Starting phenix.real_space_refine on Sun Apr 7 13:11:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckx_16705/04_2024/8ckx_16705.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckx_16705/04_2024/8ckx_16705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckx_16705/04_2024/8ckx_16705.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckx_16705/04_2024/8ckx_16705.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckx_16705/04_2024/8ckx_16705.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckx_16705/04_2024/8ckx_16705.pdb" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 726 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 71 5.16 5 C 6224 2.51 5 N 1709 2.21 5 O 1853 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9857 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1650 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1641 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 196} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1649 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 196} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1637 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1637 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1643 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 196} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 5.51, per 1000 atoms: 0.56 Number of scatterers: 9857 At special positions: 0 Unit cell: (113.46, 109.74, 77.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 71 16.00 O 1853 8.00 N 1709 7.00 C 6224 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.86 Conformation dependent library (CDL) restraints added in 1.6 seconds 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2374 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 6 sheets defined 73.0% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 119 Processing helix chain 'A' and resid 125 through 145 removed outlier: 3.562A pdb=" N LYS A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 173 Processing helix chain 'A' and resid 178 through 193 removed outlier: 4.292A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'B' and resid 16 through 31 Processing helix chain 'B' and resid 35 through 44 Processing helix chain 'B' and resid 48 through 58 Processing helix chain 'B' and resid 62 through 84 Processing helix chain 'B' and resid 100 through 105 Processing helix chain 'B' and resid 110 through 120 Processing helix chain 'B' and resid 125 through 145 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 160 through 176 removed outlier: 3.560A pdb=" N ALA B 174 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 193 removed outlier: 4.246A pdb=" N LEU B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 205 Processing helix chain 'B' and resid 210 through 218 Processing helix chain 'C' and resid 16 through 31 Processing helix chain 'C' and resid 35 through 44 Processing helix chain 'C' and resid 48 through 58 Processing helix chain 'C' and resid 62 through 84 Processing helix chain 'C' and resid 100 through 105 Processing helix chain 'C' and resid 110 through 120 Processing helix chain 'C' and resid 125 through 146 removed outlier: 3.600A pdb=" N MET C 144 " --> pdb=" O LYS C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 160 through 175 removed outlier: 3.793A pdb=" N ALA C 174 " --> pdb=" O LYS C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 193 removed outlier: 4.207A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 205 Processing helix chain 'C' and resid 210 through 218 Processing helix chain 'D' and resid 16 through 31 Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 48 through 58 Processing helix chain 'D' and resid 62 through 84 Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 110 through 119 Processing helix chain 'D' and resid 125 through 146 removed outlier: 3.619A pdb=" N LYS D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 160 through 175 removed outlier: 3.736A pdb=" N ALA D 174 " --> pdb=" O LYS D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 193 removed outlier: 4.368A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 Processing helix chain 'D' and resid 210 through 218 Processing helix chain 'E' and resid 16 through 31 Processing helix chain 'E' and resid 35 through 44 Processing helix chain 'E' and resid 48 through 58 Processing helix chain 'E' and resid 62 through 84 Processing helix chain 'E' and resid 100 through 105 Processing helix chain 'E' and resid 110 through 120 Processing helix chain 'E' and resid 125 through 146 Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'E' and resid 160 through 174 removed outlier: 3.916A pdb=" N ALA E 174 " --> pdb=" O LYS E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 193 removed outlier: 4.190A pdb=" N LEU E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 205 Processing helix chain 'E' and resid 210 through 219 Processing helix chain 'F' and resid 16 through 31 Processing helix chain 'F' and resid 35 through 43 Processing helix chain 'F' and resid 48 through 58 Processing helix chain 'F' and resid 62 through 84 Processing helix chain 'F' and resid 100 through 105 Processing helix chain 'F' and resid 110 through 120 Processing helix chain 'F' and resid 125 through 145 Processing helix chain 'F' and resid 149 through 153 Processing helix chain 'F' and resid 160 through 175 removed outlier: 3.864A pdb=" N ALA F 174 " --> pdb=" O LYS F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 193 removed outlier: 4.213A pdb=" N LEU F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 205 Processing helix chain 'F' and resid 210 through 218 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'B' and resid 2 through 4 Processing sheet with id=AA3, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AA4, first strand: chain 'D' and resid 2 through 4 Processing sheet with id=AA5, first strand: chain 'E' and resid 2 through 4 Processing sheet with id=AA6, first strand: chain 'F' and resid 2 through 4 636 hydrogen bonds defined for protein. 1878 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: 2.71 Time building geometry restraints manager: 4.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3263 1.34 - 1.46: 1252 1.46 - 1.58: 5422 1.58 - 1.70: 0 1.70 - 1.81: 130 Bond restraints: 10067 Sorted by residual: bond pdb=" CB PRO A 1 " pdb=" CG PRO A 1 " ideal model delta sigma weight residual 1.492 1.571 -0.079 5.00e-02 4.00e+02 2.50e+00 bond pdb=" CB PRO C 1 " pdb=" CG PRO C 1 " ideal model delta sigma weight residual 1.492 1.568 -0.076 5.00e-02 4.00e+02 2.32e+00 bond pdb=" CB PRO B 1 " pdb=" CG PRO B 1 " ideal model delta sigma weight residual 1.492 1.568 -0.076 5.00e-02 4.00e+02 2.31e+00 bond pdb=" CB PRO F 1 " pdb=" CG PRO F 1 " ideal model delta sigma weight residual 1.492 1.560 -0.068 5.00e-02 4.00e+02 1.86e+00 bond pdb=" CB PRO D 1 " pdb=" CG PRO D 1 " ideal model delta sigma weight residual 1.492 1.553 -0.061 5.00e-02 4.00e+02 1.47e+00 ... (remaining 10062 not shown) Histogram of bond angle deviations from ideal: 100.29 - 107.06: 477 107.06 - 113.82: 5607 113.82 - 120.59: 4061 120.59 - 127.35: 3356 127.35 - 134.11: 174 Bond angle restraints: 13675 Sorted by residual: angle pdb=" CB LEU D 6 " pdb=" CG LEU D 6 " pdb=" CD1 LEU D 6 " ideal model delta sigma weight residual 110.70 126.69 -15.99 3.00e+00 1.11e-01 2.84e+01 angle pdb=" CA LEU F 111 " pdb=" CB LEU F 111 " pdb=" CG LEU F 111 " ideal model delta sigma weight residual 116.30 126.71 -10.41 3.50e+00 8.16e-02 8.84e+00 angle pdb=" CB GLU E 28 " pdb=" CG GLU E 28 " pdb=" CD GLU E 28 " ideal model delta sigma weight residual 112.60 117.27 -4.67 1.70e+00 3.46e-01 7.55e+00 angle pdb=" CA TYR A 169 " pdb=" CB TYR A 169 " pdb=" CG TYR A 169 " ideal model delta sigma weight residual 113.90 109.28 4.62 1.80e+00 3.09e-01 6.59e+00 angle pdb=" CA GLU E 28 " pdb=" CB GLU E 28 " pdb=" CG GLU E 28 " ideal model delta sigma weight residual 114.10 119.16 -5.06 2.00e+00 2.50e-01 6.40e+00 ... (remaining 13670 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 5720 17.90 - 35.79: 356 35.79 - 53.69: 72 53.69 - 71.58: 12 71.58 - 89.48: 5 Dihedral angle restraints: 6165 sinusoidal: 2514 harmonic: 3651 Sorted by residual: dihedral pdb=" CA ASN A 121 " pdb=" C ASN A 121 " pdb=" N PRO A 122 " pdb=" CA PRO A 122 " ideal model delta harmonic sigma weight residual 180.00 150.69 29.31 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA PHE D 32 " pdb=" C PHE D 32 " pdb=" N SER D 33 " pdb=" CA SER D 33 " ideal model delta harmonic sigma weight residual 180.00 150.96 29.04 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N SER E 33 " pdb=" CA SER E 33 " ideal model delta harmonic sigma weight residual 180.00 151.34 28.66 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 6162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.235: 1544 0.235 - 0.471: 0 0.471 - 0.706: 0 0.706 - 0.941: 0 0.941 - 1.176: 1 Chirality restraints: 1545 Sorted by residual: chirality pdb=" CG LEU D 6 " pdb=" CB LEU D 6 " pdb=" CD1 LEU D 6 " pdb=" CD2 LEU D 6 " both_signs ideal model delta sigma weight residual False -2.59 -1.41 -1.18 2.00e-01 2.50e+01 3.46e+01 chirality pdb=" CA PHE E 32 " pdb=" N PHE E 32 " pdb=" C PHE E 32 " pdb=" CB PHE E 32 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.00e-01 chirality pdb=" CA PHE D 32 " pdb=" N PHE D 32 " pdb=" C PHE D 32 " pdb=" CB PHE D 32 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.76e-01 ... (remaining 1542 not shown) Planarity restraints: 1769 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 154 " 0.295 9.50e-02 1.11e+02 1.32e-01 1.11e+01 pdb=" NE ARG F 154 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG F 154 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG F 154 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG F 154 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 173 " -0.285 9.50e-02 1.11e+02 1.28e-01 1.00e+01 pdb=" NE ARG D 173 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG D 173 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG D 173 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 173 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 173 " 0.276 9.50e-02 1.11e+02 1.24e-01 9.62e+00 pdb=" NE ARG C 173 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG C 173 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG C 173 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 173 " 0.007 2.00e-02 2.50e+03 ... (remaining 1766 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 4236 2.94 - 3.43: 10602 3.43 - 3.92: 17251 3.92 - 4.41: 19436 4.41 - 4.90: 31359 Nonbonded interactions: 82884 Sorted by model distance: nonbonded pdb=" OD1 ASP D 103 " pdb=" OG1 THR D 108 " model vdw 2.453 2.440 nonbonded pdb=" OD1 ASN E 53 " pdb=" OH TYR E 130 " model vdw 2.488 2.440 nonbonded pdb=" OD1 ASN A 53 " pdb=" OH TYR A 130 " model vdw 2.492 2.440 nonbonded pdb=" OD1 ASN D 53 " pdb=" OH TYR D 130 " model vdw 2.495 2.440 nonbonded pdb=" OD1 ASP E 103 " pdb=" OG1 THR E 108 " model vdw 2.496 2.440 ... (remaining 82879 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 3 or (resid 4 through 7 and (name N or name CA o \ r name C or name O or name CB )) or resid 8 through 85 or resid 97 through 221)) \ selection = (chain 'B' and (resid 1 through 5 or (resid 6 through 7 and (name N or name CA o \ r name C or name O or name CB )) or (resid 8 through 11 and (name N or name CA o \ r name C or name O or name CB )) or resid 12 through 85 or resid 97 through 221) \ ) selection = (chain 'C' and (resid 1 through 3 or (resid 4 through 7 and (name N or name CA o \ r name C or name O or name CB )) or resid 8 or (resid 9 through 11 and (name N o \ r name CA or name C or name O or name CB )) or resid 12 through 85 or resid 97 t \ hrough 221)) selection = (chain 'D' and (resid 1 through 3 or (resid 4 through 7 and (name N or name CA o \ r name C or name O or name CB )) or (resid 8 through 11 and (name N or name CA o \ r name C or name O or name CB )) or resid 12 through 221)) selection = (chain 'E' and (resid 1 through 3 or (resid 4 through 7 and (name N or name CA o \ r name C or name O or name CB )) or (resid 8 through 11 and (name N or name CA o \ r name C or name O or name CB )) or resid 12 through 221)) selection = (chain 'F' and (resid 1 through 3 or (resid 4 through 7 and (name N or name CA o \ r name C or name O or name CB )) or resid 8 through 85 or resid 97 through 221)) \ } 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: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 12.020 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 28.650 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.040 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:12.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 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 : 0.005 0.079 10067 Z= 0.313 Angle : 0.867 15.988 13675 Z= 0.514 Chirality : 0.059 1.176 1545 Planarity : 0.013 0.132 1769 Dihedral : 12.698 89.480 3791 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.19 % Allowed : 0.75 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.20), residues: 1241 helix: -0.92 (0.14), residues: 881 sheet: -1.34 (0.78), residues: 27 loop : 0.49 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP B 117 HIS 0.011 0.004 HIS B 84 PHE 0.021 0.004 PHE B 40 TYR 0.021 0.006 TYR B 164 ARG 0.022 0.003 ARG F 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 205 time to evaluate : 1.058 Fit side-chains REVERT: A 68 MET cc_start: 0.8669 (mtp) cc_final: 0.8403 (mtp) REVERT: A 74 ASN cc_start: 0.8129 (m-40) cc_final: 0.7863 (m-40) REVERT: A 79 GLU cc_start: 0.7073 (tt0) cc_final: 0.6686 (mt-10) REVERT: A 163 ASP cc_start: 0.7895 (m-30) cc_final: 0.7646 (m-30) REVERT: A 212 GLU cc_start: 0.7374 (tt0) cc_final: 0.6767 (pm20) REVERT: B 170 LYS cc_start: 0.7759 (tttm) cc_final: 0.7535 (tptt) REVERT: B 192 GLN cc_start: 0.7559 (mt0) cc_final: 0.7321 (mm110) REVERT: C 81 ASP cc_start: 0.8662 (m-30) cc_final: 0.8428 (m-30) REVERT: C 118 MET cc_start: 0.8591 (mtp) cc_final: 0.8286 (mtp) REVERT: C 154 ARG cc_start: 0.7313 (mtt-85) cc_final: 0.7087 (mtp-110) REVERT: C 170 LYS cc_start: 0.8576 (tttm) cc_final: 0.8282 (tttp) REVERT: C 179 GLN cc_start: 0.7378 (tp40) cc_final: 0.7083 (mm-40) REVERT: C 212 GLU cc_start: 0.7132 (tt0) cc_final: 0.6349 (tp30) REVERT: D 140 LYS cc_start: 0.8485 (mttt) cc_final: 0.8262 (mttm) REVERT: D 170 LYS cc_start: 0.8432 (tttm) cc_final: 0.7826 (ttpp) REVERT: D 212 GLU cc_start: 0.7142 (tt0) cc_final: 0.6769 (pm20) REVERT: E 68 MET cc_start: 0.8318 (mtp) cc_final: 0.8082 (mtp) REVERT: E 200 THR cc_start: 0.7516 (m) cc_final: 0.7231 (p) REVERT: E 212 GLU cc_start: 0.7525 (tt0) cc_final: 0.6530 (mt-10) REVERT: E 216 THR cc_start: 0.7842 (m) cc_final: 0.7567 (p) REVERT: F 55 MET cc_start: 0.8562 (mtp) cc_final: 0.8208 (mtp) REVERT: F 74 ASN cc_start: 0.8697 (m-40) cc_final: 0.8402 (m-40) REVERT: F 102 SER cc_start: 0.8451 (m) cc_final: 0.8170 (p) REVERT: F 151 LEU cc_start: 0.8818 (mt) cc_final: 0.8574 (mm) REVERT: F 216 THR cc_start: 0.8268 (m) cc_final: 0.7786 (p) outliers start: 2 outliers final: 0 residues processed: 206 average time/residue: 1.5211 time to fit residues: 331.5154 Evaluate side-chains 152 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.9980 chunk 95 optimal weight: 0.0770 chunk 52 optimal weight: 0.3980 chunk 32 optimal weight: 0.0170 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 98 optimal weight: 0.0870 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.2554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS B 120 HIS B 193 ASN C 193 ASN C 195 ASN D 193 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10067 Z= 0.180 Angle : 0.524 5.709 13675 Z= 0.271 Chirality : 0.041 0.163 1545 Planarity : 0.005 0.037 1769 Dihedral : 4.717 28.506 1337 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 2.07 % Allowed : 7.14 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.23), residues: 1241 helix: 1.05 (0.17), residues: 879 sheet: -0.99 (0.77), residues: 27 loop : 0.95 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 117 HIS 0.002 0.001 HIS E 120 PHE 0.015 0.002 PHE D 32 TYR 0.013 0.001 TYR E 169 ARG 0.005 0.000 ARG D 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 1.011 Fit side-chains REVERT: A 75 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7127 (pt0) REVERT: A 79 GLU cc_start: 0.7061 (tt0) cc_final: 0.6684 (mt-10) REVERT: A 163 ASP cc_start: 0.7827 (m-30) cc_final: 0.7594 (m-30) REVERT: A 212 GLU cc_start: 0.7364 (tt0) cc_final: 0.6626 (pm20) REVERT: B 165 VAL cc_start: 0.7993 (t) cc_final: 0.7640 (m) REVERT: B 170 LYS cc_start: 0.7769 (tttm) cc_final: 0.7554 (tptt) REVERT: C 118 MET cc_start: 0.8453 (mtp) cc_final: 0.8150 (mtp) REVERT: C 170 LYS cc_start: 0.8477 (tttm) cc_final: 0.8144 (tttp) REVERT: C 212 GLU cc_start: 0.7132 (tt0) cc_final: 0.6614 (tp30) REVERT: D 140 LYS cc_start: 0.8380 (mttt) cc_final: 0.8081 (mttm) REVERT: D 170 LYS cc_start: 0.8333 (tttm) cc_final: 0.7621 (ttpp) REVERT: D 212 GLU cc_start: 0.7219 (tt0) cc_final: 0.6842 (pm20) REVERT: E 170 LYS cc_start: 0.8442 (tttm) cc_final: 0.8206 (tptt) REVERT: F 55 MET cc_start: 0.8424 (mtp) cc_final: 0.8006 (mtp) REVERT: F 74 ASN cc_start: 0.8468 (m-40) cc_final: 0.8203 (m-40) REVERT: F 75 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6855 (pt0) REVERT: F 143 ARG cc_start: 0.6946 (ttp80) cc_final: 0.6672 (mtt90) REVERT: F 154 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7413 (mtt90) outliers start: 22 outliers final: 4 residues processed: 156 average time/residue: 1.5417 time to fit residues: 254.8796 Evaluate side-chains 140 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 133 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 154 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 95 optimal weight: 0.3980 chunk 77 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 113 optimal weight: 0.0470 chunk 39 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN B 193 ASN C 179 GLN D 193 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10067 Z= 0.225 Angle : 0.519 7.856 13675 Z= 0.261 Chirality : 0.042 0.158 1545 Planarity : 0.005 0.037 1769 Dihedral : 4.407 29.582 1337 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 2.35 % Allowed : 8.08 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.23), residues: 1241 helix: 1.33 (0.17), residues: 881 sheet: -0.89 (0.80), residues: 27 loop : 1.02 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 184 HIS 0.002 0.001 HIS E 120 PHE 0.012 0.002 PHE C 32 TYR 0.015 0.002 TYR E 169 ARG 0.003 0.000 ARG D 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 142 time to evaluate : 1.049 Fit side-chains REVERT: A 75 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7075 (pt0) REVERT: A 79 GLU cc_start: 0.7195 (tt0) cc_final: 0.6833 (mt-10) REVERT: A 163 ASP cc_start: 0.7836 (m-30) cc_final: 0.7633 (m-30) REVERT: A 212 GLU cc_start: 0.7211 (tt0) cc_final: 0.6601 (pm20) REVERT: B 112 GLN cc_start: 0.6411 (mm-40) cc_final: 0.6005 (tp40) REVERT: B 165 VAL cc_start: 0.7972 (t) cc_final: 0.7635 (m) REVERT: B 192 GLN cc_start: 0.7308 (mt0) cc_final: 0.7025 (mm110) REVERT: C 50 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7995 (tt0) REVERT: C 118 MET cc_start: 0.8541 (mtp) cc_final: 0.8198 (mtp) REVERT: C 170 LYS cc_start: 0.8487 (tttm) cc_final: 0.8160 (tttp) REVERT: D 140 LYS cc_start: 0.8438 (mttt) cc_final: 0.8056 (mttm) REVERT: D 170 LYS cc_start: 0.8304 (tttm) cc_final: 0.7588 (ttpp) REVERT: D 212 GLU cc_start: 0.7307 (tt0) cc_final: 0.6832 (pm20) REVERT: E 170 LYS cc_start: 0.8469 (tttm) cc_final: 0.8125 (tttt) REVERT: F 29 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6997 (mt-10) REVERT: F 55 MET cc_start: 0.8397 (mtp) cc_final: 0.8033 (mtp) REVERT: F 74 ASN cc_start: 0.8462 (m-40) cc_final: 0.8211 (m-40) REVERT: F 75 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6891 (pt0) outliers start: 25 outliers final: 7 residues processed: 154 average time/residue: 1.6825 time to fit residues: 274.0390 Evaluate side-chains 142 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 102 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 chunk 121 optimal weight: 0.0470 chunk 60 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10067 Z= 0.198 Angle : 0.490 7.986 13675 Z= 0.245 Chirality : 0.041 0.152 1545 Planarity : 0.005 0.037 1769 Dihedral : 4.197 29.479 1337 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.44 % Allowed : 9.11 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.24), residues: 1241 helix: 1.48 (0.17), residues: 886 sheet: -0.77 (0.85), residues: 27 loop : 0.98 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 184 HIS 0.002 0.001 HIS D 12 PHE 0.011 0.002 PHE C 32 TYR 0.013 0.001 TYR E 169 ARG 0.003 0.000 ARG D 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 133 time to evaluate : 1.105 Fit side-chains REVERT: A 75 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7063 (pt0) REVERT: A 79 GLU cc_start: 0.7115 (tt0) cc_final: 0.6810 (mt-10) REVERT: A 212 GLU cc_start: 0.7200 (tt0) cc_final: 0.6591 (pm20) REVERT: B 112 GLN cc_start: 0.6436 (mm-40) cc_final: 0.6103 (tp40) REVERT: B 165 VAL cc_start: 0.7978 (t) cc_final: 0.7667 (m) REVERT: B 192 GLN cc_start: 0.7341 (mt0) cc_final: 0.7036 (mm-40) REVERT: C 118 MET cc_start: 0.8523 (mtp) cc_final: 0.8217 (mtp) REVERT: C 170 LYS cc_start: 0.8500 (tttm) cc_final: 0.8076 (tptp) REVERT: D 21 ASN cc_start: 0.8028 (m-40) cc_final: 0.7700 (m110) REVERT: D 103 ASP cc_start: 0.8326 (m-30) cc_final: 0.8037 (m-30) REVERT: D 140 LYS cc_start: 0.8429 (mttt) cc_final: 0.8051 (mttm) REVERT: D 170 LYS cc_start: 0.8308 (tttm) cc_final: 0.7592 (ttpp) REVERT: D 212 GLU cc_start: 0.7248 (tt0) cc_final: 0.7005 (pt0) REVERT: E 170 LYS cc_start: 0.8467 (tttm) cc_final: 0.8136 (tttt) REVERT: F 55 MET cc_start: 0.8374 (mtp) cc_final: 0.7985 (mtp) REVERT: F 75 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6864 (pt0) outliers start: 26 outliers final: 9 residues processed: 145 average time/residue: 1.6115 time to fit residues: 246.9227 Evaluate side-chains 138 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 127 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 102 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 0.0270 chunk 103 optimal weight: 0.0050 chunk 84 optimal weight: 0.0570 chunk 0 optimal weight: 3.9990 chunk 62 optimal weight: 0.0970 chunk 109 optimal weight: 1.9990 chunk 30 optimal weight: 0.0970 overall best weight: 0.0566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 193 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10067 Z= 0.130 Angle : 0.449 8.350 13675 Z= 0.227 Chirality : 0.039 0.143 1545 Planarity : 0.004 0.041 1769 Dihedral : 3.825 28.593 1337 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.31 % Allowed : 10.14 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.24), residues: 1241 helix: 1.88 (0.18), residues: 886 sheet: -0.64 (0.92), residues: 27 loop : 0.95 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 184 HIS 0.001 0.000 HIS E 12 PHE 0.010 0.001 PHE C 32 TYR 0.008 0.001 TYR E 169 ARG 0.003 0.000 ARG D 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 1.015 Fit side-chains REVERT: A 75 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7097 (pt0) REVERT: A 79 GLU cc_start: 0.7104 (tt0) cc_final: 0.6786 (mt-10) REVERT: A 212 GLU cc_start: 0.7268 (tt0) cc_final: 0.6718 (pm20) REVERT: B 165 VAL cc_start: 0.7985 (t) cc_final: 0.7678 (m) REVERT: C 170 LYS cc_start: 0.8357 (tttm) cc_final: 0.7999 (tptp) REVERT: D 55 MET cc_start: 0.8376 (mtp) cc_final: 0.8034 (mtp) REVERT: D 140 LYS cc_start: 0.8366 (mttt) cc_final: 0.8021 (mttm) REVERT: D 170 LYS cc_start: 0.8265 (tttm) cc_final: 0.7541 (ttpp) REVERT: E 170 LYS cc_start: 0.8455 (tttm) cc_final: 0.8243 (tptt) REVERT: F 55 MET cc_start: 0.8314 (mtp) cc_final: 0.8018 (mtp) REVERT: F 75 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6870 (pt0) outliers start: 14 outliers final: 6 residues processed: 130 average time/residue: 1.5190 time to fit residues: 209.6019 Evaluate side-chains 129 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 121 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 102 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 30 optimal weight: 0.0770 chunk 121 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10067 Z= 0.217 Angle : 0.480 5.668 13675 Z= 0.242 Chirality : 0.041 0.146 1545 Planarity : 0.005 0.042 1769 Dihedral : 3.953 28.320 1337 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.78 % Allowed : 10.70 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.24), residues: 1241 helix: 1.73 (0.18), residues: 887 sheet: -0.62 (0.92), residues: 27 loop : 0.95 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 184 HIS 0.002 0.001 HIS C 12 PHE 0.012 0.002 PHE C 32 TYR 0.017 0.001 TYR E 169 ARG 0.003 0.000 ARG C 100 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 0.980 Fit side-chains REVERT: A 75 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7076 (pt0) REVERT: A 79 GLU cc_start: 0.7049 (tt0) cc_final: 0.6753 (mt-10) REVERT: A 212 GLU cc_start: 0.7307 (tt0) cc_final: 0.6752 (pm20) REVERT: B 165 VAL cc_start: 0.8006 (t) cc_final: 0.7686 (m) REVERT: B 192 GLN cc_start: 0.7366 (mt0) cc_final: 0.7085 (mm110) REVERT: C 50 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.8038 (tt0) REVERT: C 167 ARG cc_start: 0.8326 (mtp-110) cc_final: 0.8023 (mtm110) REVERT: C 170 LYS cc_start: 0.8488 (tttm) cc_final: 0.8124 (tptp) REVERT: D 21 ASN cc_start: 0.8072 (m-40) cc_final: 0.7756 (m110) REVERT: D 103 ASP cc_start: 0.8373 (m-30) cc_final: 0.8087 (m-30) REVERT: D 140 LYS cc_start: 0.8455 (mttt) cc_final: 0.8085 (mttm) REVERT: D 170 LYS cc_start: 0.8270 (tttm) cc_final: 0.7556 (ttpp) REVERT: D 212 GLU cc_start: 0.7215 (tt0) cc_final: 0.6935 (pt0) REVERT: E 10 MET cc_start: 0.3879 (mmp) cc_final: 0.3007 (pp-130) REVERT: E 170 LYS cc_start: 0.8494 (tttm) cc_final: 0.8278 (tptt) REVERT: F 55 MET cc_start: 0.8365 (mtp) cc_final: 0.7968 (mtp) REVERT: F 75 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6862 (pt0) outliers start: 19 outliers final: 9 residues processed: 137 average time/residue: 1.6572 time to fit residues: 239.8603 Evaluate side-chains 141 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 102 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 121 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 74 optimal weight: 0.0010 chunk 56 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN D 193 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10067 Z= 0.193 Angle : 0.469 5.490 13675 Z= 0.235 Chirality : 0.041 0.143 1545 Planarity : 0.005 0.042 1769 Dihedral : 3.929 28.273 1337 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.69 % Allowed : 11.64 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.24), residues: 1241 helix: 1.72 (0.18), residues: 886 sheet: -0.41 (0.91), residues: 27 loop : 0.96 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 184 HIS 0.002 0.001 HIS D 12 PHE 0.011 0.002 PHE C 32 TYR 0.013 0.001 TYR E 169 ARG 0.002 0.000 ARG D 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 1.029 Fit side-chains REVERT: A 75 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7129 (pt0) REVERT: A 79 GLU cc_start: 0.7054 (tt0) cc_final: 0.6755 (mt-10) REVERT: A 212 GLU cc_start: 0.7255 (tt0) cc_final: 0.6745 (pm20) REVERT: B 112 GLN cc_start: 0.6799 (tp40) cc_final: 0.5732 (mm-40) REVERT: B 165 VAL cc_start: 0.8001 (t) cc_final: 0.7662 (m) REVERT: B 192 GLN cc_start: 0.7333 (mt0) cc_final: 0.7058 (mm110) REVERT: C 39 MET cc_start: 0.7879 (tpt) cc_final: 0.7420 (tpt) REVERT: C 50 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.8017 (tt0) REVERT: C 167 ARG cc_start: 0.8343 (mtp-110) cc_final: 0.8031 (mtm110) REVERT: C 170 LYS cc_start: 0.8491 (tttm) cc_final: 0.8108 (tptp) REVERT: D 21 ASN cc_start: 0.8087 (m-40) cc_final: 0.7768 (m110) REVERT: D 103 ASP cc_start: 0.8389 (m-30) cc_final: 0.8099 (m-30) REVERT: D 140 LYS cc_start: 0.8465 (mttt) cc_final: 0.8072 (mttm) REVERT: D 170 LYS cc_start: 0.8274 (tttm) cc_final: 0.7545 (ttpp) REVERT: E 170 LYS cc_start: 0.8456 (tttm) cc_final: 0.8239 (tptt) REVERT: F 55 MET cc_start: 0.8367 (mtp) cc_final: 0.7965 (mtp) REVERT: F 75 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6888 (pt0) outliers start: 18 outliers final: 6 residues processed: 130 average time/residue: 1.7493 time to fit residues: 241.2439 Evaluate side-chains 127 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 118 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 102 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 116 optimal weight: 0.8980 chunk 106 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10067 Z= 0.258 Angle : 0.513 6.352 13675 Z= 0.256 Chirality : 0.042 0.150 1545 Planarity : 0.005 0.042 1769 Dihedral : 4.085 28.211 1337 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.31 % Allowed : 12.30 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.23), residues: 1241 helix: 1.53 (0.17), residues: 884 sheet: -0.44 (0.86), residues: 27 loop : 0.89 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 80 HIS 0.003 0.001 HIS D 12 PHE 0.012 0.002 PHE C 32 TYR 0.016 0.002 TYR E 169 ARG 0.002 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 132 time to evaluate : 1.174 Fit side-chains REVERT: A 75 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6980 (pt0) REVERT: A 79 GLU cc_start: 0.7063 (tt0) cc_final: 0.6738 (mt-10) REVERT: A 212 GLU cc_start: 0.7345 (tt0) cc_final: 0.6697 (pm20) REVERT: B 192 GLN cc_start: 0.7429 (mt0) cc_final: 0.7136 (mm110) REVERT: C 50 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.8032 (tt0) REVERT: C 103 ASP cc_start: 0.8154 (m-30) cc_final: 0.7940 (m-30) REVERT: C 167 ARG cc_start: 0.8352 (mtp-110) cc_final: 0.8126 (mtm110) REVERT: C 170 LYS cc_start: 0.8558 (tttm) cc_final: 0.8122 (tptp) REVERT: D 21 ASN cc_start: 0.8108 (m-40) cc_final: 0.7789 (m110) REVERT: D 103 ASP cc_start: 0.8456 (m-30) cc_final: 0.8197 (m-30) REVERT: D 140 LYS cc_start: 0.8476 (mttt) cc_final: 0.8201 (mttm) REVERT: D 170 LYS cc_start: 0.8297 (tttm) cc_final: 0.7626 (ttpp) REVERT: D 212 GLU cc_start: 0.7227 (tt0) cc_final: 0.6999 (pt0) REVERT: E 10 MET cc_start: 0.4108 (mmp) cc_final: 0.3332 (pp-130) REVERT: E 170 LYS cc_start: 0.8422 (tttm) cc_final: 0.8119 (tttt) REVERT: F 55 MET cc_start: 0.8402 (mtp) cc_final: 0.8023 (mtp) outliers start: 14 outliers final: 8 residues processed: 140 average time/residue: 1.6799 time to fit residues: 248.3646 Evaluate side-chains 135 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain F residue 102 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 119 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 193 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10067 Z= 0.235 Angle : 0.499 6.393 13675 Z= 0.250 Chirality : 0.042 0.150 1545 Planarity : 0.005 0.043 1769 Dihedral : 4.046 28.289 1337 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.88 % Allowed : 11.83 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.24), residues: 1241 helix: 1.52 (0.17), residues: 884 sheet: -0.38 (0.87), residues: 27 loop : 0.84 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 184 HIS 0.003 0.001 HIS D 12 PHE 0.011 0.002 PHE C 32 TYR 0.014 0.001 TYR E 169 ARG 0.003 0.000 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 1.039 Fit side-chains REVERT: A 75 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7055 (pt0) REVERT: A 79 GLU cc_start: 0.7042 (tt0) cc_final: 0.6717 (mt-10) REVERT: A 212 GLU cc_start: 0.7392 (tt0) cc_final: 0.6769 (pm20) REVERT: B 112 GLN cc_start: 0.6802 (tp40) cc_final: 0.5810 (mp10) REVERT: B 192 GLN cc_start: 0.7438 (mt0) cc_final: 0.7143 (mm110) REVERT: C 50 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: C 167 ARG cc_start: 0.8352 (mtp-110) cc_final: 0.8135 (mtm110) REVERT: C 170 LYS cc_start: 0.8549 (tttm) cc_final: 0.8102 (tptp) REVERT: C 192 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7560 (mm-40) REVERT: D 21 ASN cc_start: 0.8094 (m-40) cc_final: 0.7761 (m110) REVERT: D 103 ASP cc_start: 0.8483 (m-30) cc_final: 0.8227 (m-30) REVERT: D 140 LYS cc_start: 0.8476 (mttt) cc_final: 0.8208 (mttm) REVERT: D 170 LYS cc_start: 0.8303 (tttm) cc_final: 0.7597 (ttpp) REVERT: D 212 GLU cc_start: 0.7198 (tt0) cc_final: 0.6995 (pt0) REVERT: E 10 MET cc_start: 0.4268 (mmp) cc_final: 0.3397 (pp-130) REVERT: F 55 MET cc_start: 0.8405 (mtp) cc_final: 0.8001 (mtp) REVERT: F 75 GLU cc_start: 0.7219 (pt0) cc_final: 0.6982 (pt0) outliers start: 20 outliers final: 11 residues processed: 138 average time/residue: 1.7533 time to fit residues: 255.2385 Evaluate side-chains 139 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 192 GLN Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain F residue 102 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 83 optimal weight: 0.1980 chunk 125 optimal weight: 0.0470 chunk 115 optimal weight: 0.1980 chunk 99 optimal weight: 0.5980 chunk 10 optimal weight: 0.0670 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 0.1980 chunk 106 optimal weight: 5.9990 overall best weight: 0.1416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 GLN C 183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10067 Z= 0.133 Angle : 0.454 6.687 13675 Z= 0.228 Chirality : 0.040 0.140 1545 Planarity : 0.004 0.042 1769 Dihedral : 3.738 27.175 1337 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.85 % Allowed : 13.05 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.24), residues: 1241 helix: 1.87 (0.18), residues: 887 sheet: -0.05 (0.95), residues: 27 loop : 0.96 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 184 HIS 0.001 0.000 HIS D 62 PHE 0.011 0.001 PHE C 32 TYR 0.007 0.001 TYR E 169 ARG 0.003 0.000 ARG D 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 125 time to evaluate : 1.285 Fit side-chains REVERT: A 75 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7151 (pt0) REVERT: A 79 GLU cc_start: 0.7083 (tt0) cc_final: 0.6728 (mt-10) REVERT: A 212 GLU cc_start: 0.7358 (tt0) cc_final: 0.6815 (pm20) REVERT: B 112 GLN cc_start: 0.6718 (tp40) cc_final: 0.5782 (mp10) REVERT: B 192 GLN cc_start: 0.7302 (mt0) cc_final: 0.7033 (mm110) REVERT: C 39 MET cc_start: 0.7880 (tpt) cc_final: 0.7377 (tpt) REVERT: C 167 ARG cc_start: 0.8339 (mtp-110) cc_final: 0.8046 (mtm110) REVERT: C 170 LYS cc_start: 0.8473 (tttm) cc_final: 0.8036 (tptp) REVERT: D 55 MET cc_start: 0.8497 (mtp) cc_final: 0.8204 (mtp) REVERT: D 140 LYS cc_start: 0.8419 (mttt) cc_final: 0.8011 (mttm) REVERT: D 170 LYS cc_start: 0.8287 (tttm) cc_final: 0.7551 (ttpp) REVERT: E 10 MET cc_start: 0.4197 (mmp) cc_final: 0.3364 (pp-130) REVERT: E 170 LYS cc_start: 0.8380 (tttm) cc_final: 0.8071 (tptt) REVERT: F 55 MET cc_start: 0.8330 (mtp) cc_final: 0.7955 (mtp) REVERT: F 75 GLU cc_start: 0.7232 (pt0) cc_final: 0.6962 (pt0) outliers start: 9 outliers final: 5 residues processed: 129 average time/residue: 1.6879 time to fit residues: 230.3714 Evaluate side-chains 128 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 122 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain E residue 144 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 0.1980 chunk 41 optimal weight: 0.0010 chunk 102 optimal weight: 5.9990 chunk 12 optimal weight: 0.2980 chunk 18 optimal weight: 0.0030 chunk 87 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 193 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.204033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.170562 restraints weight = 9216.207| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 1.96 r_work: 0.3724 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10067 Z= 0.156 Angle : 0.462 7.238 13675 Z= 0.230 Chirality : 0.040 0.168 1545 Planarity : 0.004 0.042 1769 Dihedral : 3.713 26.806 1337 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.94 % Allowed : 12.96 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.24), residues: 1241 helix: 1.91 (0.18), residues: 887 sheet: -0.03 (0.96), residues: 27 loop : 0.99 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 184 HIS 0.001 0.000 HIS D 12 PHE 0.010 0.001 PHE C 32 TYR 0.011 0.001 TYR E 169 ARG 0.003 0.000 ARG A 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4245.22 seconds wall clock time: 76 minutes 30.00 seconds (4590.00 seconds total)