Starting phenix.real_space_refine on Sat Nov 16 12:21:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7y_36053/11_2024/8j7y_36053.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7y_36053/11_2024/8j7y_36053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7y_36053/11_2024/8j7y_36053.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7y_36053/11_2024/8j7y_36053.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7y_36053/11_2024/8j7y_36053.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7y_36053/11_2024/8j7y_36053.cif" } resolution = 3.4 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= 0.005 sd= 0.055 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 Zn 2 6.06 5 S 46 5.16 5 C 7044 2.51 5 N 1830 2.21 5 O 2086 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 11008 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2193 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 9, 'TRANS': 270} Chain breaks: 3 Chain: "E" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1638 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1672 Classifications: {'peptide': 215} Link IDs: {'PCIS': 4, 'PTRANS': 7, 'TRANS': 203} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: D, B, F Time building chain proxies: 7.00, per 1000 atoms: 0.64 Number of scatterers: 11008 At special positions: 0 Unit cell: (76.7, 116.82, 159.3, 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) Zn 2 29.99 S 46 16.00 O 2086 8.00 N 1830 7.00 C 7044 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 200 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 198 " distance=2.03 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: 2.77 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 240 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 240 " 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2668 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 26 sheets defined 31.3% alpha, 36.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 23 through 32 removed outlier: 3.986A pdb=" N ARG A 27 " --> pdb=" O SER A 23 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP A 32 " --> pdb=" O SER A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 57 Processing helix chain 'A' and resid 61 through 88 removed outlier: 4.222A pdb=" N SER A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 132 Processing helix chain 'A' and resid 143 through 159 Processing helix chain 'A' and resid 232 through 259 Processing helix chain 'A' and resid 267 through 294 Proline residue: A 284 - end of helix Processing helix chain 'A' and resid 303 through 314 removed outlier: 4.475A pdb=" N GLN A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 362 Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.527A pdb=" N ALA C 87 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 132 Processing helix chain 'C' and resid 187 through 192 Processing helix chain 'F' and resid 86 through 90 Processing helix chain 'F' and resid 161 through 163 No H-bonds generated for 'chain 'F' and resid 161 through 163' Processing helix chain 'B' and resid 23 through 32 removed outlier: 3.986A pdb=" N ARG B 27 " --> pdb=" O SER B 23 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP B 32 " --> pdb=" O SER B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 57 Processing helix chain 'B' and resid 61 through 88 removed outlier: 4.222A pdb=" N SER B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 132 Processing helix chain 'B' and resid 143 through 159 Processing helix chain 'B' and resid 232 through 259 Processing helix chain 'B' and resid 267 through 294 Proline residue: B 284 - end of helix Processing helix chain 'B' and resid 303 through 314 removed outlier: 4.475A pdb=" N GLN B 307 " --> pdb=" O ASN B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 362 Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.527A pdb=" N ALA D 87 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 132 Processing helix chain 'D' and resid 187 through 192 Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 328 removed outlier: 5.558A pdb=" N LEU A 321 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE A 341 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLU A 323 " --> pdb=" O LYS A 339 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS A 339 " --> pdb=" O GLU A 323 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN A 366 " --> pdb=" O TYR A 334 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.666A pdb=" N THR E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.510A pdb=" N THR E 112 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR E 93 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER E 40 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY E 44 " --> pdb=" O SER E 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.510A pdb=" N THR E 112 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR E 93 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR E 107 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 125 through 129 removed outlier: 3.861A pdb=" N GLY E 144 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER E 184 " --> pdb=" O CYS E 145 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR E 180 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 125 through 129 removed outlier: 3.861A pdb=" N GLY E 144 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER E 184 " --> pdb=" O CYS E 145 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR E 180 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 156 through 159 removed outlier: 3.856A pdb=" N CYS E 200 " --> pdb=" O LYS E 213 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS E 213 " --> pdb=" O CYS E 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.512A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LYS C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL C 13 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET C 37 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N TYR C 53 " --> pdb=" O MET C 37 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TRP C 39 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.512A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LYS C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL C 13 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR C 101 " --> pdb=" O GLN C 94 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AB3, first strand: chain 'C' and resid 118 through 122 removed outlier: 3.818A pdb=" N ASN C 141 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL C 137 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TYR C 177 " --> pdb=" O ASN C 142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 157 through 159 removed outlier: 4.659A pdb=" N TRP C 152 " --> pdb=" O ARG C 159 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N HIS C 202 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N SER C 207 " --> pdb=" O HIS C 202 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.666A pdb=" N THR F 21 " --> pdb=" O SER F 7 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.510A pdb=" N THR F 112 " --> pdb=" O TYR F 93 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR F 93 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL F 34 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL F 50 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER F 40 " --> pdb=" O GLY F 44 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY F 44 " --> pdb=" O SER F 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.510A pdb=" N THR F 112 " --> pdb=" O TYR F 93 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR F 93 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR F 107 " --> pdb=" O ARG F 97 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 125 through 129 removed outlier: 3.862A pdb=" N GLY F 144 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER F 184 " --> pdb=" O CYS F 145 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR F 180 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 125 through 129 removed outlier: 3.862A pdb=" N GLY F 144 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER F 184 " --> pdb=" O CYS F 145 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR F 180 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 156 through 159 removed outlier: 3.856A pdb=" N CYS F 200 " --> pdb=" O LYS F 213 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS F 213 " --> pdb=" O CYS F 200 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 318 through 328 removed outlier: 5.558A pdb=" N LEU B 321 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE B 341 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLU B 323 " --> pdb=" O LYS B 339 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS B 339 " --> pdb=" O GLU B 323 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN B 366 " --> pdb=" O TYR B 334 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 14 removed outlier: 6.512A pdb=" N LEU D 11 " --> pdb=" O GLU D 109 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LYS D 111 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL D 13 " --> pdb=" O LYS D 111 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET D 37 " --> pdb=" O TYR D 53 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N TYR D 53 " --> pdb=" O MET D 37 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TRP D 39 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 10 through 14 removed outlier: 6.512A pdb=" N LEU D 11 " --> pdb=" O GLU D 109 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LYS D 111 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL D 13 " --> pdb=" O LYS D 111 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR D 101 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AC7, first strand: chain 'D' and resid 118 through 122 removed outlier: 3.819A pdb=" N ASN D 141 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL D 137 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TYR D 177 " --> pdb=" O ASN D 142 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 157 through 159 removed outlier: 4.660A pdb=" N TRP D 152 " --> pdb=" O ARG D 159 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N HIS D 202 " --> pdb=" O SER D 207 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N SER D 207 " --> pdb=" O HIS D 202 " (cutoff:3.500A) 620 hydrogen bonds defined for protein. 1716 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: 4.20 Time building geometry restraints manager: 3.24 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: 3484 1.34 - 1.46: 2685 1.46 - 1.58: 5033 1.58 - 1.70: 0 1.70 - 1.81: 66 Bond restraints: 11268 Sorted by residual: bond pdb=" CG PRO C 145 " pdb=" CD PRO C 145 " ideal model delta sigma weight residual 1.512 1.486 0.026 2.70e-02 1.37e+03 9.13e-01 bond pdb=" C ASP A 267 " pdb=" N PRO A 268 " ideal model delta sigma weight residual 1.335 1.346 -0.012 1.28e-02 6.10e+03 8.51e-01 bond pdb=" CG PRO D 145 " pdb=" CD PRO D 145 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.70e-02 1.37e+03 8.42e-01 bond pdb=" C ASP B 267 " pdb=" N PRO B 268 " ideal model delta sigma weight residual 1.335 1.346 -0.012 1.28e-02 6.10e+03 8.18e-01 bond pdb=" CG PRO C 99 " pdb=" CD PRO C 99 " ideal model delta sigma weight residual 1.512 1.489 0.023 2.70e-02 1.37e+03 7.08e-01 ... (remaining 11263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 15014 1.40 - 2.80: 255 2.80 - 4.21: 53 4.21 - 5.61: 10 5.61 - 7.01: 10 Bond angle restraints: 15342 Sorted by residual: angle pdb=" C VAL E 188 " pdb=" CA VAL E 188 " pdb=" CB VAL E 188 " ideal model delta sigma weight residual 109.33 112.33 -3.00 9.80e-01 1.04e+00 9.39e+00 angle pdb=" C VAL F 188 " pdb=" CA VAL F 188 " pdb=" CB VAL F 188 " ideal model delta sigma weight residual 109.33 112.33 -3.00 9.80e-01 1.04e+00 9.37e+00 angle pdb=" CA VAL F 188 " pdb=" C VAL F 188 " pdb=" N PRO F 189 " ideal model delta sigma weight residual 116.57 119.43 -2.86 9.80e-01 1.04e+00 8.55e+00 angle pdb=" CA VAL E 188 " pdb=" C VAL E 188 " pdb=" N PRO E 189 " ideal model delta sigma weight residual 116.57 119.40 -2.83 9.80e-01 1.04e+00 8.37e+00 angle pdb=" CA LYS C 153 " pdb=" CB LYS C 153 " pdb=" CG LYS C 153 " ideal model delta sigma weight residual 114.10 119.54 -5.44 2.00e+00 2.50e-01 7.40e+00 ... (remaining 15337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 6093 17.88 - 35.77: 458 35.77 - 53.65: 70 53.65 - 71.54: 19 71.54 - 89.42: 8 Dihedral angle restraints: 6648 sinusoidal: 2514 harmonic: 4134 Sorted by residual: dihedral pdb=" CB CYS E 145 " pdb=" SG CYS E 145 " pdb=" SG CYS E 200 " pdb=" CB CYS E 200 " ideal model delta sinusoidal sigma weight residual 93.00 149.73 -56.73 1 1.00e+01 1.00e-02 4.33e+01 dihedral pdb=" CB CYS C 23 " pdb=" SG CYS C 23 " pdb=" SG CYS C 92 " pdb=" CB CYS C 92 " ideal model delta sinusoidal sigma weight residual 93.00 57.49 35.51 1 1.00e+01 1.00e-02 1.79e+01 dihedral pdb=" CA ASP B 267 " pdb=" CB ASP B 267 " pdb=" CG ASP B 267 " pdb=" OD1 ASP B 267 " ideal model delta sinusoidal sigma weight residual -30.00 -85.71 55.71 1 2.00e+01 2.50e-03 1.05e+01 ... (remaining 6645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1107 0.029 - 0.057: 406 0.057 - 0.086: 144 0.086 - 0.115: 94 0.115 - 0.144: 15 Chirality restraints: 1766 Sorted by residual: chirality pdb=" CA ILE E 92 " pdb=" N ILE E 92 " pdb=" C ILE E 92 " pdb=" CB ILE E 92 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA ILE F 92 " pdb=" N ILE F 92 " pdb=" C ILE F 92 " pdb=" CB ILE F 92 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ASN B 152 " pdb=" N ASN B 152 " pdb=" C ASN B 152 " pdb=" CB ASN B 152 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 1763 not shown) Planarity restraints: 1938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU F 153 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO F 154 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO F 154 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 154 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 153 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO E 154 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 154 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 154 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 188 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO F 189 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO F 189 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 189 " -0.023 5.00e-02 4.00e+02 ... (remaining 1935 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 66 2.51 - 3.11: 8096 3.11 - 3.71: 16902 3.71 - 4.30: 23705 4.30 - 4.90: 40316 Nonbonded interactions: 89085 Sorted by model distance: nonbonded pdb=" CG ASP A 74 " pdb="ZN ZN A 501 " model vdw 1.914 2.460 nonbonded pdb=" CG ASP B 74 " pdb="ZN ZN B 501 " model vdw 1.914 2.460 nonbonded pdb=" OD1 ASP A 74 " pdb="ZN ZN A 501 " model vdw 2.008 2.230 nonbonded pdb=" OD1 ASP B 74 " pdb="ZN ZN B 501 " model vdw 2.009 2.230 nonbonded pdb=" SG CYS D 23 " pdb=" SG CYS D 92 " model vdw 2.033 3.760 ... (remaining 89080 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 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 1.630 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: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 31.100 Find NCS groups from input model: 0.300 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: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 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 : 0.002 0.037 11268 Z= 0.131 Angle : 0.505 7.010 15342 Z= 0.261 Chirality : 0.040 0.144 1766 Planarity : 0.003 0.050 1938 Dihedral : 13.140 89.420 3968 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.16 % Allowed : 0.33 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % 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: 1.40 (0.23), residues: 1402 helix: 2.44 (0.25), residues: 422 sheet: 0.89 (0.25), residues: 470 loop : -0.29 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 152 HIS 0.009 0.001 HIS A 240 PHE 0.005 0.001 PHE C 102 TYR 0.017 0.001 TYR E 101 ARG 0.001 0.000 ARG E 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 322 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8169 (pp20) cc_final: 0.7904 (pp20) REVERT: A 128 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7634 (mt-10) REVERT: A 319 TYR cc_start: 0.7798 (m-80) cc_final: 0.7569 (m-80) REVERT: C 4 LEU cc_start: 0.8703 (mt) cc_final: 0.8475 (mt) REVERT: C 78 THR cc_start: 0.8820 (m) cc_final: 0.8502 (p) REVERT: C 79 ILE cc_start: 0.8362 (mt) cc_final: 0.8128 (mt) REVERT: C 151 LYS cc_start: 0.8139 (mtpp) cc_final: 0.7564 (mmmt) REVERT: B 33 LYS cc_start: 0.9496 (pptt) cc_final: 0.9287 (tppt) REVERT: B 37 ASN cc_start: 0.9189 (m110) cc_final: 0.8798 (m-40) REVERT: B 50 PHE cc_start: 0.8885 (m-10) cc_final: 0.8529 (m-10) REVERT: B 73 PHE cc_start: 0.6674 (m-10) cc_final: 0.6469 (m-10) REVERT: B 120 PHE cc_start: 0.8059 (m-10) cc_final: 0.7826 (m-10) REVERT: B 154 ILE cc_start: 0.8674 (mm) cc_final: 0.8401 (mm) REVERT: B 257 MET cc_start: 0.5897 (tmm) cc_final: 0.5556 (ptm) REVERT: D 107 LYS cc_start: 0.8171 (mtpp) cc_final: 0.7971 (mmmt) REVERT: D 151 LYS cc_start: 0.8290 (mtpp) cc_final: 0.8080 (mmmt) REVERT: D 179 MET cc_start: 0.8227 (ttp) cc_final: 0.7978 (ttp) outliers start: 2 outliers final: 0 residues processed: 322 average time/residue: 0.2162 time to fit residues: 100.4928 Evaluate side-chains 197 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.0370 chunk 106 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS A 295 GLN A 361 GLN C 57 ASN C 165 ASN F 73 ASN B 295 GLN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11268 Z= 0.244 Angle : 0.605 11.281 15342 Z= 0.317 Chirality : 0.044 0.181 1766 Planarity : 0.004 0.054 1938 Dihedral : 3.796 15.519 1520 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.30 % Allowed : 11.16 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % 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: 1.22 (0.22), residues: 1402 helix: 2.25 (0.25), residues: 424 sheet: 0.84 (0.24), residues: 460 loop : -0.40 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 47 HIS 0.005 0.001 HIS A 240 PHE 0.018 0.001 PHE B 359 TYR 0.014 0.001 TYR E 150 ARG 0.007 0.000 ARG C 65 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 211 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8631 (t0) cc_final: 0.8206 (t0) REVERT: A 37 ASN cc_start: 0.9262 (m110) cc_final: 0.9057 (p0) REVERT: A 52 GLU cc_start: 0.8136 (pp20) cc_final: 0.7849 (pp20) REVERT: A 128 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7707 (mt-10) REVERT: E 176 GLN cc_start: 0.7531 (tm-30) cc_final: 0.7168 (tm-30) REVERT: E 214 LYS cc_start: 0.8411 (tptp) cc_final: 0.8172 (tptp) REVERT: C 37 MET cc_start: 0.7750 (tpp) cc_final: 0.7440 (tpp) REVERT: F 32 TYR cc_start: 0.8572 (m-80) cc_final: 0.8341 (m-80) REVERT: F 72 ASP cc_start: 0.7658 (t0) cc_final: 0.7206 (t0) REVERT: B 50 PHE cc_start: 0.8871 (m-10) cc_final: 0.8497 (m-10) REVERT: B 74 ASP cc_start: 0.6762 (m-30) cc_final: 0.6456 (m-30) REVERT: B 154 ILE cc_start: 0.8704 (mm) cc_final: 0.8439 (mm) REVERT: B 338 LEU cc_start: 0.8895 (tp) cc_final: 0.8627 (mp) outliers start: 16 outliers final: 11 residues processed: 221 average time/residue: 0.2195 time to fit residues: 71.6741 Evaluate side-chains 193 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 182 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 197 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 137 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN B 70 HIS D 160 GLN D 214 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11268 Z= 0.251 Angle : 0.579 10.359 15342 Z= 0.300 Chirality : 0.044 0.151 1766 Planarity : 0.004 0.052 1938 Dihedral : 3.866 14.892 1520 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.12 % Allowed : 12.30 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % 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: 1.08 (0.22), residues: 1402 helix: 2.18 (0.25), residues: 424 sheet: 0.70 (0.23), residues: 460 loop : -0.46 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 58 HIS 0.005 0.001 HIS A 240 PHE 0.014 0.001 PHE A 149 TYR 0.016 0.002 TYR C 190 ARG 0.004 0.000 ARG C 159 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8612 (t0) cc_final: 0.8074 (t70) REVERT: A 52 GLU cc_start: 0.7996 (pp20) cc_final: 0.7743 (pp20) REVERT: A 128 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7703 (mt-10) REVERT: A 288 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7363 (tm-30) REVERT: E 92 ILE cc_start: 0.9062 (mp) cc_final: 0.8859 (mt) REVERT: E 176 GLN cc_start: 0.7726 (tm-30) cc_final: 0.7256 (tm-30) REVERT: C 83 GLU cc_start: 0.7729 (pt0) cc_final: 0.7435 (pt0) REVERT: F 43 LYS cc_start: 0.8730 (ptpt) cc_final: 0.8427 (ptpt) REVERT: B 50 PHE cc_start: 0.8832 (m-10) cc_final: 0.8536 (m-10) REVERT: B 154 ILE cc_start: 0.8699 (mm) cc_final: 0.8442 (mm) REVERT: B 332 ASP cc_start: 0.7323 (p0) cc_final: 0.7049 (p0) outliers start: 26 outliers final: 18 residues processed: 213 average time/residue: 0.2048 time to fit residues: 64.8853 Evaluate side-chains 185 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 197 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8333 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11268 Z= 0.239 Angle : 0.571 11.794 15342 Z= 0.294 Chirality : 0.043 0.165 1766 Planarity : 0.004 0.049 1938 Dihedral : 3.838 14.656 1520 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.71 % Allowed : 14.41 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % 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: 1.07 (0.22), residues: 1402 helix: 2.13 (0.25), residues: 428 sheet: 0.70 (0.23), residues: 460 loop : -0.46 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 327 HIS 0.006 0.001 HIS A 240 PHE 0.013 0.001 PHE B 149 TYR 0.015 0.001 TYR C 190 ARG 0.006 0.000 ARG C 159 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8464 (t0) cc_final: 0.7978 (t0) REVERT: A 52 GLU cc_start: 0.8060 (pp20) cc_final: 0.7792 (pp20) REVERT: A 128 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7709 (mt-10) REVERT: A 288 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7458 (tm-30) REVERT: E 176 GLN cc_start: 0.7833 (tm-30) cc_final: 0.7310 (tm-30) REVERT: B 50 PHE cc_start: 0.8828 (m-10) cc_final: 0.8512 (m-10) REVERT: B 154 ILE cc_start: 0.8727 (mm) cc_final: 0.8472 (mm) REVERT: B 332 ASP cc_start: 0.7479 (p0) cc_final: 0.7216 (p0) REVERT: D 127 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7982 (mp0) outliers start: 21 outliers final: 15 residues processed: 197 average time/residue: 0.2093 time to fit residues: 61.1238 Evaluate side-chains 193 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 197 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 115 optimal weight: 0.5980 chunk 93 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 GLN D 214 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11268 Z= 0.247 Angle : 0.563 7.992 15342 Z= 0.293 Chirality : 0.043 0.150 1766 Planarity : 0.004 0.050 1938 Dihedral : 3.836 14.764 1520 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.79 % Allowed : 14.66 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % 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: 1.08 (0.22), residues: 1402 helix: 2.13 (0.24), residues: 428 sheet: 0.62 (0.23), residues: 468 loop : -0.35 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 58 HIS 0.003 0.001 HIS E 35 PHE 0.021 0.001 PHE A 149 TYR 0.026 0.001 TYR E 150 ARG 0.003 0.000 ARG F 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8516 (t0) cc_final: 0.8043 (t0) REVERT: A 52 GLU cc_start: 0.8097 (pp20) cc_final: 0.7790 (pp20) REVERT: A 74 ASP cc_start: 0.6774 (m-30) cc_final: 0.6491 (m-30) REVERT: A 128 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7694 (mt-10) REVERT: A 288 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7576 (tm-30) REVERT: A 347 ASP cc_start: 0.8302 (t0) cc_final: 0.8095 (t0) REVERT: E 138 ASN cc_start: 0.9017 (p0) cc_final: 0.8808 (p0) REVERT: E 176 GLN cc_start: 0.7911 (tm-30) cc_final: 0.7506 (tm-30) REVERT: B 50 PHE cc_start: 0.8857 (m-10) cc_final: 0.8523 (m-10) REVERT: B 74 ASP cc_start: 0.7007 (m-30) cc_final: 0.6675 (m-30) REVERT: B 154 ILE cc_start: 0.8714 (mm) cc_final: 0.8464 (mm) outliers start: 22 outliers final: 18 residues processed: 202 average time/residue: 0.2182 time to fit residues: 65.0743 Evaluate side-chains 198 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 197 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.9980 chunk 26 optimal weight: 0.0670 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 128 GLN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11268 Z= 0.222 Angle : 0.578 13.889 15342 Z= 0.297 Chirality : 0.043 0.155 1766 Planarity : 0.004 0.048 1938 Dihedral : 3.810 14.671 1520 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.20 % Allowed : 15.15 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % 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 (0.22), residues: 1402 helix: 2.12 (0.25), residues: 428 sheet: 0.63 (0.23), residues: 468 loop : -0.29 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 58 HIS 0.003 0.001 HIS A 240 PHE 0.019 0.001 PHE A 149 TYR 0.026 0.001 TYR E 150 ARG 0.004 0.000 ARG D 215 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 1.238 Fit side-chains revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8429 (t0) cc_final: 0.7982 (t0) REVERT: A 52 GLU cc_start: 0.8092 (pp20) cc_final: 0.7839 (pp20) REVERT: A 74 ASP cc_start: 0.6799 (m-30) cc_final: 0.6510 (m-30) REVERT: A 128 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7861 (mt-10) REVERT: A 288 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7647 (tm-30) REVERT: E 138 ASN cc_start: 0.9019 (p0) cc_final: 0.8709 (p0) REVERT: E 176 GLN cc_start: 0.7950 (tm-30) cc_final: 0.7523 (tm-30) REVERT: C 127 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8435 (mp0) REVERT: B 50 PHE cc_start: 0.8858 (m-10) cc_final: 0.8531 (m-10) REVERT: B 153 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8980 (pp) REVERT: B 154 ILE cc_start: 0.8625 (mm) cc_final: 0.8300 (mm) outliers start: 27 outliers final: 17 residues processed: 203 average time/residue: 0.2064 time to fit residues: 61.7531 Evaluate side-chains 193 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 197 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 76 optimal weight: 0.0060 chunk 114 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 83 optimal weight: 0.0570 overall best weight: 0.5114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 GLN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11268 Z= 0.192 Angle : 0.584 16.093 15342 Z= 0.297 Chirality : 0.043 0.156 1766 Planarity : 0.004 0.050 1938 Dihedral : 3.827 15.580 1520 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.47 % Allowed : 16.21 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % 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 (0.22), residues: 1402 helix: 2.05 (0.25), residues: 428 sheet: 0.64 (0.23), residues: 468 loop : -0.24 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 58 HIS 0.002 0.000 HIS A 161 PHE 0.028 0.001 PHE B 114 TYR 0.027 0.001 TYR E 150 ARG 0.002 0.000 ARG F 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 189 time to evaluate : 1.316 Fit side-chains revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8400 (t0) cc_final: 0.7946 (t0) REVERT: A 52 GLU cc_start: 0.8077 (pp20) cc_final: 0.7841 (pp20) REVERT: A 74 ASP cc_start: 0.6828 (m-30) cc_final: 0.6535 (m-30) REVERT: A 128 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7858 (mt-10) REVERT: A 288 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7643 (tm-30) REVERT: A 347 ASP cc_start: 0.8286 (t0) cc_final: 0.8016 (t0) REVERT: E 32 TYR cc_start: 0.8931 (m-80) cc_final: 0.8728 (m-80) REVERT: E 138 ASN cc_start: 0.9021 (p0) cc_final: 0.8755 (p0) REVERT: E 176 GLN cc_start: 0.7965 (tm-30) cc_final: 0.7535 (tm-30) REVERT: B 50 PHE cc_start: 0.8789 (m-10) cc_final: 0.8446 (m-10) REVERT: B 74 ASP cc_start: 0.7169 (m-30) cc_final: 0.6875 (m-30) REVERT: B 154 ILE cc_start: 0.8571 (mm) cc_final: 0.8194 (mm) outliers start: 18 outliers final: 14 residues processed: 200 average time/residue: 0.2037 time to fit residues: 60.3544 Evaluate side-chains 191 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 136 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.0000 chunk 80 optimal weight: 0.9980 chunk 40 optimal weight: 0.0050 chunk 26 optimal weight: 0.9980 chunk 85 optimal weight: 0.0770 chunk 91 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- 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: 0.8348 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11268 Z= 0.186 Angle : 0.622 15.624 15342 Z= 0.313 Chirality : 0.043 0.159 1766 Planarity : 0.004 0.051 1938 Dihedral : 3.772 16.521 1520 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.87 % Allowed : 16.53 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % 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: 1.12 (0.22), residues: 1402 helix: 2.03 (0.25), residues: 428 sheet: 0.67 (0.23), residues: 468 loop : -0.22 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 159 HIS 0.002 0.000 HIS E 35 PHE 0.024 0.001 PHE B 114 TYR 0.027 0.001 TYR E 150 ARG 0.002 0.000 ARG C 159 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 1.239 Fit side-chains revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8378 (t0) cc_final: 0.7924 (t0) REVERT: A 52 GLU cc_start: 0.8082 (pp20) cc_final: 0.7860 (pp20) REVERT: A 74 ASP cc_start: 0.6827 (m-30) cc_final: 0.6541 (m-30) REVERT: A 128 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7855 (mt-10) REVERT: A 288 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7613 (tm-30) REVERT: A 347 ASP cc_start: 0.8212 (t0) cc_final: 0.7988 (t0) REVERT: E 32 TYR cc_start: 0.8937 (m-80) cc_final: 0.8735 (m-80) REVERT: E 138 ASN cc_start: 0.9026 (p0) cc_final: 0.8767 (p0) REVERT: E 176 GLN cc_start: 0.7968 (tm-30) cc_final: 0.7542 (tm-30) REVERT: B 50 PHE cc_start: 0.8819 (m-10) cc_final: 0.8441 (m-10) REVERT: B 74 ASP cc_start: 0.7191 (m-30) cc_final: 0.6891 (m-30) REVERT: B 154 ILE cc_start: 0.8581 (mm) cc_final: 0.8273 (mm) REVERT: D 144 TYR cc_start: 0.8807 (t80) cc_final: 0.8587 (t80) outliers start: 23 outliers final: 19 residues processed: 202 average time/residue: 0.2029 time to fit residues: 60.9277 Evaluate side-chains 201 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 197 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.0020 chunk 125 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 132 optimal weight: 0.3980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 214 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11268 Z= 0.204 Angle : 0.626 14.815 15342 Z= 0.315 Chirality : 0.043 0.262 1766 Planarity : 0.004 0.051 1938 Dihedral : 3.794 16.385 1520 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.71 % Allowed : 16.78 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % 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: 1.12 (0.22), residues: 1402 helix: 1.99 (0.25), residues: 428 sheet: 0.69 (0.23), residues: 468 loop : -0.21 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 58 HIS 0.002 0.000 HIS E 35 PHE 0.026 0.001 PHE A 149 TYR 0.027 0.001 TYR E 150 ARG 0.003 0.000 ARG D 159 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 1.257 Fit side-chains revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8384 (t0) cc_final: 0.7922 (t0) REVERT: A 52 GLU cc_start: 0.8167 (pp20) cc_final: 0.7955 (pp20) REVERT: A 74 ASP cc_start: 0.6852 (m-30) cc_final: 0.6573 (m-30) REVERT: A 128 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7853 (mt-10) REVERT: A 288 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7629 (tm-30) REVERT: E 138 ASN cc_start: 0.8982 (p0) cc_final: 0.8709 (p0) REVERT: E 176 GLN cc_start: 0.7975 (tm-30) cc_final: 0.7552 (tm-30) REVERT: B 50 PHE cc_start: 0.8762 (m-10) cc_final: 0.8378 (m-10) REVERT: B 74 ASP cc_start: 0.7209 (m-30) cc_final: 0.6919 (m-30) REVERT: B 154 ILE cc_start: 0.8566 (mm) cc_final: 0.8262 (mm) REVERT: D 144 TYR cc_start: 0.8793 (t80) cc_final: 0.8560 (t80) outliers start: 21 outliers final: 21 residues processed: 201 average time/residue: 0.1993 time to fit residues: 59.3187 Evaluate side-chains 199 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 197 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.3980 chunk 63 optimal weight: 0.0980 chunk 92 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 111 optimal weight: 0.0770 chunk 11 optimal weight: 4.9990 chunk 85 optimal weight: 0.3980 chunk 68 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- 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: 0.8344 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11268 Z= 0.186 Angle : 0.637 15.812 15342 Z= 0.319 Chirality : 0.043 0.237 1766 Planarity : 0.004 0.051 1938 Dihedral : 3.781 16.662 1520 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.87 % Allowed : 16.86 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % 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: 1.15 (0.22), residues: 1402 helix: 2.01 (0.25), residues: 428 sheet: 0.71 (0.23), residues: 468 loop : -0.19 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 58 HIS 0.002 0.000 HIS E 35 PHE 0.025 0.001 PHE A 149 TYR 0.027 0.001 TYR E 150 ARG 0.003 0.000 ARG C 159 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 1.354 Fit side-chains revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8386 (t0) cc_final: 0.7941 (t0) REVERT: A 74 ASP cc_start: 0.6896 (m-30) cc_final: 0.6611 (m-30) REVERT: A 128 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7846 (mt-10) REVERT: A 288 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7629 (tm-30) REVERT: E 6 GLU cc_start: 0.8395 (mp0) cc_final: 0.8120 (mp0) REVERT: E 138 ASN cc_start: 0.9008 (p0) cc_final: 0.8761 (p0) REVERT: E 176 GLN cc_start: 0.7896 (tm-30) cc_final: 0.7487 (tm-30) REVERT: B 50 PHE cc_start: 0.8737 (m-10) cc_final: 0.8345 (m-10) REVERT: B 154 ILE cc_start: 0.8579 (mm) cc_final: 0.8301 (mm) REVERT: B 332 ASP cc_start: 0.7728 (p0) cc_final: 0.7311 (p0) REVERT: D 144 TYR cc_start: 0.8851 (t80) cc_final: 0.8626 (t80) outliers start: 23 outliers final: 19 residues processed: 204 average time/residue: 0.2082 time to fit residues: 62.2434 Evaluate side-chains 203 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain E residue 1 GLU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 197 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 111 optimal weight: 0.0060 chunk 46 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 14 optimal weight: 0.0270 chunk 20 optimal weight: 0.0670 chunk 97 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 overall best weight: 0.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 169 HIS D 214 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.120111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.082430 restraints weight = 20119.923| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.51 r_work: 0.3023 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11268 Z= 0.176 Angle : 0.641 15.541 15342 Z= 0.320 Chirality : 0.043 0.230 1766 Planarity : 0.004 0.051 1938 Dihedral : 3.750 16.251 1520 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.47 % Allowed : 17.10 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % 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: 1.13 (0.22), residues: 1402 helix: 1.92 (0.25), residues: 428 sheet: 0.73 (0.24), residues: 468 loop : -0.17 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 58 HIS 0.002 0.000 HIS A 325 PHE 0.027 0.001 PHE A 149 TYR 0.029 0.001 TYR E 150 ARG 0.003 0.000 ARG D 159 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2646.13 seconds wall clock time: 49 minutes 27.97 seconds (2967.97 seconds total)