Starting phenix.real_space_refine on Wed Mar 4 01:17:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wfg_32465/03_2026/7wfg_32465.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wfg_32465/03_2026/7wfg_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_32465/03_2026/7wfg_32465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wfg_32465/03_2026/7wfg_32465.map" model { file = "/net/cci-nas-00/data/ceres_data/7wfg_32465/03_2026/7wfg_32465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wfg_32465/03_2026/7wfg_32465.cif" } resolution = 4.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'TYR:plan': 2, 'PHE:plan': 5, 'ARG:plan': 4, 'GLU:plan': 2, 'GLN:plan1': 4, 'TRP:plan': 1} 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: {'ARG:plan': 2, 'TYR:plan': 4, 'PHE:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 1, 'TRP:plan': 1, 'ASN:plan1': 1} 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: {'TRP:plan': 2, 'ARG:plan': 4, 'HIS:plan': 3, 'PHE:plan': 3, 'TYR:plan': 4, 'GLN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 3, 'ASN:plan1': 3} 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: {'PHE:plan': 4, 'ASP:plan': 1, 'ARG:plan': 5, 'ASN:plan1': 3, 'GLN:plan1': 1, 'GLU:plan': 1, 'TYR:plan': 1} 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: {'ARG:plan': 1, 'PHE:plan': 4} 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: {'ARG:plan': 2, 'TYR:plan': 5, 'ASP:plan': 7, 'GLU:plan': 5, 'GLN:plan1': 4, 'PHE:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1} 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: {'ASP:plan': 3, 'TRP:plan': 5, 'GLN:plan1': 4, 'GLU:plan': 7, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 4, 'PHE:plan': 3, 'ARG:plan': 6} 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: {'TYR:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'TRP: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: 2.33, per 1000 atoms: 0.24 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: 0.75 Conformation dependent library (CDL) restraints added in 394.0 milliseconds 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: 0.28 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: 1.23 Time building geometry restraints manager: 1.03 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: 4.650 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.580 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.920 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.015 0.001 ARG H 69 TYR 0.016 0.002 TYR J 57 PHE 0.016 0.002 PHE H 182 TRP 0.024 0.002 TRP H 117 HIS 0.008 0.001 HIS M 169 Details of bonding type rmsd covalent geometry : bond 0.00573 (10036) covalent geometry : angle 1.00837 (13644) hydrogen bonds : bond 0.15863 ( 354) hydrogen bonds : angle 7.14889 ( 1005) metal coordination : bond 0.89549 ( 6) metal coordination : angle 28.84825 ( 18) *********************** 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 : 0.362 Fit side-chains revert: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.7825 (tpt) cc_final: 0.7366 (tpp) REVERT: H 47 LEU cc_start: 0.9296 (tp) cc_final: 0.8852 (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: 0.9128 (t0) REVERT: H 171 TRP cc_start: 0.9322 (t60) cc_final: 0.9040 (t60) REVERT: H 261 TYR cc_start: 0.8837 (t80) cc_final: 0.8624 (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: 0.8783 (mmp) REVERT: H 384 ILE cc_start: 0.9671 (mm) cc_final: 0.9320 (tp) REVERT: H 390 GLU cc_start: 0.9130 (pt0) cc_final: 0.8801 (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: 0.7637 (t70) REVERT: I 101 PHE cc_start: 0.9240 (m-10) cc_final: 0.8991 (m-80) REVERT: I 103 ILE cc_start: 0.9528 (mm) cc_final: 0.9168 (mm) REVERT: I 134 GLU cc_start: 0.8639 (tt0) cc_final: 0.8427 (tm-30) REVERT: I 137 TYR cc_start: 0.7528 (m-10) cc_final: 0.6807 (m-10) REVERT: J 51 LEU cc_start: 0.8577 (tp) cc_final: 0.8372 (tp) REVERT: J 71 LEU cc_start: 0.8562 (tp) cc_final: 0.8172 (tp) REVERT: J 111 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8534 (mm-30) REVERT: J 128 LEU cc_start: 0.8978 (tp) cc_final: 0.8568 (mt) REVERT: K 103 ILE cc_start: 0.9291 (mm) cc_final: 0.8895 (mp) REVERT: K 144 GLU cc_start: 0.8132 (mp0) cc_final: 0.7814 (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: 0.8470 (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: 0.8870 (p) outliers start: 9 outliers final: 3 residues processed: 268 average time/residue: 0.1000 time to fit residues: 36.4714 Evaluate side-chains 175 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 171 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.0770 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.0870 chunk 55 optimal weight: 10.0000 overall best weight: 1.2118 ------------------------------------------------------------------------------- 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** H 363 GLN I 10 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.054271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.047765 restraints weight = 111482.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.048507 restraints weight = 84003.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.049043 restraints weight = 66789.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.049459 restraints weight = 55643.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.049771 restraints weight = 47930.345| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10042 Z= 0.139 Angle : 0.869 32.083 13662 Z= 0.334 Chirality : 0.045 0.151 1563 Planarity : 0.006 0.061 1745 Dihedral : 5.108 29.298 1452 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 0.36 % Allowed : 4.43 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.66 (0.21), residues: 1214 helix: -1.42 (0.22), residues: 435 sheet: -2.05 (0.50), residues: 93 loop : -3.33 (0.21), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 152 TYR 0.017 0.001 TYR M 100 PHE 0.023 0.001 PHE H 182 TRP 0.022 0.001 TRP H 117 HIS 0.013 0.001 HIS M 96 Details of bonding type rmsd covalent geometry : bond 0.00299 (10036) covalent geometry : angle 0.66000 (13644) hydrogen bonds : bond 0.03294 ( 354) hydrogen bonds : angle 4.85839 ( 1005) metal coordination : bond 0.01896 ( 6) metal coordination : angle 15.58355 ( 18) *********************** 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 206 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 203 time to evaluate : 0.324 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.7637 (tpt) cc_final: 0.7257 (tpp) REVERT: H 26 LEU cc_start: 0.9051 (mp) cc_final: 0.8801 (mp) REVERT: H 47 LEU cc_start: 0.9396 (tp) cc_final: 0.9065 (tp) REVERT: H 76 MET cc_start: 0.8861 (mtt) cc_final: 0.8492 (mtm) REVERT: H 156 ASN cc_start: 0.9409 (t0) cc_final: 0.9176 (t0) REVERT: H 171 TRP cc_start: 0.9162 (t60) cc_final: 0.8907 (t60) REVERT: H 261 TYR cc_start: 0.8631 (t80) cc_final: 0.8343 (t80) REVERT: H 262 LEU cc_start: 0.9557 (mt) cc_final: 0.9235 (pp) REVERT: H 381 LEU cc_start: 0.9350 (pp) cc_final: 0.8675 (pp) REVERT: H 384 ILE cc_start: 0.9663 (mm) cc_final: 0.9332 (tp) REVERT: H 390 GLU cc_start: 0.8980 (pt0) cc_final: 0.8588 (pt0) REVERT: I 85 LEU cc_start: 0.8980 (mt) cc_final: 0.8515 (tp) REVERT: I 100 ASP cc_start: 0.8660 (t0) cc_final: 0.7734 (t70) REVERT: I 101 PHE cc_start: 0.9196 (m-10) cc_final: 0.8774 (m-10) REVERT: I 103 ILE cc_start: 0.9657 (mm) cc_final: 0.9359 (mm) REVERT: I 134 GLU cc_start: 0.8719 (tt0) cc_final: 0.8509 (tm-30) REVERT: J 128 LEU cc_start: 0.9103 (tp) cc_final: 0.8884 (tp) REVERT: J 133 MET cc_start: 0.8367 (mmm) cc_final: 0.7741 (mmt) REVERT: K 114 MET cc_start: 0.8961 (pmm) cc_final: 0.8467 (pmm) REVERT: K 144 GLU cc_start: 0.8411 (mp0) cc_final: 0.7949 (tp30) REVERT: K 164 ASP cc_start: 0.7750 (t0) cc_final: 0.7451 (p0) REVERT: L 128 MET cc_start: 0.9222 (mmm) cc_final: 0.8794 (mmt) REVERT: M 100 TYR cc_start: 0.8197 (m-80) cc_final: 0.7969 (m-80) outliers start: 3 outliers final: 3 residues processed: 204 average time/residue: 0.0954 time to fit residues: 27.5026 Evaluate side-chains 165 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 162 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 52 optimal weight: 5.9990 chunk 116 optimal weight: 0.1980 chunk 47 optimal weight: 7.9990 chunk 124 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 chunk 92 optimal weight: 0.9980 chunk 128 optimal weight: 10.0000 chunk 8 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.050047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.043748 restraints weight = 111319.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.044493 restraints weight = 82079.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.044918 restraints weight = 64601.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.045373 restraints weight = 54876.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.045692 restraints weight = 46904.346| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10042 Z= 0.160 Angle : 0.903 37.744 13662 Z= 0.336 Chirality : 0.045 0.148 1563 Planarity : 0.006 0.068 1745 Dihedral : 4.982 25.121 1452 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.96 % Favored : 88.96 % Rotamer: Outliers : 0.36 % Allowed : 3.47 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.23), residues: 1214 helix: -0.59 (0.24), residues: 455 sheet: -2.13 (0.46), residues: 101 loop : -3.09 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG J 96 TYR 0.015 0.001 TYR J 122 PHE 0.018 0.002 PHE K 45 TRP 0.016 0.002 TRP H 217 HIS 0.006 0.001 HIS H 155 Details of bonding type rmsd covalent geometry : bond 0.00342 (10036) covalent geometry : angle 0.66167 (13644) hydrogen bonds : bond 0.03217 ( 354) hydrogen bonds : angle 4.54869 ( 1005) metal coordination : bond 0.01562 ( 6) metal coordination : angle 16.93405 ( 18) *********************** 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 194 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 191 time to evaluate : 0.370 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: H 15 MET cc_start: 0.8244 (tpt) cc_final: 0.7739 (tpp) REVERT: H 154 MET cc_start: 0.7191 (mtm) cc_final: 0.6946 (mtm) REVERT: H 171 TRP cc_start: 0.9147 (t60) cc_final: 0.8945 (t60) REVERT: H 261 TYR cc_start: 0.8870 (t80) cc_final: 0.8614 (t80) REVERT: H 262 LEU cc_start: 0.9610 (mt) cc_final: 0.9282 (pp) REVERT: H 340 PHE cc_start: 0.8517 (t80) cc_final: 0.8282 (t80) REVERT: H 390 GLU cc_start: 0.9060 (pt0) cc_final: 0.8612 (pt0) REVERT: I 85 LEU cc_start: 0.9053 (mt) cc_final: 0.8720 (tp) REVERT: I 100 ASP cc_start: 0.8691 (t0) cc_final: 0.8086 (t0) REVERT: I 101 PHE cc_start: 0.8898 (m-10) cc_final: 0.7691 (m-10) REVERT: I 103 ILE cc_start: 0.9563 (mm) cc_final: 0.9326 (mm) REVERT: I 137 TYR cc_start: 0.8068 (m-80) cc_final: 0.7068 (m-80) REVERT: J 111 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8279 (mm-30) REVERT: J 128 LEU cc_start: 0.9204 (tp) cc_final: 0.8840 (tp) REVERT: K 83 MET cc_start: 0.8540 (ppp) cc_final: 0.8305 (tpp) REVERT: K 114 MET cc_start: 0.8866 (pmm) cc_final: 0.8238 (pmm) REVERT: K 144 GLU cc_start: 0.8592 (mp0) cc_final: 0.8094 (tp30) REVERT: L 128 MET cc_start: 0.9174 (mmm) cc_final: 0.8754 (mmt) REVERT: M 100 TYR cc_start: 0.8431 (m-80) cc_final: 0.8187 (m-80) outliers start: 3 outliers final: 3 residues processed: 192 average time/residue: 0.0870 time to fit residues: 24.1442 Evaluate side-chains 155 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 152 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 69 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 67 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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** ** H 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN ** M 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 169 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.050605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.044447 restraints weight = 116787.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.045190 restraints weight = 84190.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.045744 restraints weight = 65449.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.046077 restraints weight = 53508.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.046403 restraints weight = 46445.769| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10042 Z= 0.177 Angle : 0.900 40.627 13662 Z= 0.345 Chirality : 0.045 0.147 1563 Planarity : 0.006 0.115 1745 Dihedral : 5.161 23.375 1452 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 0.36 % Allowed : 4.07 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.23), residues: 1214 helix: -0.39 (0.24), residues: 458 sheet: -2.15 (0.49), residues: 89 loop : -2.94 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 161 TYR 0.016 0.002 TYR H 327 PHE 0.014 0.001 PHE K 115 TRP 0.015 0.002 TRP H 350 HIS 0.007 0.002 HIS H 155 Details of bonding type rmsd covalent geometry : bond 0.00374 (10036) covalent geometry : angle 0.67876 (13644) hydrogen bonds : bond 0.03213 ( 354) hydrogen bonds : angle 4.52443 ( 1005) metal coordination : bond 0.01693 ( 6) metal coordination : angle 16.30593 ( 18) *********************** 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 175 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 172 time to evaluate : 0.341 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: 0.8378 (tpt) cc_final: 0.7968 (tpp) REVERT: H 47 LEU cc_start: 0.9583 (tp) cc_final: 0.9297 (tp) REVERT: H 154 MET cc_start: 0.7429 (mtm) cc_final: 0.7019 (mtm) REVERT: H 261 TYR cc_start: 0.8949 (t80) cc_final: 0.8726 (t80) REVERT: H 262 LEU cc_start: 0.9646 (mt) cc_final: 0.9316 (pp) REVERT: H 340 PHE cc_start: 0.8814 (t80) cc_final: 0.8556 (t80) REVERT: H 390 GLU cc_start: 0.9151 (pt0) cc_final: 0.8707 (pt0) REVERT: I 85 LEU cc_start: 0.9103 (mt) cc_final: 0.8665 (tp) REVERT: I 100 ASP cc_start: 0.8613 (t0) cc_final: 0.8409 (t70) REVERT: I 113 TYR cc_start: 0.9085 (m-80) cc_final: 0.8795 (m-80) REVERT: J 70 HIS cc_start: 0.7928 (m90) cc_final: 0.6930 (m90) REVERT: K 114 MET cc_start: 0.9000 (pmm) cc_final: 0.8255 (pmm) REVERT: K 144 GLU cc_start: 0.8870 (mp0) cc_final: 0.8058 (tp30) REVERT: K 148 ASP cc_start: 0.8472 (m-30) cc_final: 0.7669 (m-30) REVERT: L 128 MET cc_start: 0.9162 (mmm) cc_final: 0.8716 (mmt) outliers start: 3 outliers final: 3 residues processed: 173 average time/residue: 0.0702 time to fit residues: 18.7348 Evaluate side-chains 143 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 140 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 83 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.0980 chunk 69 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- 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 48 HIS H 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.047542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.041851 restraints weight = 120845.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.042544 restraints weight = 87417.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.043039 restraints weight = 68046.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.043347 restraints weight = 55782.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.043657 restraints weight = 48415.220| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.6558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10042 Z= 0.206 Angle : 1.012 45.037 13662 Z= 0.368 Chirality : 0.047 0.207 1563 Planarity : 0.006 0.066 1745 Dihedral : 5.431 23.314 1452 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.51 % Favored : 86.41 % Rotamer: Outliers : 0.36 % Allowed : 2.99 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.24), residues: 1214 helix: -0.44 (0.24), residues: 470 sheet: -2.28 (0.51), residues: 83 loop : -2.83 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 69 TYR 0.014 0.002 TYR J 57 PHE 0.015 0.002 PHE K 115 TRP 0.018 0.002 TRP H 350 HIS 0.009 0.002 HIS H 114 Details of bonding type rmsd covalent geometry : bond 0.00433 (10036) covalent geometry : angle 0.70910 (13644) hydrogen bonds : bond 0.03489 ( 354) hydrogen bonds : angle 4.75297 ( 1005) metal coordination : bond 0.02192 ( 6) metal coordination : angle 19.89141 ( 18) *********************** 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 170 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 167 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.8800 (tpt) cc_final: 0.8202 (tpp) REVERT: H 79 GLU cc_start: 0.8862 (tt0) cc_final: 0.7969 (tm-30) REVERT: H 262 LEU cc_start: 0.9648 (mt) cc_final: 0.9334 (pp) REVERT: H 390 GLU cc_start: 0.9151 (pt0) cc_final: 0.8704 (pt0) REVERT: I 85 LEU cc_start: 0.9073 (mt) cc_final: 0.8492 (tp) REVERT: I 100 ASP cc_start: 0.8633 (t0) cc_final: 0.7820 (t70) REVERT: I 103 ILE cc_start: 0.9503 (mm) cc_final: 0.9103 (mm) REVERT: I 113 TYR cc_start: 0.9319 (m-80) cc_final: 0.9046 (m-80) REVERT: I 137 TYR cc_start: 0.7786 (m-80) cc_final: 0.7517 (m-80) REVERT: J 85 CYS cc_start: 0.8714 (t) cc_final: 0.8308 (p) REVERT: J 128 LEU cc_start: 0.9286 (tp) cc_final: 0.9070 (tp) REVERT: K 85 MET cc_start: 0.9024 (mmp) cc_final: 0.8704 (mmp) REVERT: K 114 MET cc_start: 0.8825 (pmm) cc_final: 0.8044 (pmm) REVERT: K 144 GLU cc_start: 0.8885 (mp0) cc_final: 0.7845 (tp30) REVERT: K 148 ASP cc_start: 0.8742 (m-30) cc_final: 0.7732 (m-30) REVERT: L 108 MET cc_start: 0.8679 (mpp) cc_final: 0.8425 (mpp) REVERT: L 128 MET cc_start: 0.9132 (mmm) cc_final: 0.8619 (mmt) REVERT: M 100 TYR cc_start: 0.8697 (m-80) cc_final: 0.8375 (m-80) outliers start: 3 outliers final: 3 residues processed: 168 average time/residue: 0.0761 time to fit residues: 19.6234 Evaluate side-chains 136 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 133 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 128 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3356 r_free = 0.3356 target = 0.048457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.042583 restraints weight = 116312.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.043208 restraints weight = 85605.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.043758 restraints weight = 67422.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.044049 restraints weight = 55540.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.044391 restraints weight = 48676.605| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.6525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10042 Z= 0.123 Angle : 0.877 37.174 13662 Z= 0.323 Chirality : 0.045 0.144 1563 Planarity : 0.005 0.063 1745 Dihedral : 5.039 22.812 1452 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.71 % Favored : 89.21 % Rotamer: Outliers : 0.36 % Allowed : 1.91 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.24), residues: 1214 helix: -0.29 (0.24), residues: 470 sheet: -2.35 (0.46), residues: 94 loop : -2.72 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 17 TYR 0.015 0.001 TYR J 57 PHE 0.027 0.001 PHE K 115 TRP 0.018 0.001 TRP H 171 HIS 0.006 0.001 HIS H 114 Details of bonding type rmsd covalent geometry : bond 0.00272 (10036) covalent geometry : angle 0.64354 (13644) hydrogen bonds : bond 0.02797 ( 354) hydrogen bonds : angle 4.50098 ( 1005) metal coordination : bond 0.01365 ( 6) metal coordination : angle 16.41971 ( 18) *********************** 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 175 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 172 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.8623 (tpt) cc_final: 0.8102 (tpp) REVERT: H 47 LEU cc_start: 0.9640 (tp) cc_final: 0.9375 (tp) REVERT: H 79 GLU cc_start: 0.8777 (tt0) cc_final: 0.7745 (mm-30) REVERT: H 154 MET cc_start: 0.7077 (mtm) cc_final: 0.6848 (mtt) REVERT: H 208 ILE cc_start: 0.9074 (pt) cc_final: 0.8656 (mm) REVERT: H 262 LEU cc_start: 0.9669 (mt) cc_final: 0.9367 (pp) REVERT: H 340 PHE cc_start: 0.8714 (t80) cc_final: 0.8443 (t80) REVERT: H 390 GLU cc_start: 0.9166 (pt0) cc_final: 0.8816 (pt0) REVERT: I 85 LEU cc_start: 0.9065 (mt) cc_final: 0.8456 (tp) REVERT: I 100 ASP cc_start: 0.8824 (t0) cc_final: 0.7987 (t70) REVERT: I 103 ILE cc_start: 0.9595 (mm) cc_final: 0.9193 (mm) REVERT: I 113 TYR cc_start: 0.9245 (m-80) cc_final: 0.9021 (m-80) REVERT: J 85 CYS cc_start: 0.8817 (t) cc_final: 0.8536 (t) REVERT: J 87 LYS cc_start: 0.8940 (mmpt) cc_final: 0.8723 (mmmt) REVERT: K 85 MET cc_start: 0.9153 (mmp) cc_final: 0.8757 (mmp) REVERT: K 114 MET cc_start: 0.8967 (pmm) cc_final: 0.8094 (pmm) REVERT: K 130 ILE cc_start: 0.9719 (mp) cc_final: 0.9470 (tt) REVERT: K 144 GLU cc_start: 0.8937 (mp0) cc_final: 0.7953 (tp30) REVERT: K 148 ASP cc_start: 0.8952 (m-30) cc_final: 0.8013 (m-30) REVERT: L 108 MET cc_start: 0.8728 (mpp) cc_final: 0.8297 (mpp) REVERT: L 128 MET cc_start: 0.9168 (mmm) cc_final: 0.8686 (mmt) REVERT: M 100 TYR cc_start: 0.8591 (m-80) cc_final: 0.8202 (m-80) outliers start: 3 outliers final: 3 residues processed: 173 average time/residue: 0.0728 time to fit residues: 19.1638 Evaluate side-chains 144 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 141 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 4 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 131 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 361 ASN ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.046820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.041440 restraints weight = 118821.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.041929 restraints weight = 87141.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.042484 restraints weight = 70473.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 15)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.042769 restraints weight = 57852.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.043082 restraints weight = 50432.683| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.7398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10042 Z= 0.217 Angle : 1.065 45.086 13662 Z= 0.371 Chirality : 0.047 0.169 1563 Planarity : 0.005 0.068 1745 Dihedral : 5.454 22.694 1452 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 20.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.26 % Favored : 86.57 % Rotamer: Outliers : 0.36 % Allowed : 2.03 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.24), residues: 1214 helix: -0.47 (0.23), residues: 470 sheet: -2.39 (0.49), residues: 83 loop : -2.70 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 69 TYR 0.017 0.002 TYR J 69 PHE 0.024 0.002 PHE K 115 TRP 0.021 0.002 TRP K 28 HIS 0.010 0.002 HIS H 114 Details of bonding type rmsd covalent geometry : bond 0.00457 (10036) covalent geometry : angle 0.71637 (13644) hydrogen bonds : bond 0.03455 ( 354) hydrogen bonds : angle 4.79523 ( 1005) metal coordination : bond 0.02243 ( 6) metal coordination : angle 21.72413 ( 18) *********************** 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 165 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 162 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.8871 (tpt) cc_final: 0.8380 (tpp) REVERT: H 79 GLU cc_start: 0.8915 (tt0) cc_final: 0.8080 (tm-30) REVERT: H 262 LEU cc_start: 0.9714 (mt) cc_final: 0.9407 (pp) REVERT: H 340 PHE cc_start: 0.8827 (t80) cc_final: 0.8501 (t80) REVERT: H 390 GLU cc_start: 0.9286 (pt0) cc_final: 0.8887 (pt0) REVERT: I 100 ASP cc_start: 0.8815 (t0) cc_final: 0.7942 (t0) REVERT: I 103 ILE cc_start: 0.9591 (mm) cc_final: 0.9220 (mm) REVERT: J 50 TYR cc_start: 0.7737 (t80) cc_final: 0.7187 (t80) REVERT: J 87 LYS cc_start: 0.9127 (mmpt) cc_final: 0.8816 (mmmt) REVERT: K 37 LEU cc_start: 0.7962 (tp) cc_final: 0.7459 (mt) REVERT: K 77 THR cc_start: 0.8836 (t) cc_final: 0.8610 (t) REVERT: K 85 MET cc_start: 0.9251 (mmp) cc_final: 0.8674 (mmm) REVERT: K 114 MET cc_start: 0.9053 (pmm) cc_final: 0.8129 (pmm) REVERT: K 144 GLU cc_start: 0.8987 (mp0) cc_final: 0.7754 (tp30) REVERT: K 148 ASP cc_start: 0.9043 (m-30) cc_final: 0.7977 (m-30) REVERT: L 108 MET cc_start: 0.8947 (mpp) cc_final: 0.8520 (mpp) REVERT: L 128 MET cc_start: 0.9098 (mmm) cc_final: 0.8593 (mmt) REVERT: M 100 TYR cc_start: 0.8693 (m-80) cc_final: 0.8424 (m-80) outliers start: 3 outliers final: 3 residues processed: 163 average time/residue: 0.0632 time to fit residues: 15.6740 Evaluate side-chains 136 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 133 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 66 optimal weight: 20.0000 chunk 87 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 0.0070 chunk 116 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 38 optimal weight: 0.0370 chunk 52 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- 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** H 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.048823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.043235 restraints weight = 108853.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 15)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.043774 restraints weight = 81751.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.044307 restraints weight = 65782.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.044622 restraints weight = 54740.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.044889 restraints weight = 47366.476| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.7167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10042 Z= 0.119 Angle : 0.889 32.990 13662 Z= 0.326 Chirality : 0.046 0.151 1563 Planarity : 0.005 0.066 1745 Dihedral : 5.022 23.845 1452 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.38 % Favored : 89.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.24), residues: 1214 helix: -0.26 (0.24), residues: 470 sheet: -2.35 (0.47), residues: 88 loop : -2.62 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 96 TYR 0.018 0.001 TYR J 122 PHE 0.029 0.001 PHE L 134 TRP 0.021 0.002 TRP H 171 HIS 0.006 0.001 HIS H 114 Details of bonding type rmsd covalent geometry : bond 0.00266 (10036) covalent geometry : angle 0.65713 (13644) hydrogen bonds : bond 0.02791 ( 354) hydrogen bonds : angle 4.53284 ( 1005) metal coordination : bond 0.01330 ( 6) metal coordination : angle 16.51886 ( 18) *********************** 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 178 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 175 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.8644 (tpt) cc_final: 0.8114 (tpp) REVERT: H 47 LEU cc_start: 0.9535 (tp) cc_final: 0.9330 (tp) REVERT: H 79 GLU cc_start: 0.8860 (tt0) cc_final: 0.8046 (tm-30) REVERT: H 154 MET cc_start: 0.6580 (mtt) cc_final: 0.5746 (mtt) REVERT: H 208 ILE cc_start: 0.9162 (pt) cc_final: 0.8773 (mm) REVERT: H 262 LEU cc_start: 0.9706 (mt) cc_final: 0.9382 (pp) REVERT: H 340 PHE cc_start: 0.8780 (t80) cc_final: 0.8493 (t80) REVERT: H 390 GLU cc_start: 0.9309 (pt0) cc_final: 0.8891 (pt0) REVERT: I 85 LEU cc_start: 0.8847 (mt) cc_final: 0.8360 (tp) REVERT: I 100 ASP cc_start: 0.8869 (t0) cc_final: 0.7992 (t70) REVERT: I 101 PHE cc_start: 0.9238 (m-10) cc_final: 0.8892 (m-10) REVERT: I 103 ILE cc_start: 0.9675 (mm) cc_final: 0.9304 (mm) REVERT: J 50 TYR cc_start: 0.7537 (t80) cc_final: 0.7034 (t80) REVERT: J 87 LYS cc_start: 0.9001 (mmpt) cc_final: 0.8757 (mmmt) REVERT: K 85 MET cc_start: 0.9169 (mmp) cc_final: 0.8640 (mmm) REVERT: K 114 MET cc_start: 0.9022 (pmm) cc_final: 0.8304 (pmm) REVERT: K 144 GLU cc_start: 0.8947 (mp0) cc_final: 0.7964 (tp30) REVERT: L 108 MET cc_start: 0.8853 (mpp) cc_final: 0.8380 (mpp) REVERT: L 128 MET cc_start: 0.9139 (mmm) cc_final: 0.8785 (mmt) REVERT: M 100 TYR cc_start: 0.8612 (m-80) cc_final: 0.8291 (m-80) outliers start: 3 outliers final: 3 residues processed: 176 average time/residue: 0.0775 time to fit residues: 20.5757 Evaluate side-chains 144 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 141 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 47 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 60 optimal weight: 0.0010 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 49 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 110 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- 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** ** K 23 ASN ** 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 = 0.3294 r_free = 0.3294 target = 0.047220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.041549 restraints weight = 116995.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.042133 restraints weight = 84037.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.042645 restraints weight = 66428.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.043067 restraints weight = 55107.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.043282 restraints weight = 46459.117| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.7629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10042 Z= 0.176 Angle : 1.042 43.487 13662 Z= 0.354 Chirality : 0.046 0.166 1563 Planarity : 0.005 0.065 1745 Dihedral : 5.232 23.206 1452 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.69 % Favored : 87.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.24), residues: 1214 helix: -0.42 (0.24), residues: 476 sheet: -2.27 (0.51), residues: 78 loop : -2.62 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 69 TYR 0.017 0.002 TYR H 261 PHE 0.018 0.001 PHE K 115 TRP 0.019 0.002 TRP H 171 HIS 0.008 0.001 HIS H 114 Details of bonding type rmsd covalent geometry : bond 0.00380 (10036) covalent geometry : angle 0.69745 (13644) hydrogen bonds : bond 0.03175 ( 354) hydrogen bonds : angle 4.70049 ( 1005) metal coordination : bond 0.01448 ( 6) metal coordination : angle 21.34719 ( 18) *********************** 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 167 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 164 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: H 15 MET cc_start: 0.8857 (tpt) cc_final: 0.8275 (tpp) REVERT: H 47 LEU cc_start: 0.9639 (tp) cc_final: 0.9363 (tp) REVERT: H 76 MET cc_start: 0.9084 (ttt) cc_final: 0.8531 (ttt) REVERT: H 79 GLU cc_start: 0.8963 (tt0) cc_final: 0.8188 (tm-30) REVERT: H 208 ILE cc_start: 0.9190 (pt) cc_final: 0.8794 (mm) REVERT: H 340 PHE cc_start: 0.8708 (t80) cc_final: 0.8379 (t80) REVERT: H 390 GLU cc_start: 0.9330 (pt0) cc_final: 0.8879 (pt0) REVERT: I 85 LEU cc_start: 0.8898 (mt) cc_final: 0.8428 (tp) REVERT: I 100 ASP cc_start: 0.8854 (t0) cc_final: 0.7953 (t70) REVERT: I 101 PHE cc_start: 0.9242 (m-10) cc_final: 0.8875 (m-10) REVERT: I 103 ILE cc_start: 0.9627 (mm) cc_final: 0.9286 (mm) REVERT: J 50 TYR cc_start: 0.7722 (t80) cc_final: 0.7032 (t80) REVERT: J 87 LYS cc_start: 0.8997 (mmpt) cc_final: 0.8765 (mmmt) REVERT: K 85 MET cc_start: 0.9210 (mmp) cc_final: 0.8858 (mmp) REVERT: K 114 MET cc_start: 0.8851 (pmm) cc_final: 0.8138 (pmm) REVERT: K 115 PHE cc_start: 0.9284 (m-10) cc_final: 0.8804 (m-10) REVERT: K 144 GLU cc_start: 0.9047 (mp0) cc_final: 0.7795 (tp30) REVERT: K 148 ASP cc_start: 0.9043 (m-30) cc_final: 0.8041 (m-30) REVERT: L 108 MET cc_start: 0.9094 (mpp) cc_final: 0.8513 (mpp) REVERT: L 128 MET cc_start: 0.9176 (mmm) cc_final: 0.8787 (mmt) REVERT: M 100 TYR cc_start: 0.8648 (m-80) cc_final: 0.8366 (m-80) outliers start: 3 outliers final: 3 residues processed: 165 average time/residue: 0.0779 time to fit residues: 19.4607 Evaluate side-chains 135 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 132 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 30 optimal weight: 8.9990 chunk 60 optimal weight: 0.5980 chunk 91 optimal weight: 0.0870 chunk 103 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 overall best weight: 1.5362 ------------------------------------------------------------------------------- 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 = 0.3307 r_free = 0.3307 target = 0.047027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.041312 restraints weight = 109804.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.041960 restraints weight = 81546.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.042355 restraints weight = 64097.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 14)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.042677 restraints weight = 53879.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.043024 restraints weight = 46958.165| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.7689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10042 Z= 0.143 Angle : 0.983 39.135 13662 Z= 0.347 Chirality : 0.047 0.390 1563 Planarity : 0.005 0.063 1745 Dihedral : 5.137 24.189 1452 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.04 % Favored : 88.88 % Rotamer: Outliers : 0.36 % Allowed : 0.36 % Favored : 99.28 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.24), residues: 1214 helix: -0.37 (0.24), residues: 476 sheet: -2.36 (0.47), residues: 88 loop : -2.55 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 17 TYR 0.014 0.001 TYR J 57 PHE 0.019 0.001 PHE K 115 TRP 0.025 0.002 TRP H 171 HIS 0.007 0.001 HIS H 114 Details of bonding type rmsd covalent geometry : bond 0.00316 (10036) covalent geometry : angle 0.70949 (13644) hydrogen bonds : bond 0.02947 ( 354) hydrogen bonds : angle 4.60214 ( 1005) metal coordination : bond 0.01442 ( 6) metal coordination : angle 18.76621 ( 18) ********************** 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 169 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 166 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: H 15 MET cc_start: 0.8747 (tpt) cc_final: 0.8242 (tpp) REVERT: H 79 GLU cc_start: 0.8963 (tt0) cc_final: 0.8059 (mm-30) REVERT: H 208 ILE cc_start: 0.9189 (pt) cc_final: 0.8783 (mm) REVERT: H 262 LEU cc_start: 0.9727 (mt) cc_final: 0.9350 (pp) REVERT: H 340 PHE cc_start: 0.8689 (t80) cc_final: 0.8431 (t80) REVERT: H 390 GLU cc_start: 0.9312 (pt0) cc_final: 0.8935 (pt0) REVERT: I 85 LEU cc_start: 0.8798 (mt) cc_final: 0.8327 (tp) REVERT: I 100 ASP cc_start: 0.8921 (t0) cc_final: 0.8064 (t70) REVERT: I 101 PHE cc_start: 0.9252 (m-10) cc_final: 0.8883 (m-10) REVERT: I 103 ILE cc_start: 0.9643 (mm) cc_final: 0.9283 (mm) REVERT: I 113 TYR cc_start: 0.9381 (m-80) cc_final: 0.9166 (m-80) REVERT: J 50 TYR cc_start: 0.7674 (t80) cc_final: 0.7011 (t80) REVERT: J 133 MET cc_start: 0.9117 (mmp) cc_final: 0.8785 (mmm) REVERT: K 37 LEU cc_start: 0.8695 (tt) cc_final: 0.8247 (tp) REVERT: K 74 LEU cc_start: 0.8625 (mp) cc_final: 0.8032 (mp) REVERT: K 85 MET cc_start: 0.9281 (mmp) cc_final: 0.8855 (mmp) REVERT: K 144 GLU cc_start: 0.9101 (mp0) cc_final: 0.7920 (tp30) REVERT: K 148 ASP cc_start: 0.9036 (m-30) cc_final: 0.8375 (m-30) REVERT: L 108 MET cc_start: 0.9086 (mpp) cc_final: 0.8581 (mpp) REVERT: L 128 MET cc_start: 0.9201 (mmm) cc_final: 0.8862 (mmt) REVERT: M 100 TYR cc_start: 0.8625 (m-80) cc_final: 0.8319 (m-80) outliers start: 3 outliers final: 3 residues processed: 167 average time/residue: 0.0761 time to fit residues: 19.2047 Evaluate side-chains 140 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 137 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 65 optimal weight: 0.4980 chunk 48 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 76 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3321 r_free = 0.3321 target = 0.049071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.043333 restraints weight = 110730.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.043941 restraints weight = 81582.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.044334 restraints weight = 64356.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.044766 restraints weight = 54333.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.045020 restraints weight = 46718.534| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.7797 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= 0.132 Angle : 0.951 38.826 13662 Z= 0.338 Chirality : 0.046 0.187 1563 Planarity : 0.005 0.058 1745 Dihedral : 4.988 23.888 1452 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.37 % Favored : 88.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.24), residues: 1214 helix: -0.32 (0.24), residues: 476 sheet: -2.34 (0.47), residues: 88 loop : -2.57 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 17 TYR 0.018 0.001 TYR J 69 PHE 0.022 0.001 PHE L 134 TRP 0.047 0.002 TRP M 131 HIS 0.007 0.001 HIS H 114 Details of bonding type rmsd covalent geometry : bond 0.00298 (10036) covalent geometry : angle 0.68600 (13644) hydrogen bonds : bond 0.02837 ( 354) hydrogen bonds : angle 4.55866 ( 1005) metal coordination : bond 0.01251 ( 6) metal coordination : angle 18.15265 ( 18) =============================================================================== Job complete usr+sys time: 1622.58 seconds wall clock time: 28 minutes 40.89 seconds (1720.89 seconds total)