442 Dihedral : 3.432 12.989 1150 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.52 % Allowed : 12.16 % Favored : 87.32 % 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: 4.55 (0.25), residues: 1095 helix: 3.25 (0.16), residues: 906 sheet: None (None), residues: 0 loop : 1.74 (0.53), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 52 TYR 0.018 0.001 TYR a 145 PHE 0.013 0.001 PHE R 74 TRP 0.010 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8265) covalent geometry : angle 0.46931 (11229) hydrogen bonds : bond 0.04292 ( 778) hydrogen bonds : angle 3.50822 ( 2325) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 75 MET cc_start: 0.7596 (tmm) cc_final: 0.7276 (tmm) REVERT: R 65 GLU cc_start: 0.7058 (pt0) cc_final: 0.6795 (pt0) REVERT: b 63 MET cc_start: 0.7656 (tmm) cc_final: 0.7367 (tmm) outliers start: 4 outliers final: 2 residues processed: 66 average time/residue: 0.1663 time to fit residues: 16.6005 Evaluate side-chains 66 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain S residue 63 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.081609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.074285 restraints weight = 75379.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.076375 restraints weight = 28022.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.077550 restraints weight = 13820.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.078436 restraints weight = 8723.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.078786 restraints weight = 6095.075| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8265 Z= 0.149 Angle : 0.478 5.301 11229 Z= 0.254 Chirality : 0.038 0.142 1323 Planarity : 0.004 0.031 1442 Dihedral : 3.432 13.040 1150 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.26 % Allowed : 12.29 % Favored : 87.45 % 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: 4.52 (0.25), residues: 1095 helix: 3.23 (0.16), residues: 906 sheet: None (None), residues: 0 loop : 1.73 (0.53), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 52 TYR 0.018 0.001 TYR a 145 PHE 0.013 0.001 PHE a 221 TRP 0.010 0.001 TRP a 218 HIS 0.003 0.001 HIS a 16 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8265) covalent geometry : angle 0.47800 (11229) hydrogen bonds : bond 0.04304 ( 778) hydrogen bonds : angle 3.51237 ( 2325) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 75 MET cc_start: 0.7569 (tmm) cc_final: 0.7263 (tmm) REVERT: R 65 GLU cc_start: 0.7120 (pt0) cc_final: 0.6845 (pt0) REVERT: a 192 ASN cc_start: 0.8392 (m-40) cc_final: 0.8182 (m-40) REVERT: b 63 MET cc_start: 0.7656 (tmm) cc_final: 0.7384 (tmm) outliers start: 2 outliers final: 2 residues processed: 66 average time/residue: 0.1659 time to fit residues: 16.5516 Evaluate side-chains 65 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain S residue 63 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 94 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 66 optimal weight: 0.1980 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.080736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.073646 restraints weight = 76084.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.075655 restraints weight = 28820.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.076778 restraints weight = 14198.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.077327 restraints weight = 9051.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.077928 restraints weight = 7220.853| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8265 Z= 0.145 Angle : 0.479 6.090 11229 Z= 0.254 Chirality : 0.038 0.142 1323 Planarity : 0.004 0.032 1442 Dihedral : 3.418 13.149 1150 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.39 % Allowed : 12.03 % Favored : 87.58 % 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: 4.58 (0.25), residues: 1095 helix: 3.28 (0.16), residues: 906 sheet: None (None), residues: 0 loop : 1.72 (0.53), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 52 TYR 0.018 0.001 TYR a 145 PHE 0.013 0.001 PHE a 221 TRP 0.010 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8265) covalent geometry : angle 0.47937 (11229) hydrogen bonds : bond 0.04290 ( 778) hydrogen bonds : angle 3.50383 ( 2325) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 75 MET cc_start: 0.7570 (tmm) cc_final: 0.7260 (tmm) REVERT: R 65 GLU cc_start: 0.7058 (pt0) cc_final: 0.6785 (pt0) REVERT: a 192 ASN cc_start: 0.8412 (m-40) cc_final: 0.8197 (m-40) REVERT: b 63 MET cc_start: 0.7668 (tmm) cc_final: 0.7399 (tmm) outliers start: 3 outliers final: 3 residues processed: 64 average time/residue: 0.1723 time to fit residues: 16.7255 Evaluate side-chains 66 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain a residue 30 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 42 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.080020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.072756 restraints weight = 76393.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.074812 restraints weight = 28698.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.076062 restraints weight = 14123.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.076581 restraints weight = 8672.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.077189 restraints weight = 6876.763| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8265 Z= 0.185 Angle : 0.504 6.248 11229 Z= 0.271 Chirality : 0.038 0.140 1323 Planarity : 0.004 0.031 1442 Dihedral : 3.487 13.334 1150 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.39 % Allowed : 12.16 % Favored : 87.45 % 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: 4.35 (0.25), residues: 1095 helix: 3.13 (0.16), residues: 906 sheet: None (None), residues: 0 loop : 1.60 (0.52), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 52 TYR 0.016 0.001 TYR a 145 PHE 0.015 0.001 PHE a 221 TRP 0.010 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 8265) covalent geometry : angle 0.50426 (11229) hydrogen bonds : bond 0.04457 ( 778) hydrogen bonds : angle 3.59864 ( 2325) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2253.09 seconds wall clock time: 39 minutes 9.41 seconds (2349.41 seconds total)