Starting phenix.real_space_refine on Thu Jul 31 18:07:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sk3_25171/07_2025/7sk3_25171_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sk3_25171/07_2025/7sk3_25171.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sk3_25171/07_2025/7sk3_25171.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sk3_25171/07_2025/7sk3_25171.map" model { file = "/net/cci-nas-00/data/ceres_data/7sk3_25171/07_2025/7sk3_25171_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sk3_25171/07_2025/7sk3_25171_trim.cif" } resolution = 3.8 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= -0.002 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 38 5.16 5 C 4480 2.51 5 N 1079 2.21 5 O 1206 1.98 5 H 6491 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13294 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 4967 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 11, 'TRANS': 292} Chain: "B" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1145 Classifications: {'peptide': 68} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain: "C" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1592 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1888 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "E" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1607 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "F" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1871 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "A" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 224 Unusual residues: {'CLR': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 7.10, per 1000 atoms: 0.53 Number of scatterers: 13294 At special positions: 0 Unit cell: (70.2, 71.28, 146.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 O 1206 8.00 N 1079 7.00 C 4480 6.00 H 6491 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 9 " - pdb=" SG CYS B 34 " distance=2.03 Simple disulfide: pdb=" SG CYS B 11 " - pdb=" SG CYS B 50 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 99 " 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: 3.43 Conformation dependent library (CDL) restraints added in 965.4 milliseconds 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1568 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 15 sheets defined 34.5% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 40 through 73 removed outlier: 3.824A pdb=" N ALA A 61 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.579A pdb=" N LEU A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A 96 " --> pdb=" O TRP A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 106 removed outlier: 3.642A pdb=" N TRP A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN A 106 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 148 removed outlier: 3.939A pdb=" N SER A 131 " --> pdb=" O ASN A 127 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 152 Processing helix chain 'A' and resid 153 through 182 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 204 through 219 removed outlier: 4.272A pdb=" N SER A 216 " --> pdb=" O MET A 212 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 242 Processing helix chain 'A' and resid 242 through 249 removed outlier: 3.590A pdb=" N LYS A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N HIS A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 280 removed outlier: 4.362A pdb=" N ILE A 254 " --> pdb=" O SER A 250 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 255 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL A 258 " --> pdb=" O ILE A 254 " (cutoff:3.500A) Proline residue: A 267 - end of helix removed outlier: 3.575A pdb=" N LEU A 273 " --> pdb=" O HIS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 311 removed outlier: 3.878A pdb=" N GLU A 290 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N HIS A 291 " --> pdb=" O CYS A 287 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N CYS A 308 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N CYS A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 316 Processing helix chain 'A' and resid 319 through 329 Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.751A pdb=" N VAL B 23 " --> pdb=" O ARG B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 68 Processing helix chain 'D' and resid 65 through 68 Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 65 through 68 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33 removed outlier: 3.583A pdb=" N VAL A 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN B 30 " --> pdb=" O VAL A 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 79 removed outlier: 3.705A pdb=" N SER F 112 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 183 through 187 Processing sheet with id=AA4, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AA5, first strand: chain 'C' and resid 5 through 8 Processing sheet with id=AA6, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.119A pdb=" N GLN C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LEU C 47 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR C 50 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 11 through 13 Processing sheet with id=AA8, first strand: chain 'D' and resid 6 through 10 Processing sheet with id=AA9, first strand: chain 'D' and resid 61 through 63 removed outlier: 3.574A pdb=" N SER D 62 " --> pdb=" O TYR D 53 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TRP D 39 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR D 53 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE D 37 " --> pdb=" O TYR D 53 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR D 117 " --> pdb=" O ARG D 101 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 61 through 63 removed outlier: 3.574A pdb=" N SER D 62 " --> pdb=" O TYR D 53 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TRP D 39 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR D 53 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE D 37 " --> pdb=" O TYR D 53 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 5 through 8 Processing sheet with id=AB3, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.691A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.638A pdb=" N GLN E 91 " --> pdb=" O THR E 98 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR E 98 " --> pdb=" O GLN E 91 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 6 through 10 Processing sheet with id=AB6, first strand: chain 'F' and resid 61 through 63 removed outlier: 3.694A pdb=" N SER F 62 " --> pdb=" O SER F 53 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER F 53 " --> pdb=" O SER F 62 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N TRP F 50 " --> pdb=" O ARG F 41 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG F 41 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER F 36 " --> pdb=" O VAL F 102 " (cutoff:3.500A) 337 hydrogen bonds defined for protein. 921 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: 4.28 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6480 1.03 - 1.23: 18 1.23 - 1.42: 2983 1.42 - 1.62: 3967 1.62 - 1.81: 51 Bond restraints: 13499 Sorted by residual: bond pdb=" C6 CLR A 608 " pdb=" C7 CLR A 608 " ideal model delta sigma weight residual 1.492 1.541 -0.049 2.00e-02 2.50e+03 5.90e+00 bond pdb=" C6 CLR A 607 " pdb=" C7 CLR A 607 " ideal model delta sigma weight residual 1.492 1.541 -0.049 2.00e-02 2.50e+03 5.90e+00 bond pdb=" C6 CLR A 605 " pdb=" C7 CLR A 605 " ideal model delta sigma weight residual 1.492 1.538 -0.046 2.00e-02 2.50e+03 5.38e+00 bond pdb=" C6 CLR A 604 " pdb=" C7 CLR A 604 " ideal model delta sigma weight residual 1.492 1.538 -0.046 2.00e-02 2.50e+03 5.31e+00 bond pdb=" C6 CLR A 606 " pdb=" C7 CLR A 606 " ideal model delta sigma weight residual 1.492 1.538 -0.046 2.00e-02 2.50e+03 5.29e+00 ... (remaining 13494 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 23859 1.69 - 3.38: 269 3.38 - 5.07: 50 5.07 - 6.76: 22 6.76 - 8.45: 8 Bond angle restraints: 24208 Sorted by residual: angle pdb=" C22 CLR A 602 " pdb=" C23 CLR A 602 " pdb=" C24 CLR A 602 " ideal model delta sigma weight residual 111.95 103.50 8.45 3.00e+00 1.11e-01 7.93e+00 angle pdb=" C22 CLR A 605 " pdb=" C23 CLR A 605 " pdb=" C24 CLR A 605 " ideal model delta sigma weight residual 111.95 103.66 8.29 3.00e+00 1.11e-01 7.64e+00 angle pdb=" C22 CLR A 604 " pdb=" C23 CLR A 604 " pdb=" C24 CLR A 604 " ideal model delta sigma weight residual 111.95 103.81 8.14 3.00e+00 1.11e-01 7.36e+00 angle pdb=" C22 CLR A 603 " pdb=" C23 CLR A 603 " pdb=" C24 CLR A 603 " ideal model delta sigma weight residual 111.95 103.94 8.01 3.00e+00 1.11e-01 7.13e+00 angle pdb=" C22 CLR A 608 " pdb=" C23 CLR A 608 " pdb=" C24 CLR A 608 " ideal model delta sigma weight residual 111.95 104.02 7.93 3.00e+00 1.11e-01 7.00e+00 ... (remaining 24203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 6249 17.78 - 35.56: 484 35.56 - 53.34: 112 53.34 - 71.12: 19 71.12 - 88.90: 5 Dihedral angle restraints: 6869 sinusoidal: 3824 harmonic: 3045 Sorted by residual: dihedral pdb=" CA TYR D 55 " pdb=" C TYR D 55 " pdb=" N SER D 56 " pdb=" CA SER D 56 " ideal model delta harmonic sigma weight residual -180.00 -159.89 -20.11 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA HIS A 269 " pdb=" C HIS A 269 " pdb=" N VAL A 270 " pdb=" CA VAL A 270 " ideal model delta harmonic sigma weight residual 180.00 161.47 18.53 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA GLY C 69 " pdb=" C GLY C 69 " pdb=" N THR C 70 " pdb=" CA THR C 70 " ideal model delta harmonic sigma weight residual 180.00 163.37 16.63 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 6866 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 979 0.080 - 0.161: 86 0.161 - 0.241: 2 0.241 - 0.321: 22 0.321 - 0.402: 8 Chirality restraints: 1097 Sorted by residual: chirality pdb=" C17 CLR A 606 " pdb=" C13 CLR A 606 " pdb=" C16 CLR A 606 " pdb=" C20 CLR A 606 " both_signs ideal model delta sigma weight residual False 2.55 2.95 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" C17 CLR A 608 " pdb=" C13 CLR A 608 " pdb=" C16 CLR A 608 " pdb=" C20 CLR A 608 " both_signs ideal model delta sigma weight residual False 2.55 2.92 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" C17 CLR A 604 " pdb=" C13 CLR A 604 " pdb=" C16 CLR A 604 " pdb=" C20 CLR A 604 " both_signs ideal model delta sigma weight residual False 2.55 2.92 -0.37 2.00e-01 2.50e+01 3.37e+00 ... (remaining 1094 not shown) Planarity restraints: 1921 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 80 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO E 81 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO E 81 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 81 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 12 " -0.111 9.50e-02 1.11e+02 3.70e-02 1.59e+00 pdb=" NE ARG B 12 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG B 12 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 12 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 12 " -0.002 2.00e-02 2.50e+03 pdb="HH11 ARG B 12 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG B 12 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG B 12 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 12 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 40 " -0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO C 41 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO C 41 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 41 " -0.015 5.00e-02 4.00e+02 ... (remaining 1918 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 2238 2.28 - 2.86: 28788 2.86 - 3.44: 31611 3.44 - 4.02: 45014 4.02 - 4.60: 67718 Nonbonded interactions: 175369 Sorted by model distance: nonbonded pdb=" OE2 GLU F 9 " pdb=" H CYS F 99 " model vdw 1.697 2.450 nonbonded pdb=" HH TYR C 37 " pdb=" OE1 GLN C 90 " model vdw 1.727 2.450 nonbonded pdb=" HE ARG F 41 " pdb=" OE2 GLU F 49 " model vdw 1.762 2.450 nonbonded pdb=" OE1 GLU C 82 " pdb=" H GLU C 82 " model vdw 1.779 2.450 nonbonded pdb="HE22 GLN A 245 " pdb=" O TYR F 104 " model vdw 1.786 2.450 ... (remaining 175364 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 'C' and (resid 3 through 91 or resid 93 through 94 or resid 98 through 10 \ 7)) selection = (chain 'E' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name CD1 or name HA or name HB or name HG12 or name HG \ 13 or name HG21 or name HG22 or name HG23 or name HD11 or name HD12 or name HD13 \ )) or resid 4 through 54 or (resid 55 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB \ 3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or \ name HD23)) or resid 56 through 91 or resid 93 through 94 or resid 98 through 1 \ 07)) } ncs_group { reference = (chain 'D' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name H \ G13 or name HG21 or name HG22 or name HG23)) or resid 6 through 31 or resid 33 o \ r resid 35 through 52 or resid 54 or resid 57 through 102 or resid 105 through 1 \ 06 or resid 111 or resid 113 or resid 116 through 127)) selection = (chain 'F' and (resid 5 through 31 or resid 33 or resid 35 through 52 or resid 5 \ 4 or resid 57 through 102 or resid 105 or resid 109 or resid 114 or resid 116 or \ resid 118 through 129)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.240 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 30.660 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 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 0.049 7015 Z= 0.231 Angle : 0.677 8.449 9606 Z= 0.281 Chirality : 0.067 0.402 1097 Planarity : 0.003 0.049 1131 Dihedral : 13.105 88.900 2881 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.15 (0.31), residues: 819 helix: 1.65 (0.35), residues: 239 sheet: 0.12 (0.38), residues: 216 loop : -0.94 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 36 HIS 0.004 0.001 HIS A 121 PHE 0.008 0.001 PHE A 53 TYR 0.009 0.001 TYR D 55 ARG 0.005 0.000 ARG B 12 Details of bonding type rmsd hydrogen bonds : bond 0.18188 ( 318) hydrogen bonds : angle 6.57519 ( 921) SS BOND : bond 0.00241 ( 7) SS BOND : angle 0.83547 ( 14) covalent geometry : bond 0.00479 ( 7008) covalent geometry : angle 0.67681 ( 9592) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8507 (t80) cc_final: 0.8295 (t80) REVERT: A 79 THR cc_start: 0.8984 (p) cc_final: 0.8759 (p) REVERT: C 107 ILE cc_start: 0.7209 (mp) cc_final: 0.6672 (mp) REVERT: F 93 ASP cc_start: 0.8440 (t0) cc_final: 0.8014 (t0) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.4017 time to fit residues: 73.0636 Evaluate side-chains 117 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.0970 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 0.1980 chunk 32 optimal weight: 0.4980 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 GLN F 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.111194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.094564 restraints weight = 28686.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.098267 restraints weight = 16167.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.100538 restraints weight = 10656.972| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7015 Z= 0.122 Angle : 0.489 4.841 9606 Z= 0.264 Chirality : 0.040 0.138 1097 Planarity : 0.003 0.039 1131 Dihedral : 5.564 59.543 1438 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.96 % Allowed : 6.31 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.17 (0.31), residues: 819 helix: 1.70 (0.34), residues: 242 sheet: 0.15 (0.37), residues: 217 loop : -1.01 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 50 HIS 0.006 0.001 HIS A 121 PHE 0.008 0.001 PHE A 231 TYR 0.010 0.001 TYR D 117 ARG 0.002 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.05858 ( 318) hydrogen bonds : angle 5.24292 ( 921) SS BOND : bond 0.00353 ( 7) SS BOND : angle 0.83728 ( 14) covalent geometry : bond 0.00255 ( 7008) covalent geometry : angle 0.48860 ( 9592) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 116 ASP cc_start: 0.7795 (m-30) cc_final: 0.7593 (m-30) REVERT: F 93 ASP cc_start: 0.8400 (t0) cc_final: 0.7900 (t0) outliers start: 7 outliers final: 5 residues processed: 130 average time/residue: 0.3781 time to fit residues: 66.1790 Evaluate side-chains 122 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 117 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 98 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 GLN F 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.109361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.092991 restraints weight = 29065.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.096452 restraints weight = 16652.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.098736 restraints weight = 11155.097| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7015 Z= 0.141 Angle : 0.489 6.163 9606 Z= 0.263 Chirality : 0.040 0.133 1097 Planarity : 0.003 0.040 1131 Dihedral : 5.174 55.957 1438 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.51 % Allowed : 7.54 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.14 (0.30), residues: 819 helix: 1.70 (0.34), residues: 243 sheet: 0.16 (0.37), residues: 224 loop : -1.08 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 50 HIS 0.005 0.001 HIS A 121 PHE 0.008 0.001 PHE A 149 TYR 0.010 0.001 TYR D 117 ARG 0.005 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.05224 ( 318) hydrogen bonds : angle 4.95465 ( 921) SS BOND : bond 0.00354 ( 7) SS BOND : angle 0.81290 ( 14) covalent geometry : bond 0.00319 ( 7008) covalent geometry : angle 0.48833 ( 9592) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 116 ASP cc_start: 0.7632 (m-30) cc_final: 0.7370 (m-30) REVERT: F 93 ASP cc_start: 0.8339 (t0) cc_final: 0.8051 (t0) outliers start: 11 outliers final: 10 residues processed: 124 average time/residue: 0.4094 time to fit residues: 68.0962 Evaluate side-chains 120 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain F residue 124 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 4 GLN F 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.107236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.090710 restraints weight = 29107.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.094219 restraints weight = 16849.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.096540 restraints weight = 11342.558| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7015 Z= 0.188 Angle : 0.515 5.945 9606 Z= 0.278 Chirality : 0.040 0.135 1097 Planarity : 0.003 0.040 1131 Dihedral : 5.216 50.517 1438 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.19 % Allowed : 8.64 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.03 (0.30), residues: 819 helix: 1.65 (0.34), residues: 243 sheet: 0.04 (0.37), residues: 219 loop : -1.23 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 36 HIS 0.006 0.001 HIS A 121 PHE 0.010 0.001 PHE A 149 TYR 0.011 0.001 TYR D 117 ARG 0.002 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.05278 ( 318) hydrogen bonds : angle 4.90676 ( 921) SS BOND : bond 0.00382 ( 7) SS BOND : angle 0.89087 ( 14) covalent geometry : bond 0.00431 ( 7008) covalent geometry : angle 0.51384 ( 9592) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 GLU cc_start: 0.7536 (tm-30) cc_final: 0.6836 (tm-30) REVERT: F 93 ASP cc_start: 0.8406 (t0) cc_final: 0.8128 (t0) outliers start: 16 outliers final: 14 residues processed: 125 average time/residue: 0.3745 time to fit residues: 62.9672 Evaluate side-chains 125 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain F residue 124 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 64 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 GLN F 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.107812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.091024 restraints weight = 29285.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.094683 restraints weight = 16558.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.097109 restraints weight = 11004.458| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7015 Z= 0.177 Angle : 0.510 6.238 9606 Z= 0.274 Chirality : 0.040 0.134 1097 Planarity : 0.003 0.040 1131 Dihedral : 5.195 46.332 1438 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.06 % Allowed : 11.25 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.07 (0.30), residues: 819 helix: 1.63 (0.33), residues: 242 sheet: 0.04 (0.37), residues: 217 loop : -1.28 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 36 HIS 0.006 0.001 HIS A 121 PHE 0.010 0.001 PHE A 149 TYR 0.010 0.001 TYR D 53 ARG 0.001 0.000 ARG D 101 Details of bonding type rmsd hydrogen bonds : bond 0.05110 ( 318) hydrogen bonds : angle 4.81939 ( 921) SS BOND : bond 0.00389 ( 7) SS BOND : angle 0.82705 ( 14) covalent geometry : bond 0.00406 ( 7008) covalent geometry : angle 0.50917 ( 9592) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7235 (tm-30) REVERT: C 106 GLU cc_start: 0.7475 (tm-30) cc_final: 0.6648 (tm-30) REVERT: F 93 ASP cc_start: 0.8477 (t0) cc_final: 0.8195 (t0) outliers start: 15 outliers final: 15 residues processed: 127 average time/residue: 0.3824 time to fit residues: 65.4022 Evaluate side-chains 130 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain F residue 124 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 3 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 GLN E 4 GLN F 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.108268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.091314 restraints weight = 29739.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.095024 restraints weight = 16814.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.097447 restraints weight = 11140.626| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7015 Z= 0.163 Angle : 0.499 6.403 9606 Z= 0.268 Chirality : 0.040 0.132 1097 Planarity : 0.003 0.040 1131 Dihedral : 5.143 42.465 1438 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.33 % Allowed : 11.39 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.07 (0.30), residues: 819 helix: 1.68 (0.33), residues: 242 sheet: 0.01 (0.37), residues: 217 loop : -1.29 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 36 HIS 0.005 0.001 HIS A 121 PHE 0.010 0.001 PHE A 149 TYR 0.009 0.001 TYR A 257 ARG 0.002 0.000 ARG F 70 Details of bonding type rmsd hydrogen bonds : bond 0.04956 ( 318) hydrogen bonds : angle 4.73368 ( 921) SS BOND : bond 0.00371 ( 7) SS BOND : angle 0.77833 ( 14) covalent geometry : bond 0.00374 ( 7008) covalent geometry : angle 0.49897 ( 9592) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 15 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7239 (tm-30) REVERT: F 93 ASP cc_start: 0.8440 (t0) cc_final: 0.8143 (t0) outliers start: 17 outliers final: 17 residues processed: 127 average time/residue: 0.3788 time to fit residues: 64.4847 Evaluate side-chains 129 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain F residue 124 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 3 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 38 optimal weight: 0.0270 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 overall best weight: 1.0442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 GLN E 101 GLN F 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.107054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.090154 restraints weight = 29439.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.093791 restraints weight = 16792.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.096208 restraints weight = 11204.164| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7015 Z= 0.175 Angle : 0.512 6.603 9606 Z= 0.275 Chirality : 0.040 0.133 1097 Planarity : 0.004 0.039 1131 Dihedral : 5.214 39.332 1438 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.74 % Allowed : 11.52 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.11 (0.30), residues: 819 helix: 1.68 (0.33), residues: 242 sheet: -0.02 (0.37), residues: 217 loop : -1.35 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 36 HIS 0.005 0.001 HIS A 121 PHE 0.010 0.001 PHE A 149 TYR 0.010 0.001 TYR D 53 ARG 0.003 0.000 ARG F 70 Details of bonding type rmsd hydrogen bonds : bond 0.04990 ( 318) hydrogen bonds : angle 4.72042 ( 921) SS BOND : bond 0.00371 ( 7) SS BOND : angle 0.80739 ( 14) covalent geometry : bond 0.00403 ( 7008) covalent geometry : angle 0.51119 ( 9592) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.7415 (m-80) cc_final: 0.7194 (m-80) REVERT: B 15 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7215 (tm-30) REVERT: C 106 GLU cc_start: 0.7743 (tp30) cc_final: 0.7484 (tm-30) REVERT: F 93 ASP cc_start: 0.8500 (t0) cc_final: 0.8195 (t0) outliers start: 20 outliers final: 19 residues processed: 125 average time/residue: 0.4027 time to fit residues: 67.8965 Evaluate side-chains 130 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain F residue 124 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 77 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 0.0770 chunk 35 optimal weight: 0.2980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 GLN E 101 GLN F 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.109433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.092815 restraints weight = 29188.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.096410 restraints weight = 16768.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.098785 restraints weight = 11215.000| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7015 Z= 0.115 Angle : 0.475 5.895 9606 Z= 0.253 Chirality : 0.039 0.130 1097 Planarity : 0.003 0.039 1131 Dihedral : 4.918 36.726 1438 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.92 % Allowed : 12.35 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.08 (0.30), residues: 819 helix: 1.83 (0.34), residues: 243 sheet: 0.13 (0.37), residues: 215 loop : -1.25 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 36 HIS 0.004 0.001 HIS A 121 PHE 0.009 0.001 PHE A 149 TYR 0.014 0.001 TYR D 60 ARG 0.003 0.000 ARG E 25 Details of bonding type rmsd hydrogen bonds : bond 0.04486 ( 318) hydrogen bonds : angle 4.56001 ( 921) SS BOND : bond 0.00325 ( 7) SS BOND : angle 0.62655 ( 14) covalent geometry : bond 0.00257 ( 7008) covalent geometry : angle 0.47425 ( 9592) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 GLU cc_start: 0.7466 (tm-30) cc_final: 0.7106 (tm-30) REVERT: F 93 ASP cc_start: 0.8454 (t0) cc_final: 0.8149 (t0) outliers start: 14 outliers final: 14 residues processed: 127 average time/residue: 0.3921 time to fit residues: 66.9566 Evaluate side-chains 127 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain F residue 124 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 22 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 70 optimal weight: 0.0870 chunk 32 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 GLN E 101 GLN F 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.109560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.092942 restraints weight = 28987.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.096450 restraints weight = 16765.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.098805 restraints weight = 11289.934| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7015 Z= 0.128 Angle : 0.489 6.919 9606 Z= 0.260 Chirality : 0.040 0.136 1097 Planarity : 0.003 0.038 1131 Dihedral : 4.902 35.996 1438 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.33 % Allowed : 12.21 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.12 (0.30), residues: 819 helix: 1.91 (0.34), residues: 243 sheet: 0.15 (0.37), residues: 215 loop : -1.26 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 36 HIS 0.005 0.001 HIS A 121 PHE 0.009 0.001 PHE A 149 TYR 0.019 0.001 TYR D 60 ARG 0.006 0.000 ARG B 12 Details of bonding type rmsd hydrogen bonds : bond 0.04485 ( 318) hydrogen bonds : angle 4.53123 ( 921) SS BOND : bond 0.00330 ( 7) SS BOND : angle 0.70227 ( 14) covalent geometry : bond 0.00294 ( 7008) covalent geometry : angle 0.48858 ( 9592) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 GLU cc_start: 0.7493 (tm-30) cc_final: 0.7131 (tm-30) REVERT: F 93 ASP cc_start: 0.8431 (t0) cc_final: 0.8116 (t0) outliers start: 17 outliers final: 16 residues processed: 124 average time/residue: 0.3822 time to fit residues: 63.8658 Evaluate side-chains 130 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 124 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 65 optimal weight: 0.1980 chunk 18 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 41 optimal weight: 0.0070 chunk 44 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 GLN E 101 GLN F 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.110973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.094471 restraints weight = 28726.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.098058 restraints weight = 16444.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.100435 restraints weight = 10981.293| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 7015 Z= 0.109 Angle : 0.476 7.361 9606 Z= 0.252 Chirality : 0.040 0.133 1097 Planarity : 0.003 0.039 1131 Dihedral : 4.726 36.954 1438 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.78 % Allowed : 12.89 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.25 (0.30), residues: 819 helix: 2.01 (0.34), residues: 243 sheet: 0.22 (0.37), residues: 215 loop : -1.18 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 36 HIS 0.004 0.001 HIS A 121 PHE 0.008 0.001 PHE A 149 TYR 0.011 0.001 TYR D 60 ARG 0.006 0.000 ARG B 12 Details of bonding type rmsd hydrogen bonds : bond 0.04218 ( 318) hydrogen bonds : angle 4.43842 ( 921) SS BOND : bond 0.00328 ( 7) SS BOND : angle 0.61954 ( 14) covalent geometry : bond 0.00248 ( 7008) covalent geometry : angle 0.47621 ( 9592) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 GLU cc_start: 0.7448 (tm-30) cc_final: 0.7110 (tm-30) outliers start: 13 outliers final: 13 residues processed: 123 average time/residue: 0.4005 time to fit residues: 65.8167 Evaluate side-chains 126 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 124 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 73 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 64 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 4 GLN E 101 GLN F 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.110372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.093730 restraints weight = 28990.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.097349 restraints weight = 16651.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.099736 restraints weight = 11143.988| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7015 Z= 0.129 Angle : 0.488 7.178 9606 Z= 0.258 Chirality : 0.039 0.132 1097 Planarity : 0.003 0.039 1131 Dihedral : 4.771 36.289 1438 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.92 % Allowed : 13.17 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.25 (0.30), residues: 819 helix: 2.03 (0.34), residues: 243 sheet: 0.28 (0.37), residues: 213 loop : -1.22 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 36 HIS 0.005 0.001 HIS A 121 PHE 0.009 0.001 PHE A 149 TYR 0.014 0.001 TYR D 60 ARG 0.006 0.000 ARG B 12 Details of bonding type rmsd hydrogen bonds : bond 0.04322 ( 318) hydrogen bonds : angle 4.44907 ( 921) SS BOND : bond 0.00328 ( 7) SS BOND : angle 0.67527 ( 14) covalent geometry : bond 0.00298 ( 7008) covalent geometry : angle 0.48773 ( 9592) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4480.81 seconds wall clock time: 77 minutes 21.17 seconds (4641.17 seconds total)