Starting phenix.real_space_refine on Sun Jun 8 17:31:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wfg_32465/06_2025/7wfg_32465.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wfg_32465/06_2025/7wfg_32465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wfg_32465/06_2025/7wfg_32465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wfg_32465/06_2025/7wfg_32465.map" model { file = "/net/cci-nas-00/data/ceres_data/7wfg_32465/06_2025/7wfg_32465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wfg_32465/06_2025/7wfg_32465.cif" } resolution = 4.33 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 Fe 12 7.16 5 S 64 5.16 5 C 6304 2.51 5 N 1677 2.21 5 O 1779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9836 Number of models: 1 Model: "" Number of chains: 11 Chain: "H" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2812 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 20, 'TRANS': 335} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'TRP:plan': 1, 'PHE:plan': 5, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 86 Chain: "I" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1236 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 152} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "J" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1120 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 146} Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 118 Chain: "K" Number of atoms: 1199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1199 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 12, 'TRANS': 154} Chain breaks: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 66 Chain: "L" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 646 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 70} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'PHE:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "M" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 767 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain breaks: 1 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 110 Chain: "N" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 909 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 13, 'TRANS': 132} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 290 Unresolved non-hydrogen angles: 396 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 5, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 7, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 183 Chain: "O" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 520 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain breaks: 2 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "T" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 603 Classifications: {'peptide': 122} Incomplete info: {'backbone_only': 7, 'truncation_to_alanine': 115} Link IDs: {'TRANS': 121} Unresolved non-hydrogen bonds: 251 Unresolved non-hydrogen angles: 380 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'UNK:plan-1': 122} Unresolved non-hydrogen planarities: 122 Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3592 SG CYS I 110 39.258 36.676 84.998 1.00144.09 S ATOM 5818 SG CYS K 108 52.007 42.309 71.485 1.00166.07 S Time building chain proxies: 6.17, per 1000 atoms: 0.63 Number of scatterers: 9836 At special positions: 0 Unit cell: (113.36, 119.6, 121.68, 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) Fe 12 26.01 S 64 16.00 O 1779 8.00 N 1677 7.00 C 6304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 2.25 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 I 201 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 110 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 104 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 74 " pdb=" SF4 I 202 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 114 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 67 " pdb=" SF4 K 301 " pdb="FE4 SF4 K 301 " - pdb=" SG CYS K 108 " Number of angles added : 18 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2568 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 10 sheets defined 41.5% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'H' and resid 50 through 58 removed outlier: 3.586A pdb=" N ILE H 54 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 64 Processing helix chain 'H' and resid 75 through 91 removed outlier: 3.691A pdb=" N GLU H 79 " --> pdb=" O THR H 75 " (cutoff:3.500A) Proline residue: H 86 - end of helix Processing helix chain 'H' and resid 95 through 125 Proline residue: H 120 - end of helix Processing helix chain 'H' and resid 134 through 149 removed outlier: 4.614A pdb=" N PHE H 140 " --> pdb=" O ARG H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 191 removed outlier: 4.180A pdb=" N CYS H 179 " --> pdb=" O CYS H 175 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASP H 180 " --> pdb=" O LEU H 176 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N THR H 184 " --> pdb=" O ASP H 180 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLU H 185 " --> pdb=" O TYR H 181 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS H 191 " --> pdb=" O VAL H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 196 Processing helix chain 'H' and resid 210 through 215 Processing helix chain 'H' and resid 221 through 226 Processing helix chain 'H' and resid 232 through 237 Processing helix chain 'H' and resid 256 through 278 Processing helix chain 'H' and resid 356 through 362 removed outlier: 3.767A pdb=" N ILE H 360 " --> pdb=" O PRO H 356 " (cutoff:3.500A) Processing helix chain 'H' and resid 363 through 365 No H-bonds generated for 'chain 'H' and resid 363 through 365' Processing helix chain 'H' and resid 376 through 384 Processing helix chain 'I' and resid 7 through 33 Processing helix chain 'I' and resid 140 through 144 removed outlier: 4.022A pdb=" N ARG I 144 " --> pdb=" O ALA I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 148 through 152 removed outlier: 4.082A pdb=" N ASP I 152 " --> pdb=" O VAL I 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 35 Processing helix chain 'J' and resid 36 through 45 Processing helix chain 'J' and resid 107 through 118 Processing helix chain 'J' and resid 151 through 155 Processing helix chain 'K' and resid 16 through 31 Processing helix chain 'K' and resid 42 through 48 removed outlier: 3.824A pdb=" N ILE K 46 " --> pdb=" O CYS K 43 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU K 47 " --> pdb=" O CYS K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 95 Processing helix chain 'K' and resid 112 through 116 removed outlier: 3.653A pdb=" N PHE K 115 " --> pdb=" O GLY K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 129 removed outlier: 3.990A pdb=" N LYS K 128 " --> pdb=" O GLY K 125 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 160 Processing helix chain 'K' and resid 161 through 166 removed outlier: 3.724A pdb=" N ASP K 164 " --> pdb=" O ILE K 161 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 107 Processing helix chain 'L' and resid 107 through 119 removed outlier: 4.213A pdb=" N ILE L 111 " --> pdb=" O VAL L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 138 Processing helix chain 'L' and resid 139 through 144 removed outlier: 3.849A pdb=" N LEU L 143 " --> pdb=" O PRO L 140 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU L 144 " --> pdb=" O GLY L 141 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 150 Processing helix chain 'M' and resid 156 through 177 Processing helix chain 'N' and resid 63 through 72 Processing helix chain 'N' and resid 86 through 95 removed outlier: 4.146A pdb=" N LEU N 90 " --> pdb=" O GLU N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 116 Processing helix chain 'N' and resid 139 through 145 Processing helix chain 'N' and resid 166 through 179 Proline residue: N 176 - end of helix Processing helix chain 'T' and resid 2 through 6 removed outlier: 4.304A pdb=" N UNK T 6 " --> pdb=" O UNK T 3 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 18 Processing helix chain 'T' and resid 25 through 39 removed outlier: 3.675A pdb=" N UNK T 39 " --> pdb=" O UNK T 35 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 62 Processing helix chain 'T' and resid 62 through 73 Processing helix chain 'T' and resid 98 through 121 removed outlier: 3.683A pdb=" N UNK T 102 " --> pdb=" O UNK T 98 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 27 through 30 removed outlier: 3.521A pdb=" N ARG H 27 " --> pdb=" O ILE H 43 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE H 29 " --> pdb=" O GLU H 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 36 through 37 removed outlier: 3.956A pdb=" N MET H 372 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 325 through 330 Processing sheet with id=AA4, first strand: chain 'I' and resid 57 through 58 Processing sheet with id=AA5, first strand: chain 'I' and resid 80 through 82 removed outlier: 6.796A pdb=" N VAL I 80 " --> pdb=" O TYR I 97 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N TYR I 97 " --> pdb=" O VAL I 80 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP I 82 " --> pdb=" O LEU I 95 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 17 through 21 removed outlier: 5.953A pdb=" N THR J 28 " --> pdb=" O LEU J 19 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU J 27 " --> pdb=" O CYS J 85 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LYS J 87 " --> pdb=" O GLU J 27 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU J 29 " --> pdb=" O LYS J 87 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N PHE J 89 " --> pdb=" O LEU J 29 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE J 31 " --> pdb=" O PHE J 89 " (cutoff:3.500A) removed outlier: 10.336A pdb=" N HIS J 91 " --> pdb=" O ILE J 31 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 96 through 98 removed outlier: 3.849A pdb=" N ASP J 123 " --> pdb=" O ILE J 97 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 102 through 104 removed outlier: 8.505A pdb=" N VAL K 102 " --> pdb=" O ASP K 133 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N TYR K 135 " --> pdb=" O VAL K 102 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ALA K 104 " --> pdb=" O TYR K 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'N' and resid 99 through 103 removed outlier: 6.687A pdb=" N TYR N 99 " --> pdb=" O VAL N 156 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL N 158 " --> pdb=" O TYR N 99 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU N 101 " --> pdb=" O VAL N 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'O' and resid 80 through 81 removed outlier: 3.827A pdb=" N GLY O 114 " --> pdb=" O VAL O 81 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU O 129 " --> pdb=" O LEU O 117 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU O 119 " --> pdb=" O TYR O 127 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR O 127 " --> pdb=" O LEU O 119 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 1005 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.14 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.42: 3991 1.42 - 1.64: 5927 1.64 - 1.86: 82 1.86 - 2.09: 0 2.09 - 2.31: 36 Bond restraints: 10036 Sorted by residual: bond pdb=" C ARG L 152 " pdb=" N LYS L 153 " ideal model delta sigma weight residual 1.332 1.201 0.132 1.40e-02 5.10e+03 8.86e+01 bond pdb=" C GLU I 68 " pdb=" N VAL I 69 " ideal model delta sigma weight residual 1.334 1.265 0.068 1.28e-02 6.10e+03 2.86e+01 bond pdb=" C PRO N 148 " pdb=" N PRO N 149 " ideal model delta sigma weight residual 1.326 1.392 -0.065 1.44e-02 4.82e+03 2.07e+01 bond pdb=" N ARG N 179 " pdb=" CA ARG N 179 " ideal model delta sigma weight residual 1.462 1.493 -0.031 7.70e-03 1.69e+04 1.62e+01 bond pdb=" N LEU N 175 " pdb=" CA LEU N 175 " ideal model delta sigma weight residual 1.463 1.490 -0.027 6.90e-03 2.10e+04 1.51e+01 ... (remaining 10031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 12868 1.95 - 3.90: 634 3.90 - 5.85: 102 5.85 - 7.80: 29 7.80 - 9.75: 11 Bond angle restraints: 13644 Sorted by residual: angle pdb=" N PRO K 140 " pdb=" CA PRO K 140 " pdb=" C PRO K 140 " ideal model delta sigma weight residual 110.70 120.21 -9.51 1.22e+00 6.72e-01 6.08e+01 angle pdb=" N SER N 177 " pdb=" CA SER N 177 " pdb=" C SER N 177 " ideal model delta sigma weight residual 113.23 104.14 9.09 1.24e+00 6.50e-01 5.37e+01 angle pdb=" N LEU K 37 " pdb=" CA LEU K 37 " pdb=" C LEU K 37 " ideal model delta sigma weight residual 113.02 106.16 6.86 1.20e+00 6.94e-01 3.27e+01 angle pdb=" N PRO L 109 " pdb=" CA PRO L 109 " pdb=" C PRO L 109 " ideal model delta sigma weight residual 110.70 117.06 -6.36 1.22e+00 6.72e-01 2.72e+01 angle pdb=" N ASN N 181 " pdb=" CA ASN N 181 " pdb=" C ASN N 181 " ideal model delta sigma weight residual 114.39 107.58 6.81 1.45e+00 4.76e-01 2.21e+01 ... (remaining 13639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.90: 5624 14.90 - 29.80: 312 29.80 - 44.70: 96 44.70 - 59.60: 26 59.60 - 74.51: 2 Dihedral angle restraints: 6060 sinusoidal: 2097 harmonic: 3963 Sorted by residual: dihedral pdb=" CA THR K 117 " pdb=" C THR K 117 " pdb=" N ASP K 118 " pdb=" CA ASP K 118 " ideal model delta harmonic sigma weight residual -180.00 -153.96 -26.04 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA GLY H 218 " pdb=" C GLY H 218 " pdb=" N LEU H 219 " pdb=" CA LEU H 219 " ideal model delta harmonic sigma weight residual 180.00 -154.68 -25.32 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA ARG L 152 " pdb=" C ARG L 152 " pdb=" N LYS L 153 " pdb=" CA LYS L 153 " ideal model delta harmonic sigma weight residual 180.00 155.93 24.07 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 6057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1231 0.070 - 0.139: 265 0.139 - 0.209: 52 0.209 - 0.278: 14 0.278 - 0.348: 1 Chirality restraints: 1563 Sorted by residual: chirality pdb=" CA LEU H 32 " pdb=" N LEU H 32 " pdb=" C LEU H 32 " pdb=" CB LEU H 32 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CA ARG M 161 " pdb=" N ARG M 161 " pdb=" C ARG M 161 " pdb=" CB ARG M 161 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB ILE I 65 " pdb=" CA ILE I 65 " pdb=" CG1 ILE I 65 " pdb=" CG2 ILE I 65 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1560 not shown) Planarity restraints: 1745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU K 136 " -0.042 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO K 137 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO K 137 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO K 137 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 64 " 0.041 5.00e-02 4.00e+02 6.15e-02 6.06e+00 pdb=" N PRO H 65 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO H 65 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 65 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP J 140 " 0.040 5.00e-02 4.00e+02 6.01e-02 5.79e+00 pdb=" N PRO J 141 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO J 141 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO J 141 " 0.033 5.00e-02 4.00e+02 ... (remaining 1742 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 834 2.74 - 3.28: 9622 3.28 - 3.82: 16282 3.82 - 4.36: 18343 4.36 - 4.90: 30572 Nonbonded interactions: 75653 Sorted by model distance: nonbonded pdb=" OE2 GLU H 146 " pdb=" N SER I 50 " model vdw 2.204 3.120 nonbonded pdb=" CB ALA H 165 " pdb=" NH1 ARG I 52 " model vdw 2.248 3.540 nonbonded pdb=" NZ LYS N 128 " pdb=" O PRO O 136 " model vdw 2.257 3.120 nonbonded pdb=" O VAL H 203 " pdb=" OG SER H 257 " model vdw 2.301 3.040 nonbonded pdb=" NH2 ARG H 136 " pdb=" O HIS I 32 " model vdw 2.304 3.120 ... (remaining 75648 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.860 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 24.850 Find NCS groups from input model: 0.140 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 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 : 0.023 1.120 10042 Z= 0.732 Angle : 1.453 45.092 13662 Z= 0.599 Chirality : 0.063 0.348 1563 Planarity : 0.007 0.064 1745 Dihedral : 11.464 74.505 3492 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.27 % Favored : 87.48 % Rotamer: Outliers : 1.08 % Allowed : 3.11 % Favored : 95.81 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % 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: -5.06 (0.18), residues: 1214 helix: -3.16 (0.16), residues: 405 sheet: -2.66 (0.48), residues: 93 loop : -3.76 (0.19), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 117 HIS 0.008 0.001 HIS M 169 PHE 0.016 0.002 PHE H 182 TYR 0.016 0.002 TYR J 57 ARG 0.015 0.001 ARG H 69 Details of bonding type rmsd hydrogen bonds : bond 0.15863 ( 354) hydrogen bonds : angle 7.14889 ( 1005) metal coordination : bond 0.89549 ( 6) metal coordination : angle 28.84825 ( 18) covalent geometry : bond 0.00573 (10036) covalent geometry : angle 1.00837 (13644) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 262 time to evaluate : 1.076 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE H 132 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.7825 (tpt) cc_final: 0.7336 (tpp) REVERT: H 47 LEU cc_start: 0.9296 (tp) cc_final: 0.8851 (tp) REVERT: H 49 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7844 (mpp80) REVERT: H 105 MET cc_start: 0.9533 (ptp) cc_final: 0.9057 (ptt) REVERT: H 156 ASN cc_start: 0.9382 (t0) cc_final: 0.9130 (t0) REVERT: H 171 TRP cc_start: 0.9322 (t60) cc_final: 0.9042 (t60) REVERT: H 261 TYR cc_start: 0.8837 (t80) cc_final: 0.8626 (t80) REVERT: H 262 LEU cc_start: 0.9547 (mt) cc_final: 0.9286 (pp) REVERT: H 378 MET cc_start: 0.9076 (mmp) cc_final: 0.8669 (mmp) REVERT: H 381 LEU cc_start: 0.9450 (pp) cc_final: 0.8455 (pp) REVERT: H 384 ILE cc_start: 0.9671 (mm) cc_final: 0.9321 (tp) REVERT: H 390 GLU cc_start: 0.9130 (pt0) cc_final: 0.8798 (pt0) REVERT: I 85 LEU cc_start: 0.8474 (mt) cc_final: 0.7835 (tp) REVERT: I 100 ASP cc_start: 0.8560 (t0) cc_final: 0.7633 (t70) REVERT: I 101 PHE cc_start: 0.9240 (m-10) cc_final: 0.8995 (m-80) REVERT: I 103 ILE cc_start: 0.9528 (mm) cc_final: 0.9170 (mm) REVERT: I 134 GLU cc_start: 0.8639 (tt0) cc_final: 0.8424 (tm-30) REVERT: I 137 TYR cc_start: 0.7528 (m-10) cc_final: 0.6809 (m-10) REVERT: J 51 LEU cc_start: 0.8577 (tp) cc_final: 0.8373 (tp) REVERT: J 71 LEU cc_start: 0.8562 (tp) cc_final: 0.8171 (tp) REVERT: J 111 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8535 (mm-30) REVERT: J 128 LEU cc_start: 0.8978 (tp) cc_final: 0.8569 (mt) REVERT: K 103 ILE cc_start: 0.9291 (mm) cc_final: 0.8892 (mp) REVERT: K 144 GLU cc_start: 0.8132 (mp0) cc_final: 0.7815 (tp30) REVERT: L 128 MET cc_start: 0.8939 (mmm) cc_final: 0.8601 (mmt) REVERT: L 142 LEU cc_start: 0.8682 (mm) cc_final: 0.8471 (mm) REVERT: L 144 LEU cc_start: 0.8174 (pt) cc_final: 0.7949 (pt) REVERT: L 160 MET cc_start: 0.7307 (mpp) cc_final: 0.6776 (tpp) REVERT: N 140 VAL cc_start: 0.9093 (m) cc_final: 0.8871 (p) outliers start: 9 outliers final: 3 residues processed: 268 average time/residue: 0.2436 time to fit residues: 88.0966 Evaluate side-chains 176 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 172 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 23 HIS ** H 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 363 GLN ** M 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 169 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.049906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.044108 restraints weight = 114792.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.044799 restraints weight = 84355.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.045296 restraints weight = 65937.519| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10042 Z= 0.248 Angle : 1.010 44.992 13662 Z= 0.410 Chirality : 0.050 0.349 1563 Planarity : 0.007 0.068 1745 Dihedral : 5.691 25.051 1452 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer: Outliers : 0.48 % Allowed : 5.02 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.64 (0.21), residues: 1214 helix: -1.38 (0.22), residues: 444 sheet: -2.51 (0.45), residues: 101 loop : -3.27 (0.21), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 117 HIS 0.014 0.002 HIS M 96 PHE 0.020 0.002 PHE H 182 TYR 0.016 0.002 TYR M 100 ARG 0.007 0.001 ARG I 56 Details of bonding type rmsd hydrogen bonds : bond 0.03996 ( 354) hydrogen bonds : angle 5.09695 ( 1005) metal coordination : bond 0.03042 ( 6) metal coordination : angle 17.43549 ( 18) covalent geometry : bond 0.00515 (10036) covalent geometry : angle 0.78773 (13644) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 189 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.8351 (tpt) cc_final: 0.7827 (tpp) REVERT: H 47 LEU cc_start: 0.9459 (tp) cc_final: 0.9013 (tp) REVERT: H 76 MET cc_start: 0.8875 (mtt) cc_final: 0.8539 (mtm) REVERT: H 171 TRP cc_start: 0.9200 (t60) cc_final: 0.8938 (t60) REVERT: H 261 TYR cc_start: 0.8813 (t80) cc_final: 0.8613 (t80) REVERT: H 384 ILE cc_start: 0.9641 (mm) cc_final: 0.9413 (tp) REVERT: I 9 MET cc_start: 0.1609 (tmm) cc_final: 0.1331 (tmm) REVERT: I 85 LEU cc_start: 0.9132 (mt) cc_final: 0.8699 (tp) REVERT: I 100 ASP cc_start: 0.8831 (t0) cc_final: 0.8057 (t70) REVERT: I 101 PHE cc_start: 0.9032 (m-10) cc_final: 0.8512 (m-80) REVERT: I 103 ILE cc_start: 0.9641 (mm) cc_final: 0.9432 (mm) REVERT: I 134 GLU cc_start: 0.8686 (tt0) cc_final: 0.8462 (tm-30) REVERT: I 137 TYR cc_start: 0.7793 (m-10) cc_final: 0.7368 (m-10) REVERT: J 151 PHE cc_start: 0.8730 (m-80) cc_final: 0.8310 (m-80) REVERT: K 114 MET cc_start: 0.9019 (pmm) cc_final: 0.8534 (pmm) REVERT: K 136 LEU cc_start: 0.8983 (tp) cc_final: 0.8748 (tp) REVERT: K 144 GLU cc_start: 0.8777 (mp0) cc_final: 0.8179 (tp30) REVERT: L 128 MET cc_start: 0.9085 (mmm) cc_final: 0.8664 (mmt) REVERT: L 144 LEU cc_start: 0.8738 (pt) cc_final: 0.8404 (pt) outliers start: 4 outliers final: 3 residues processed: 192 average time/residue: 0.2035 time to fit residues: 56.1978 Evaluate side-chains 150 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 147 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 5 optimal weight: 0.8980 chunk 111 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 67 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 18 HIS ** H 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.048541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.042500 restraints weight = 113955.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.043198 restraints weight = 84491.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.043688 restraints weight = 66343.965| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10042 Z= 0.156 Angle : 0.902 42.342 13662 Z= 0.335 Chirality : 0.045 0.136 1563 Planarity : 0.006 0.089 1745 Dihedral : 5.195 24.910 1452 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.12 % Favored : 88.88 % Rotamer: Outliers : 0.36 % Allowed : 3.35 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.23), residues: 1214 helix: -0.61 (0.24), residues: 448 sheet: -2.64 (0.43), residues: 110 loop : -2.98 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 217 HIS 0.008 0.001 HIS H 155 PHE 0.013 0.002 PHE K 115 TYR 0.012 0.002 TYR J 57 ARG 0.008 0.001 ARG H 138 Details of bonding type rmsd hydrogen bonds : bond 0.03246 ( 354) hydrogen bonds : angle 4.72891 ( 1005) metal coordination : bond 0.01578 ( 6) metal coordination : angle 17.18738 ( 18) covalent geometry : bond 0.00332 (10036) covalent geometry : angle 0.65150 (13644) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 187 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.8530 (tpt) cc_final: 0.7911 (tpp) REVERT: H 47 LEU cc_start: 0.9481 (tp) cc_final: 0.9192 (tp) REVERT: H 76 MET cc_start: 0.8868 (mtt) cc_final: 0.8563 (mtm) REVERT: H 79 GLU cc_start: 0.8604 (tt0) cc_final: 0.7806 (tt0) REVERT: H 154 MET cc_start: 0.7018 (mtt) cc_final: 0.6654 (mtt) REVERT: H 262 LEU cc_start: 0.9661 (mt) cc_final: 0.9334 (pp) REVERT: H 390 GLU cc_start: 0.9096 (pt0) cc_final: 0.8634 (pt0) REVERT: I 85 LEU cc_start: 0.9135 (mt) cc_final: 0.8661 (tp) REVERT: I 100 ASP cc_start: 0.8662 (t0) cc_final: 0.8005 (t70) REVERT: I 101 PHE cc_start: 0.9103 (m-10) cc_final: 0.8470 (m-80) REVERT: I 103 ILE cc_start: 0.9580 (mm) cc_final: 0.9293 (mm) REVERT: I 137 TYR cc_start: 0.8069 (m-10) cc_final: 0.7460 (m-10) REVERT: J 70 HIS cc_start: 0.8179 (m90) cc_final: 0.7913 (m90) REVERT: J 128 LEU cc_start: 0.9171 (tp) cc_final: 0.8879 (tp) REVERT: J 151 PHE cc_start: 0.8806 (m-80) cc_final: 0.8467 (m-80) REVERT: K 83 MET cc_start: 0.8571 (ppp) cc_final: 0.8356 (tpt) REVERT: K 103 ILE cc_start: 0.8862 (mm) cc_final: 0.8653 (mm) REVERT: K 114 MET cc_start: 0.9031 (pmm) cc_final: 0.8349 (pmm) REVERT: K 144 GLU cc_start: 0.8878 (mp0) cc_final: 0.8065 (tp30) REVERT: K 148 ASP cc_start: 0.8557 (m-30) cc_final: 0.7487 (m-30) REVERT: L 108 MET cc_start: 0.8693 (mpp) cc_final: 0.8373 (mpp) REVERT: L 128 MET cc_start: 0.9129 (mmm) cc_final: 0.8659 (mmt) REVERT: M 100 TYR cc_start: 0.8376 (m-80) cc_final: 0.7994 (m-80) outliers start: 3 outliers final: 3 residues processed: 188 average time/residue: 0.2009 time to fit residues: 54.3391 Evaluate side-chains 151 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 148 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 76 optimal weight: 9.9990 chunk 33 optimal weight: 0.0020 chunk 34 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 81 optimal weight: 0.0040 chunk 35 optimal weight: 0.8980 chunk 122 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 overall best weight: 0.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 48 HIS ** M 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.049668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.043395 restraints weight = 108215.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.044137 restraints weight = 79856.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.044676 restraints weight = 62620.450| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10042 Z= 0.110 Angle : 0.815 36.558 13662 Z= 0.309 Chirality : 0.045 0.139 1563 Planarity : 0.005 0.069 1745 Dihedral : 4.841 25.622 1452 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 0.36 % Allowed : 2.51 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.24), residues: 1214 helix: -0.29 (0.25), residues: 448 sheet: -2.51 (0.43), residues: 111 loop : -2.85 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 217 HIS 0.007 0.001 HIS H 155 PHE 0.021 0.001 PHE H 182 TYR 0.017 0.001 TYR H 327 ARG 0.009 0.000 ARG J 96 Details of bonding type rmsd hydrogen bonds : bond 0.02713 ( 354) hydrogen bonds : angle 4.47536 ( 1005) metal coordination : bond 0.01211 ( 6) metal coordination : angle 14.46114 ( 18) covalent geometry : bond 0.00244 (10036) covalent geometry : angle 0.62354 (13644) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 182 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.8341 (tpt) cc_final: 0.7825 (tpp) REVERT: H 76 MET cc_start: 0.8775 (mtt) cc_final: 0.8475 (mtm) REVERT: H 79 GLU cc_start: 0.8589 (tt0) cc_final: 0.7858 (mm-30) REVERT: H 154 MET cc_start: 0.6755 (mtt) cc_final: 0.6207 (mtt) REVERT: H 340 PHE cc_start: 0.8782 (t80) cc_final: 0.8452 (t80) REVERT: H 390 GLU cc_start: 0.9152 (pt0) cc_final: 0.8676 (pt0) REVERT: I 85 LEU cc_start: 0.9052 (mt) cc_final: 0.8578 (tp) REVERT: J 151 PHE cc_start: 0.8942 (m-80) cc_final: 0.8631 (m-80) REVERT: K 77 THR cc_start: 0.8970 (t) cc_final: 0.8548 (t) REVERT: K 83 MET cc_start: 0.8624 (ppp) cc_final: 0.8323 (tpt) REVERT: K 114 MET cc_start: 0.8974 (pmm) cc_final: 0.8384 (pmm) REVERT: K 136 LEU cc_start: 0.8686 (tp) cc_final: 0.8251 (tt) REVERT: K 144 GLU cc_start: 0.8806 (mp0) cc_final: 0.8067 (tp30) REVERT: K 148 ASP cc_start: 0.8432 (m-30) cc_final: 0.7907 (m-30) REVERT: L 108 MET cc_start: 0.8669 (mpp) cc_final: 0.8309 (mpp) REVERT: L 128 MET cc_start: 0.9136 (mmm) cc_final: 0.8684 (mmt) REVERT: L 138 PHE cc_start: 0.9493 (m-80) cc_final: 0.9221 (m-80) REVERT: L 144 LEU cc_start: 0.8548 (pt) cc_final: 0.8311 (tp) REVERT: M 100 TYR cc_start: 0.8428 (m-80) cc_final: 0.8055 (m-80) outliers start: 3 outliers final: 3 residues processed: 183 average time/residue: 0.1708 time to fit residues: 47.2838 Evaluate side-chains 152 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 149 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 54 optimal weight: 0.9990 chunk 115 optimal weight: 0.0770 chunk 2 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 27 optimal weight: 0.0970 chunk 45 optimal weight: 0.4980 chunk 56 optimal weight: 10.0000 chunk 126 optimal weight: 20.0000 chunk 128 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.050947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.044492 restraints weight = 109233.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.045248 restraints weight = 79721.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.045792 restraints weight = 62655.811| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10042 Z= 0.104 Angle : 0.792 34.250 13662 Z= 0.300 Chirality : 0.044 0.138 1563 Planarity : 0.004 0.061 1745 Dihedral : 4.628 25.228 1452 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 0.36 % Allowed : 3.23 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.24), residues: 1214 helix: -0.14 (0.25), residues: 452 sheet: -2.12 (0.46), residues: 101 loop : -2.72 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 217 HIS 0.007 0.001 HIS H 23 PHE 0.022 0.001 PHE L 134 TYR 0.013 0.001 TYR J 57 ARG 0.004 0.000 ARG I 17 Details of bonding type rmsd hydrogen bonds : bond 0.02559 ( 354) hydrogen bonds : angle 4.28432 ( 1005) metal coordination : bond 0.01469 ( 6) metal coordination : angle 14.02813 ( 18) covalent geometry : bond 0.00229 (10036) covalent geometry : angle 0.60638 (13644) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 178 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.8260 (tpt) cc_final: 0.7726 (tpp) REVERT: H 76 MET cc_start: 0.8756 (mtt) cc_final: 0.8467 (mtm) REVERT: H 208 ILE cc_start: 0.8868 (pt) cc_final: 0.8426 (mm) REVERT: H 262 LEU cc_start: 0.9651 (mt) cc_final: 0.9323 (pp) REVERT: H 340 PHE cc_start: 0.8693 (t80) cc_final: 0.8387 (t80) REVERT: H 390 GLU cc_start: 0.9139 (pt0) cc_final: 0.8667 (pt0) REVERT: I 85 LEU cc_start: 0.9022 (mt) cc_final: 0.8557 (tp) REVERT: I 100 ASP cc_start: 0.8767 (t0) cc_final: 0.8545 (t70) REVERT: I 137 TYR cc_start: 0.8048 (m-80) cc_final: 0.7677 (m-10) REVERT: J 151 PHE cc_start: 0.8938 (m-80) cc_final: 0.8615 (m-80) REVERT: K 83 MET cc_start: 0.8685 (ppp) cc_final: 0.8467 (tpt) REVERT: K 85 MET cc_start: 0.9046 (mmp) cc_final: 0.8825 (mmp) REVERT: K 114 MET cc_start: 0.8989 (pmm) cc_final: 0.8267 (pmm) REVERT: K 136 LEU cc_start: 0.8546 (tp) cc_final: 0.8282 (tt) REVERT: K 144 GLU cc_start: 0.8847 (mp0) cc_final: 0.8170 (tp30) REVERT: K 148 ASP cc_start: 0.8563 (m-30) cc_final: 0.8210 (m-30) REVERT: L 128 MET cc_start: 0.9125 (mmm) cc_final: 0.8619 (mmt) REVERT: L 138 PHE cc_start: 0.9482 (m-80) cc_final: 0.9250 (m-80) REVERT: M 100 TYR cc_start: 0.8399 (m-80) cc_final: 0.8065 (m-80) outliers start: 3 outliers final: 3 residues processed: 179 average time/residue: 0.1742 time to fit residues: 46.5992 Evaluate side-chains 149 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 146 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 60 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 18 HIS ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 GLN H 361 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.047254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.041602 restraints weight = 120205.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.042320 restraints weight = 85943.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.042832 restraints weight = 65860.107| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.6543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10042 Z= 0.214 Angle : 1.021 52.190 13662 Z= 0.372 Chirality : 0.047 0.156 1563 Planarity : 0.006 0.073 1745 Dihedral : 5.306 22.953 1452 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.60 % Favored : 87.31 % Rotamer: Outliers : 0.36 % Allowed : 2.27 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.24), residues: 1214 helix: -0.47 (0.24), residues: 469 sheet: -2.00 (0.50), residues: 86 loop : -2.73 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 145 HIS 0.008 0.002 HIS H 114 PHE 0.022 0.002 PHE K 115 TYR 0.022 0.002 TYR K 135 ARG 0.008 0.001 ARG H 69 Details of bonding type rmsd hydrogen bonds : bond 0.03613 ( 354) hydrogen bonds : angle 4.74915 ( 1005) metal coordination : bond 0.02130 ( 6) metal coordination : angle 19.99877 ( 18) covalent geometry : bond 0.00450 (10036) covalent geometry : angle 0.71810 (13644) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 163 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.8805 (tpt) cc_final: 0.8269 (tpp) REVERT: H 76 MET cc_start: 0.8943 (mtt) cc_final: 0.8573 (ttm) REVERT: H 105 MET cc_start: 0.9233 (ptt) cc_final: 0.8800 (ptt) REVERT: H 154 MET cc_start: 0.6483 (mtt) cc_final: 0.6016 (mtt) REVERT: H 208 ILE cc_start: 0.9121 (pt) cc_final: 0.8694 (mm) REVERT: H 262 LEU cc_start: 0.9692 (mt) cc_final: 0.9346 (pp) REVERT: H 390 GLU cc_start: 0.9143 (pt0) cc_final: 0.8729 (pt0) REVERT: I 85 LEU cc_start: 0.9174 (mt) cc_final: 0.8599 (tp) REVERT: I 100 ASP cc_start: 0.8851 (t0) cc_final: 0.8073 (t70) REVERT: I 103 ILE cc_start: 0.9571 (mm) cc_final: 0.9264 (mm) REVERT: I 137 TYR cc_start: 0.8187 (m-80) cc_final: 0.7680 (m-80) REVERT: J 151 PHE cc_start: 0.9095 (m-80) cc_final: 0.8678 (m-80) REVERT: K 85 MET cc_start: 0.9048 (mmp) cc_final: 0.8802 (mmm) REVERT: K 114 MET cc_start: 0.9067 (pmm) cc_final: 0.8181 (pmm) REVERT: K 136 LEU cc_start: 0.8754 (tp) cc_final: 0.8465 (tt) REVERT: K 144 GLU cc_start: 0.8950 (mp0) cc_final: 0.7921 (tp30) REVERT: K 148 ASP cc_start: 0.8660 (m-30) cc_final: 0.7740 (m-30) REVERT: L 108 MET cc_start: 0.8739 (mpp) cc_final: 0.8513 (mpp) REVERT: L 128 MET cc_start: 0.9127 (mmm) cc_final: 0.8618 (mmt) REVERT: L 138 PHE cc_start: 0.9499 (m-80) cc_final: 0.9252 (m-80) REVERT: M 100 TYR cc_start: 0.8692 (m-10) cc_final: 0.8440 (m-80) outliers start: 3 outliers final: 3 residues processed: 164 average time/residue: 0.1758 time to fit residues: 43.0742 Evaluate side-chains 139 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 136 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 18 optimal weight: 0.0980 chunk 3 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.047274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.041466 restraints weight = 118251.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.042088 restraints weight = 84668.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.042554 restraints weight = 66298.140| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.6874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10042 Z= 0.162 Angle : 0.939 44.652 13662 Z= 0.334 Chirality : 0.045 0.142 1563 Planarity : 0.005 0.075 1745 Dihedral : 5.134 24.450 1452 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.29 % Favored : 88.63 % Rotamer: Outliers : 0.36 % Allowed : 1.79 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.24), residues: 1214 helix: -0.29 (0.24), residues: 469 sheet: -2.28 (0.46), residues: 89 loop : -2.63 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 28 HIS 0.006 0.001 HIS H 114 PHE 0.029 0.001 PHE I 101 TYR 0.018 0.001 TYR H 261 ARG 0.010 0.001 ARG M 161 Details of bonding type rmsd hydrogen bonds : bond 0.03036 ( 354) hydrogen bonds : angle 4.60838 ( 1005) metal coordination : bond 0.01831 ( 6) metal coordination : angle 18.62926 ( 18) covalent geometry : bond 0.00345 (10036) covalent geometry : angle 0.65168 (13644) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 168 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.8680 (tpt) cc_final: 0.8090 (tpp) REVERT: H 76 MET cc_start: 0.8733 (mtt) cc_final: 0.8458 (ttm) REVERT: H 79 GLU cc_start: 0.8863 (tt0) cc_final: 0.8475 (tt0) REVERT: H 105 MET cc_start: 0.9190 (ptt) cc_final: 0.8826 (ptt) REVERT: H 208 ILE cc_start: 0.9172 (pt) cc_final: 0.8791 (mm) REVERT: H 262 LEU cc_start: 0.9707 (mt) cc_final: 0.9376 (pp) REVERT: H 340 PHE cc_start: 0.8761 (t80) cc_final: 0.8445 (t80) REVERT: H 390 GLU cc_start: 0.9249 (pt0) cc_final: 0.8877 (pt0) REVERT: I 85 LEU cc_start: 0.9174 (mt) cc_final: 0.8535 (tp) REVERT: I 100 ASP cc_start: 0.8859 (t0) cc_final: 0.8059 (t70) REVERT: I 103 ILE cc_start: 0.9627 (mm) cc_final: 0.9313 (mm) REVERT: J 133 MET cc_start: 0.8969 (mmm) cc_final: 0.8602 (mmm) REVERT: J 151 PHE cc_start: 0.9124 (m-80) cc_final: 0.8716 (m-80) REVERT: K 85 MET cc_start: 0.9165 (mmp) cc_final: 0.8788 (mmp) REVERT: K 114 MET cc_start: 0.9068 (pmm) cc_final: 0.8344 (pmm) REVERT: K 144 GLU cc_start: 0.9010 (mp0) cc_final: 0.7900 (tp30) REVERT: K 148 ASP cc_start: 0.8981 (m-30) cc_final: 0.7644 (m-30) REVERT: L 108 MET cc_start: 0.8889 (mpp) cc_final: 0.8461 (mpp) REVERT: L 128 MET cc_start: 0.9140 (mmm) cc_final: 0.8784 (mmt) REVERT: M 100 TYR cc_start: 0.8666 (m-10) cc_final: 0.8453 (m-80) outliers start: 3 outliers final: 3 residues processed: 169 average time/residue: 0.2081 time to fit residues: 51.2518 Evaluate side-chains 146 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 143 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 131 optimal weight: 10.0000 chunk 106 optimal weight: 0.0670 chunk 7 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 95 optimal weight: 0.5980 chunk 27 optimal weight: 9.9990 overall best weight: 2.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 18 HIS ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.054710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.049654 restraints weight = 119383.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.050415 restraints weight = 77512.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.051000 restraints weight = 56546.876| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.7635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10042 Z= 0.219 Angle : 1.118 50.007 13662 Z= 0.378 Chirality : 0.048 0.225 1563 Planarity : 0.006 0.080 1745 Dihedral : 5.559 23.252 1452 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.92 % Favored : 86.00 % Rotamer: Outliers : 0.36 % Allowed : 1.20 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.24), residues: 1214 helix: -0.55 (0.23), residues: 472 sheet: -2.40 (0.50), residues: 78 loop : -2.60 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP K 28 HIS 0.009 0.002 HIS H 114 PHE 0.021 0.002 PHE K 115 TYR 0.032 0.002 TYR K 135 ARG 0.009 0.001 ARG H 69 Details of bonding type rmsd hydrogen bonds : bond 0.03540 ( 354) hydrogen bonds : angle 4.87304 ( 1005) metal coordination : bond 0.02281 ( 6) metal coordination : angle 23.42636 ( 18) covalent geometry : bond 0.00459 (10036) covalent geometry : angle 0.72685 (13644) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 161 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.8926 (tpt) cc_final: 0.8355 (tpp) REVERT: H 76 MET cc_start: 0.9022 (mtt) cc_final: 0.8752 (mtm) REVERT: H 79 GLU cc_start: 0.8938 (tt0) cc_final: 0.8528 (tt0) REVERT: H 154 MET cc_start: 0.6336 (mtt) cc_final: 0.5993 (mtt) REVERT: H 208 ILE cc_start: 0.9283 (pt) cc_final: 0.8896 (mm) REVERT: H 262 LEU cc_start: 0.9749 (mt) cc_final: 0.9374 (pp) REVERT: H 340 PHE cc_start: 0.9006 (t80) cc_final: 0.8548 (t80) REVERT: H 390 GLU cc_start: 0.9276 (pt0) cc_final: 0.8929 (pt0) REVERT: I 100 ASP cc_start: 0.8878 (t0) cc_final: 0.8152 (t70) REVERT: I 103 ILE cc_start: 0.9657 (mm) cc_final: 0.9416 (mm) REVERT: I 105 ILE cc_start: 0.9120 (tt) cc_final: 0.8915 (pt) REVERT: J 50 TYR cc_start: 0.7956 (t80) cc_final: 0.7125 (t80) REVERT: J 133 MET cc_start: 0.9028 (mmm) cc_final: 0.8498 (mmm) REVERT: J 151 PHE cc_start: 0.9297 (m-80) cc_final: 0.8664 (m-80) REVERT: K 34 LEU cc_start: 0.9008 (mm) cc_final: 0.8754 (mm) REVERT: K 85 MET cc_start: 0.9070 (mmp) cc_final: 0.8574 (mmp) REVERT: K 114 MET cc_start: 0.8969 (pmm) cc_final: 0.8457 (pmm) REVERT: K 115 PHE cc_start: 0.9269 (m-10) cc_final: 0.8843 (m-10) REVERT: L 108 MET cc_start: 0.8849 (mpp) cc_final: 0.8572 (mpp) REVERT: L 128 MET cc_start: 0.8990 (mmm) cc_final: 0.8517 (mmt) outliers start: 3 outliers final: 3 residues processed: 162 average time/residue: 0.2188 time to fit residues: 52.4823 Evaluate side-chains 138 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 135 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 55 optimal weight: 1.9990 chunk 74 optimal weight: 0.0470 chunk 11 optimal weight: 2.9990 chunk 27 optimal weight: 0.0470 chunk 49 optimal weight: 0.4980 chunk 28 optimal weight: 8.9990 chunk 128 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 361 ASN J 110 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.049248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.043550 restraints weight = 110017.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.044225 restraints weight = 80424.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.044644 restraints weight = 62688.998| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.7461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10042 Z= 0.124 Angle : 0.955 35.920 13662 Z= 0.335 Chirality : 0.046 0.310 1563 Planarity : 0.005 0.074 1745 Dihedral : 5.079 24.762 1452 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.54 % Favored : 89.37 % Rotamer: Outliers : 0.36 % Allowed : 0.84 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.24), residues: 1214 helix: -0.32 (0.24), residues: 476 sheet: -2.55 (0.44), residues: 88 loop : -2.54 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 131 HIS 0.006 0.001 HIS H 155 PHE 0.015 0.001 PHE K 115 TYR 0.017 0.001 TYR H 261 ARG 0.004 0.000 ARG M 95 Details of bonding type rmsd hydrogen bonds : bond 0.02805 ( 354) hydrogen bonds : angle 4.67911 ( 1005) metal coordination : bond 0.01676 ( 6) metal coordination : angle 18.42744 ( 18) covalent geometry : bond 0.00276 (10036) covalent geometry : angle 0.68150 (13644) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 174 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.8622 (tpt) cc_final: 0.8208 (tpp) REVERT: H 76 MET cc_start: 0.8751 (mtt) cc_final: 0.8535 (ttm) REVERT: H 79 GLU cc_start: 0.8834 (tt0) cc_final: 0.7982 (mm-30) REVERT: H 208 ILE cc_start: 0.9218 (pt) cc_final: 0.8823 (mm) REVERT: H 262 LEU cc_start: 0.9695 (mt) cc_final: 0.9345 (pp) REVERT: H 340 PHE cc_start: 0.8899 (t80) cc_final: 0.8535 (t80) REVERT: H 390 GLU cc_start: 0.9296 (pt0) cc_final: 0.8947 (pt0) REVERT: I 85 LEU cc_start: 0.8830 (mt) cc_final: 0.8343 (tp) REVERT: I 100 ASP cc_start: 0.9021 (t0) cc_final: 0.8287 (t70) REVERT: I 103 ILE cc_start: 0.9655 (mm) cc_final: 0.9418 (mm) REVERT: J 50 TYR cc_start: 0.7638 (t80) cc_final: 0.7075 (t80) REVERT: J 133 MET cc_start: 0.9009 (mmm) cc_final: 0.8395 (mmm) REVERT: J 151 PHE cc_start: 0.9234 (m-80) cc_final: 0.8661 (m-80) REVERT: J 153 GLU cc_start: 0.8861 (pp20) cc_final: 0.8186 (pp20) REVERT: K 85 MET cc_start: 0.9142 (mmp) cc_final: 0.8725 (mmp) REVERT: K 136 LEU cc_start: 0.8059 (tp) cc_final: 0.7807 (tt) REVERT: K 144 GLU cc_start: 0.9214 (mp0) cc_final: 0.7983 (tp30) REVERT: K 148 ASP cc_start: 0.9162 (m-30) cc_final: 0.8323 (m-30) REVERT: L 108 MET cc_start: 0.9025 (mpp) cc_final: 0.8669 (mpp) REVERT: L 128 MET cc_start: 0.9097 (mmm) cc_final: 0.8803 (mmt) REVERT: M 100 TYR cc_start: 0.8580 (m-80) cc_final: 0.8224 (m-80) outliers start: 3 outliers final: 3 residues processed: 175 average time/residue: 0.2178 time to fit residues: 55.7497 Evaluate side-chains 146 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 143 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 70 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 115 optimal weight: 8.9990 chunk 117 optimal weight: 0.8980 chunk 46 optimal weight: 0.0170 chunk 24 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 45 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 18 HIS ** M 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.048644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.042853 restraints weight = 113980.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.043576 restraints weight = 82375.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.044066 restraints weight = 63523.440| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.7386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10042 Z= 0.119 Angle : 0.935 38.438 13662 Z= 0.332 Chirality : 0.045 0.150 1563 Planarity : 0.005 0.065 1745 Dihedral : 4.912 24.138 1452 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.29 % Favored : 88.63 % Rotamer: Outliers : 0.36 % Allowed : 0.48 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.24), residues: 1214 helix: -0.21 (0.24), residues: 473 sheet: -2.31 (0.46), residues: 89 loop : -2.57 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 171 HIS 0.006 0.001 HIS H 23 PHE 0.021 0.001 PHE K 115 TYR 0.017 0.001 TYR H 261 ARG 0.011 0.001 ARG I 54 Details of bonding type rmsd hydrogen bonds : bond 0.02616 ( 354) hydrogen bonds : angle 4.54379 ( 1005) metal coordination : bond 0.01393 ( 6) metal coordination : angle 17.86943 ( 18) covalent geometry : bond 0.00268 (10036) covalent geometry : angle 0.67322 (13644) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 169 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.8639 (tpt) cc_final: 0.8309 (tpp) REVERT: H 47 LEU cc_start: 0.9661 (tp) cc_final: 0.9427 (tp) REVERT: H 76 MET cc_start: 0.8719 (mtt) cc_final: 0.8429 (ttm) REVERT: H 79 GLU cc_start: 0.8763 (tt0) cc_final: 0.8011 (mm-30) REVERT: H 105 MET cc_start: 0.9158 (ptt) cc_final: 0.8754 (ptt) REVERT: H 156 ASN cc_start: 0.9240 (t0) cc_final: 0.9018 (t0) REVERT: H 208 ILE cc_start: 0.9154 (pt) cc_final: 0.8781 (mm) REVERT: H 262 LEU cc_start: 0.9689 (mt) cc_final: 0.9344 (pp) REVERT: H 340 PHE cc_start: 0.8787 (t80) cc_final: 0.8442 (t80) REVERT: H 378 MET cc_start: 0.8850 (mmp) cc_final: 0.8199 (mmt) REVERT: H 390 GLU cc_start: 0.9297 (pt0) cc_final: 0.8885 (pt0) REVERT: I 85 LEU cc_start: 0.8928 (mt) cc_final: 0.8440 (tp) REVERT: I 100 ASP cc_start: 0.8971 (t0) cc_final: 0.8746 (t70) REVERT: J 50 TYR cc_start: 0.7466 (t80) cc_final: 0.6892 (t80) REVERT: J 133 MET cc_start: 0.9016 (mmm) cc_final: 0.8609 (mmm) REVERT: J 151 PHE cc_start: 0.9206 (m-80) cc_final: 0.8628 (m-80) REVERT: J 153 GLU cc_start: 0.8765 (pp20) cc_final: 0.8208 (pp20) REVERT: K 85 MET cc_start: 0.9026 (mmp) cc_final: 0.8774 (mmm) REVERT: K 144 GLU cc_start: 0.9220 (mp0) cc_final: 0.7896 (tp30) REVERT: K 148 ASP cc_start: 0.9025 (m-30) cc_final: 0.8083 (m-30) REVERT: L 108 MET cc_start: 0.9031 (mpp) cc_final: 0.8592 (mpp) REVERT: L 128 MET cc_start: 0.9158 (mmm) cc_final: 0.8796 (mmt) REVERT: L 144 LEU cc_start: 0.7943 (tp) cc_final: 0.7539 (pp) REVERT: M 100 TYR cc_start: 0.8523 (m-80) cc_final: 0.8108 (m-80) outliers start: 3 outliers final: 3 residues processed: 170 average time/residue: 0.1761 time to fit residues: 44.4620 Evaluate side-chains 147 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 144 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 74 optimal weight: 7.9990 chunk 107 optimal weight: 0.3980 chunk 55 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 83 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 361 ASN ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.055031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.050059 restraints weight = 117084.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.050862 restraints weight = 76299.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.051413 restraints weight = 54317.773| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.8083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10042 Z= 0.209 Angle : 1.149 48.098 13662 Z= 0.381 Chirality : 0.048 0.167 1563 Planarity : 0.005 0.069 1745 Dihedral : 5.468 23.028 1452 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.92 % Favored : 86.00 % Rotamer: Outliers : 0.36 % Allowed : 0.60 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.24), residues: 1214 helix: -0.37 (0.24), residues: 472 sheet: -2.38 (0.51), residues: 78 loop : -2.58 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP K 35 HIS 0.009 0.002 HIS H 114 PHE 0.016 0.002 PHE K 115 TYR 0.023 0.002 TYR J 69 ARG 0.009 0.001 ARG H 69 Details of bonding type rmsd hydrogen bonds : bond 0.03455 ( 354) hydrogen bonds : angle 4.89123 ( 1005) metal coordination : bond 0.01968 ( 6) metal coordination : angle 24.20985 ( 18) covalent geometry : bond 0.00442 (10036) covalent geometry : angle 0.74023 (13644) =============================================================================== Job complete usr+sys time: 3533.45 seconds wall clock time: 63 minutes 40.20 seconds (3820.20 seconds total)