Starting phenix.real_space_refine on Sun Dec 29 04:22:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wfg_32465/12_2024/7wfg_32465.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wfg_32465/12_2024/7wfg_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_32465/12_2024/7wfg_32465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wfg_32465/12_2024/7wfg_32465.map" model { file = "/net/cci-nas-00/data/ceres_data/7wfg_32465/12_2024/7wfg_32465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wfg_32465/12_2024/7wfg_32465.cif" } resolution = 4.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 12 7.16 5 S 64 5.16 5 C 6304 2.51 5 N 1677 2.21 5 O 1779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9836 Number of models: 1 Model: "" Number of chains: 11 Chain: "H" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2812 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 20, 'TRANS': 335} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'TRP:plan': 1, 'PHE:plan': 5, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 86 Chain: "I" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1236 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 152} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "J" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1120 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 146} Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 118 Chain: "K" Number of atoms: 1199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1199 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 12, 'TRANS': 154} Chain breaks: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 66 Chain: "L" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 646 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 70} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'PHE:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "M" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 767 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain breaks: 1 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 110 Chain: "N" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 909 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 13, 'TRANS': 132} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 290 Unresolved non-hydrogen angles: 396 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 5, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 7, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 183 Chain: "O" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 520 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain breaks: 2 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "T" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 603 Classifications: {'peptide': 122} Incomplete info: {'backbone_only': 7, 'truncation_to_alanine': 115} Link IDs: {'TRANS': 121} Unresolved non-hydrogen bonds: 251 Unresolved non-hydrogen angles: 380 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'UNK:plan-1': 122} Unresolved non-hydrogen planarities: 122 Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3592 SG CYS I 110 39.258 36.676 84.998 1.00144.09 S ATOM 5818 SG CYS K 108 52.007 42.309 71.485 1.00166.07 S Time building chain proxies: 7.08, per 1000 atoms: 0.72 Number of scatterers: 9836 At special positions: 0 Unit cell: (113.36, 119.6, 121.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 12 26.01 S 64 16.00 O 1779 8.00 N 1677 7.00 C 6304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 I 201 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 110 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 104 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 74 " pdb=" SF4 I 202 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 114 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 67 " pdb=" SF4 K 301 " pdb="FE4 SF4 K 301 " - pdb=" SG CYS K 108 " Number of angles added : 18 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2568 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 10 sheets defined 41.5% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'H' and resid 50 through 58 removed outlier: 3.586A pdb=" N ILE H 54 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 64 Processing helix chain 'H' and resid 75 through 91 removed outlier: 3.691A pdb=" N GLU H 79 " --> pdb=" O THR H 75 " (cutoff:3.500A) Proline residue: H 86 - end of helix Processing helix chain 'H' and resid 95 through 125 Proline residue: H 120 - end of helix Processing helix chain 'H' and resid 134 through 149 removed outlier: 4.614A pdb=" N PHE H 140 " --> pdb=" O ARG H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 191 removed outlier: 4.180A pdb=" N CYS H 179 " --> pdb=" O CYS H 175 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASP H 180 " --> pdb=" O LEU H 176 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N THR H 184 " --> pdb=" O ASP H 180 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLU H 185 " --> pdb=" O TYR H 181 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS H 191 " --> pdb=" O VAL H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 196 Processing helix chain 'H' and resid 210 through 215 Processing helix chain 'H' and resid 221 through 226 Processing helix chain 'H' and resid 232 through 237 Processing helix chain 'H' and resid 256 through 278 Processing helix chain 'H' and resid 356 through 362 removed outlier: 3.767A pdb=" N ILE H 360 " --> pdb=" O PRO H 356 " (cutoff:3.500A) Processing helix chain 'H' and resid 363 through 365 No H-bonds generated for 'chain 'H' and resid 363 through 365' Processing helix chain 'H' and resid 376 through 384 Processing helix chain 'I' and resid 7 through 33 Processing helix chain 'I' and resid 140 through 144 removed outlier: 4.022A pdb=" N ARG I 144 " --> pdb=" O ALA I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 148 through 152 removed outlier: 4.082A pdb=" N ASP I 152 " --> pdb=" O VAL I 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 35 Processing helix chain 'J' and resid 36 through 45 Processing helix chain 'J' and resid 107 through 118 Processing helix chain 'J' and resid 151 through 155 Processing helix chain 'K' and resid 16 through 31 Processing helix chain 'K' and resid 42 through 48 removed outlier: 3.824A pdb=" N ILE K 46 " --> pdb=" O CYS K 43 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU K 47 " --> pdb=" O CYS K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 95 Processing helix chain 'K' and resid 112 through 116 removed outlier: 3.653A pdb=" N PHE K 115 " --> pdb=" O GLY K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 129 removed outlier: 3.990A pdb=" N LYS K 128 " --> pdb=" O GLY K 125 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 160 Processing helix chain 'K' and resid 161 through 166 removed outlier: 3.724A pdb=" N ASP K 164 " --> pdb=" O ILE K 161 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 107 Processing helix chain 'L' and resid 107 through 119 removed outlier: 4.213A pdb=" N ILE L 111 " --> pdb=" O VAL L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 138 Processing helix chain 'L' and resid 139 through 144 removed outlier: 3.849A pdb=" N LEU L 143 " --> pdb=" O PRO L 140 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU L 144 " --> pdb=" O GLY L 141 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 150 Processing helix chain 'M' and resid 156 through 177 Processing helix chain 'N' and resid 63 through 72 Processing helix chain 'N' and resid 86 through 95 removed outlier: 4.146A pdb=" N LEU N 90 " --> pdb=" O GLU N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 116 Processing helix chain 'N' and resid 139 through 145 Processing helix chain 'N' and resid 166 through 179 Proline residue: N 176 - end of helix Processing helix chain 'T' and resid 2 through 6 removed outlier: 4.304A pdb=" N UNK T 6 " --> pdb=" O UNK T 3 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 18 Processing helix chain 'T' and resid 25 through 39 removed outlier: 3.675A pdb=" N UNK T 39 " --> pdb=" O UNK T 35 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 62 Processing helix chain 'T' and resid 62 through 73 Processing helix chain 'T' and resid 98 through 121 removed outlier: 3.683A pdb=" N UNK T 102 " --> pdb=" O UNK T 98 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 27 through 30 removed outlier: 3.521A pdb=" N ARG H 27 " --> pdb=" O ILE H 43 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE H 29 " --> pdb=" O GLU H 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 36 through 37 removed outlier: 3.956A pdb=" N MET H 372 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 325 through 330 Processing sheet with id=AA4, first strand: chain 'I' and resid 57 through 58 Processing sheet with id=AA5, first strand: chain 'I' and resid 80 through 82 removed outlier: 6.796A pdb=" N VAL I 80 " --> pdb=" O TYR I 97 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N TYR I 97 " --> pdb=" O VAL I 80 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP I 82 " --> pdb=" O LEU I 95 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 17 through 21 removed outlier: 5.953A pdb=" N THR J 28 " --> pdb=" O LEU J 19 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU J 27 " --> pdb=" O CYS J 85 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LYS J 87 " --> pdb=" O GLU J 27 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU J 29 " --> pdb=" O LYS J 87 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N PHE J 89 " --> pdb=" O LEU J 29 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE J 31 " --> pdb=" O PHE J 89 " (cutoff:3.500A) removed outlier: 10.336A pdb=" N HIS J 91 " --> pdb=" O ILE J 31 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 96 through 98 removed outlier: 3.849A pdb=" N ASP J 123 " --> pdb=" O ILE J 97 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 102 through 104 removed outlier: 8.505A pdb=" N VAL K 102 " --> pdb=" O ASP K 133 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N TYR K 135 " --> pdb=" O VAL K 102 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ALA K 104 " --> pdb=" O TYR K 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'N' and resid 99 through 103 removed outlier: 6.687A pdb=" N TYR N 99 " --> pdb=" O VAL N 156 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL N 158 " --> pdb=" O TYR N 99 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU N 101 " --> pdb=" O VAL N 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'O' and resid 80 through 81 removed outlier: 3.827A pdb=" N GLY O 114 " --> pdb=" O VAL O 81 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU O 129 " --> pdb=" O LEU O 117 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU O 119 " --> pdb=" O TYR O 127 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR O 127 " --> pdb=" O LEU O 119 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 1005 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.48 Time building geometry restraints manager: 2.79 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: 4.040 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.970 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.540 ------------------------------------------------------------------------------- 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 : 0.006 0.132 10036 Z= 0.378 Angle : 1.008 9.753 13644 Z= 0.593 Chirality : 0.063 0.348 1563 Planarity : 0.007 0.064 1745 Dihedral : 11.464 74.505 3492 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.27 % Favored : 87.48 % Rotamer: Outliers : 1.08 % Allowed : 3.11 % Favored : 95.81 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.06 (0.18), residues: 1214 helix: -3.16 (0.16), residues: 405 sheet: -2.66 (0.48), residues: 93 loop : -3.76 (0.19), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 117 HIS 0.008 0.001 HIS M 169 PHE 0.016 0.002 PHE H 182 TYR 0.016 0.002 TYR J 57 ARG 0.015 0.001 ARG H 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 262 time to evaluate : 1.174 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE H 132 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.7825 (tpt) cc_final: 0.7336 (tpp) REVERT: H 47 LEU cc_start: 0.9296 (tp) cc_final: 0.8851 (tp) REVERT: H 49 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7844 (mpp80) REVERT: H 105 MET cc_start: 0.9533 (ptp) cc_final: 0.9057 (ptt) REVERT: H 156 ASN cc_start: 0.9382 (t0) cc_final: 0.9130 (t0) REVERT: H 171 TRP cc_start: 0.9322 (t60) cc_final: 0.9042 (t60) REVERT: H 261 TYR cc_start: 0.8837 (t80) cc_final: 0.8626 (t80) REVERT: H 262 LEU cc_start: 0.9547 (mt) cc_final: 0.9286 (pp) REVERT: H 378 MET cc_start: 0.9076 (mmp) cc_final: 0.8669 (mmp) REVERT: H 381 LEU cc_start: 0.9450 (pp) cc_final: 0.8455 (pp) REVERT: H 384 ILE cc_start: 0.9671 (mm) cc_final: 0.9321 (tp) REVERT: H 390 GLU cc_start: 0.9130 (pt0) cc_final: 0.8798 (pt0) REVERT: I 85 LEU cc_start: 0.8474 (mt) cc_final: 0.7835 (tp) REVERT: I 100 ASP cc_start: 0.8560 (t0) cc_final: 0.7633 (t70) REVERT: I 101 PHE cc_start: 0.9240 (m-10) cc_final: 0.8995 (m-80) REVERT: I 103 ILE cc_start: 0.9528 (mm) cc_final: 0.9170 (mm) REVERT: I 134 GLU cc_start: 0.8639 (tt0) cc_final: 0.8424 (tm-30) REVERT: I 137 TYR cc_start: 0.7528 (m-10) cc_final: 0.6809 (m-10) REVERT: J 51 LEU cc_start: 0.8577 (tp) cc_final: 0.8373 (tp) REVERT: J 71 LEU cc_start: 0.8562 (tp) cc_final: 0.8171 (tp) REVERT: J 111 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8535 (mm-30) REVERT: J 128 LEU cc_start: 0.8978 (tp) cc_final: 0.8569 (mt) REVERT: K 103 ILE cc_start: 0.9291 (mm) cc_final: 0.8892 (mp) REVERT: K 144 GLU cc_start: 0.8132 (mp0) cc_final: 0.7815 (tp30) REVERT: L 128 MET cc_start: 0.8939 (mmm) cc_final: 0.8601 (mmt) REVERT: L 142 LEU cc_start: 0.8682 (mm) cc_final: 0.8471 (mm) REVERT: L 144 LEU cc_start: 0.8174 (pt) cc_final: 0.7949 (pt) REVERT: L 160 MET cc_start: 0.7307 (mpp) cc_final: 0.6776 (tpp) REVERT: N 140 VAL cc_start: 0.9093 (m) cc_final: 0.8871 (p) outliers start: 9 outliers final: 3 residues processed: 268 average time/residue: 0.2436 time to fit residues: 88.0506 Evaluate side-chains 176 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 172 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 48 HIS H 363 GLN J 110 GLN ** M 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 169 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.5231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 10036 Z= 0.417 Angle : 0.887 11.798 13644 Z= 0.462 Chirality : 0.053 0.371 1563 Planarity : 0.007 0.071 1745 Dihedral : 6.191 25.890 1452 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 24.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.45 % Favored : 88.47 % Rotamer: Outliers : 0.48 % Allowed : 5.50 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.21), residues: 1214 helix: -1.31 (0.22), residues: 422 sheet: -2.75 (0.42), residues: 111 loop : -3.23 (0.21), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP H 350 HIS 0.017 0.003 HIS M 96 PHE 0.021 0.002 PHE K 115 TYR 0.016 0.002 TYR O 127 ARG 0.008 0.001 ARG J 112 *********************** 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 183 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 179 time to evaluate : 1.130 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: H 15 MET cc_start: 0.8434 (tpt) cc_final: 0.7968 (tpp) REVERT: H 76 MET cc_start: 0.9121 (mtt) cc_final: 0.8713 (mtm) REVERT: H 105 MET cc_start: 0.9470 (ptp) cc_final: 0.9247 (ptp) REVERT: H 223 MET cc_start: 0.9357 (mpp) cc_final: 0.9082 (mpp) REVERT: I 85 LEU cc_start: 0.9154 (mt) cc_final: 0.8708 (tp) REVERT: I 100 ASP cc_start: 0.8935 (t0) cc_final: 0.8275 (t70) REVERT: I 101 PHE cc_start: 0.9179 (m-10) cc_final: 0.8669 (m-80) REVERT: I 137 TYR cc_start: 0.8323 (m-10) cc_final: 0.7664 (m-10) REVERT: J 86 ILE cc_start: 0.9362 (mp) cc_final: 0.9125 (tt) REVERT: J 133 MET cc_start: 0.8873 (mmm) cc_final: 0.8573 (mmm) REVERT: J 151 PHE cc_start: 0.8887 (m-80) cc_final: 0.8418 (m-80) REVERT: K 85 MET cc_start: 0.9413 (mmp) cc_final: 0.9158 (mmm) REVERT: K 105 MET cc_start: 0.8365 (ptp) cc_final: 0.8128 (ptp) REVERT: K 114 MET cc_start: 0.8944 (pmm) cc_final: 0.8714 (pmm) REVERT: K 136 LEU cc_start: 0.9098 (tp) cc_final: 0.8857 (tp) REVERT: K 144 GLU cc_start: 0.9011 (mp0) cc_final: 0.8179 (tp30) REVERT: K 148 ASP cc_start: 0.8729 (m-30) cc_final: 0.7972 (m-30) REVERT: L 128 MET cc_start: 0.8876 (mmm) cc_final: 0.8522 (mmt) REVERT: L 144 LEU cc_start: 0.8622 (pt) cc_final: 0.8276 (pt) outliers start: 4 outliers final: 3 residues processed: 183 average time/residue: 0.2070 time to fit residues: 54.2283 Evaluate side-chains 141 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 138 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 33 optimal weight: 0.0040 chunk 120 optimal weight: 4.9990 chunk 130 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 41 optimal weight: 0.0020 chunk 97 optimal weight: 6.9990 overall best weight: 0.5600 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10036 Z= 0.163 Angle : 0.641 9.481 13644 Z= 0.317 Chirality : 0.045 0.147 1563 Planarity : 0.006 0.109 1745 Dihedral : 5.160 25.432 1452 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 0.48 % Allowed : 3.23 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.23), residues: 1214 helix: -0.55 (0.25), residues: 441 sheet: -2.69 (0.42), residues: 111 loop : -3.00 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 117 HIS 0.007 0.001 HIS H 155 PHE 0.020 0.001 PHE L 134 TYR 0.017 0.001 TYR K 93 ARG 0.013 0.001 ARG M 161 *********************** 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 192 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 188 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.8242 (tpt) cc_final: 0.7638 (tpp) REVERT: H 76 MET cc_start: 0.8881 (mtt) cc_final: 0.8522 (mtm) REVERT: H 79 GLU cc_start: 0.8738 (tt0) cc_final: 0.7613 (tt0) REVERT: H 154 MET cc_start: 0.6930 (mtt) cc_final: 0.6496 (mtm) REVERT: H 262 LEU cc_start: 0.9690 (mt) cc_final: 0.9406 (pp) REVERT: H 364 ILE cc_start: 0.9208 (mm) cc_final: 0.8988 (mm) REVERT: H 390 GLU cc_start: 0.9271 (pt0) cc_final: 0.8913 (pt0) REVERT: I 85 LEU cc_start: 0.8978 (mt) cc_final: 0.8507 (tp) REVERT: I 100 ASP cc_start: 0.8621 (t0) cc_final: 0.7782 (t70) REVERT: I 103 ILE cc_start: 0.9560 (mm) cc_final: 0.9112 (mm) REVERT: J 51 LEU cc_start: 0.8841 (tp) cc_final: 0.8588 (tp) REVERT: J 69 TYR cc_start: 0.8225 (m-10) cc_final: 0.7864 (m-10) REVERT: J 128 LEU cc_start: 0.9059 (tp) cc_final: 0.8835 (tp) REVERT: J 151 PHE cc_start: 0.8847 (m-80) cc_final: 0.8507 (m-80) REVERT: K 83 MET cc_start: 0.8805 (ppp) cc_final: 0.8400 (tpt) REVERT: K 105 MET cc_start: 0.8440 (ptp) cc_final: 0.8223 (ptp) REVERT: K 114 MET cc_start: 0.8979 (pmm) cc_final: 0.8742 (pmm) REVERT: K 144 GLU cc_start: 0.8948 (mp0) cc_final: 0.8087 (tp30) REVERT: K 148 ASP cc_start: 0.8565 (m-30) cc_final: 0.7516 (m-30) REVERT: L 108 MET cc_start: 0.8760 (mpp) cc_final: 0.8419 (mpp) REVERT: L 128 MET cc_start: 0.8847 (mmm) cc_final: 0.8496 (mmt) REVERT: L 144 LEU cc_start: 0.8471 (pt) cc_final: 0.8251 (tp) REVERT: M 100 TYR cc_start: 0.8391 (m-80) cc_final: 0.7970 (m-80) REVERT: N 108 LEU cc_start: 0.8805 (tp) cc_final: 0.8489 (tt) outliers start: 4 outliers final: 3 residues processed: 189 average time/residue: 0.2052 time to fit residues: 55.4515 Evaluate side-chains 147 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 144 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 0.7980 chunk 90 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 81 optimal weight: 0.3980 chunk 121 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 overall best weight: 4.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 93 GLN H 361 ASN ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.6504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 10036 Z= 0.378 Angle : 0.785 11.039 13644 Z= 0.406 Chirality : 0.048 0.166 1563 Planarity : 0.007 0.074 1745 Dihedral : 5.875 27.338 1452 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.76 % Favored : 86.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.23), residues: 1214 helix: -0.83 (0.23), residues: 469 sheet: -2.85 (0.44), residues: 99 loop : -2.92 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 217 HIS 0.009 0.003 HIS H 114 PHE 0.024 0.002 PHE K 115 TYR 0.022 0.002 TYR H 261 ARG 0.011 0.001 ARG H 69 *********************** 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 164 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 161 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.8798 (tpt) cc_final: 0.8404 (tpp) REVERT: H 76 MET cc_start: 0.9197 (mtt) cc_final: 0.8924 (ttm) REVERT: H 223 MET cc_start: 0.9254 (mpp) cc_final: 0.9043 (mpp) REVERT: H 340 PHE cc_start: 0.8956 (t80) cc_final: 0.8609 (t80) REVERT: H 390 GLU cc_start: 0.9378 (pt0) cc_final: 0.9087 (pt0) REVERT: I 85 LEU cc_start: 0.9095 (mt) cc_final: 0.8520 (tp) REVERT: I 100 ASP cc_start: 0.8988 (t0) cc_final: 0.8451 (t70) REVERT: I 103 ILE cc_start: 0.9651 (mm) cc_final: 0.9414 (mm) REVERT: I 137 TYR cc_start: 0.8455 (m-80) cc_final: 0.7897 (m-10) REVERT: J 50 TYR cc_start: 0.8517 (t80) cc_final: 0.7924 (t80) REVERT: J 151 PHE cc_start: 0.9148 (m-80) cc_final: 0.8507 (m-80) REVERT: K 83 MET cc_start: 0.9046 (ppp) cc_final: 0.8722 (tpt) REVERT: K 85 MET cc_start: 0.9395 (mmp) cc_final: 0.8766 (mmm) REVERT: K 114 MET cc_start: 0.9147 (pmm) cc_final: 0.8397 (pmm) REVERT: K 144 GLU cc_start: 0.9036 (mp0) cc_final: 0.8070 (tp30) REVERT: K 148 ASP cc_start: 0.8804 (m-30) cc_final: 0.8129 (m-30) REVERT: L 128 MET cc_start: 0.8918 (mmm) cc_final: 0.8506 (mmt) REVERT: M 100 TYR cc_start: 0.8700 (m-80) cc_final: 0.8454 (m-80) REVERT: N 108 LEU cc_start: 0.8805 (tp) cc_final: 0.8436 (tt) outliers start: 3 outliers final: 3 residues processed: 164 average time/residue: 0.2033 time to fit residues: 48.1278 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 : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 8.9990 chunk 72 optimal weight: 0.0980 chunk 1 optimal weight: 4.9990 chunk 95 optimal weight: 0.0870 chunk 53 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 overall best weight: 2.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.6710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10036 Z= 0.241 Angle : 0.664 10.027 13644 Z= 0.338 Chirality : 0.045 0.157 1563 Planarity : 0.005 0.077 1745 Dihedral : 5.449 25.234 1452 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.45 % Favored : 88.47 % Rotamer: Outliers : 0.36 % Allowed : 3.23 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.24), residues: 1214 helix: -0.53 (0.24), residues: 468 sheet: -2.83 (0.42), residues: 103 loop : -2.79 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 35 HIS 0.007 0.001 HIS H 114 PHE 0.018 0.001 PHE K 115 TYR 0.016 0.002 TYR K 93 ARG 0.005 0.001 ARG H 69 *********************** 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 166 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 163 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.8681 (tpt) cc_final: 0.8228 (tpp) REVERT: H 76 MET cc_start: 0.9033 (mtt) cc_final: 0.8668 (mtm) REVERT: H 154 MET cc_start: 0.6842 (mtt) cc_final: 0.6071 (mtt) REVERT: H 208 ILE cc_start: 0.9173 (pt) cc_final: 0.8733 (mm) REVERT: H 340 PHE cc_start: 0.8806 (t80) cc_final: 0.8518 (t80) REVERT: H 390 GLU cc_start: 0.9354 (pt0) cc_final: 0.9029 (pt0) REVERT: I 85 LEU cc_start: 0.9087 (mt) cc_final: 0.8394 (tp) REVERT: I 100 ASP cc_start: 0.8914 (t0) cc_final: 0.8403 (t70) REVERT: I 103 ILE cc_start: 0.9626 (mm) cc_final: 0.9368 (mm) REVERT: J 50 TYR cc_start: 0.8182 (t80) cc_final: 0.7490 (t80) REVERT: J 151 PHE cc_start: 0.9139 (m-80) cc_final: 0.8664 (m-80) REVERT: K 37 LEU cc_start: 0.7160 (tp) cc_final: 0.6948 (tp) REVERT: K 83 MET cc_start: 0.8976 (ppp) cc_final: 0.8610 (tpt) REVERT: K 85 MET cc_start: 0.9271 (mmp) cc_final: 0.8746 (mmm) REVERT: K 105 MET cc_start: 0.8432 (ptp) cc_final: 0.8131 (ptp) REVERT: K 114 MET cc_start: 0.9012 (pmm) cc_final: 0.8570 (pmm) REVERT: K 144 GLU cc_start: 0.9100 (mp0) cc_final: 0.8001 (tp30) REVERT: K 148 ASP cc_start: 0.9096 (m-30) cc_final: 0.8192 (m-30) REVERT: L 108 MET cc_start: 0.8858 (mpp) cc_final: 0.8435 (mpp) REVERT: L 128 MET cc_start: 0.8916 (mmm) cc_final: 0.8651 (mmt) REVERT: M 100 TYR cc_start: 0.8648 (m-10) cc_final: 0.8443 (m-80) REVERT: N 108 LEU cc_start: 0.8943 (tp) cc_final: 0.8593 (tt) outliers start: 3 outliers final: 3 residues processed: 165 average time/residue: 0.2178 time to fit residues: 51.6526 Evaluate side-chains 142 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 139 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.6873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10036 Z= 0.206 Angle : 0.668 11.890 13644 Z= 0.333 Chirality : 0.045 0.138 1563 Planarity : 0.006 0.074 1745 Dihedral : 5.251 25.185 1452 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.27 % Favored : 87.64 % Rotamer: Outliers : 0.36 % Allowed : 1.67 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.24), residues: 1214 helix: -0.37 (0.24), residues: 464 sheet: -2.92 (0.41), residues: 109 loop : -2.70 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 35 HIS 0.010 0.001 HIS J 70 PHE 0.019 0.001 PHE K 115 TYR 0.015 0.001 TYR J 57 ARG 0.015 0.001 ARG M 161 *********************** 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 168 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 165 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.8671 (tpt) cc_final: 0.8232 (tpp) REVERT: H 79 GLU cc_start: 0.9054 (tt0) cc_final: 0.7990 (mm-30) REVERT: H 208 ILE cc_start: 0.9219 (pt) cc_final: 0.8818 (mm) REVERT: H 340 PHE cc_start: 0.8783 (t80) cc_final: 0.8509 (t80) REVERT: H 390 GLU cc_start: 0.9418 (pt0) cc_final: 0.9125 (pt0) REVERT: I 85 LEU cc_start: 0.9106 (mt) cc_final: 0.8764 (mt) REVERT: I 100 ASP cc_start: 0.9008 (t0) cc_final: 0.8462 (t70) REVERT: I 103 ILE cc_start: 0.9628 (mm) cc_final: 0.9389 (mm) REVERT: I 137 TYR cc_start: 0.8423 (m-80) cc_final: 0.7855 (m-10) REVERT: J 50 TYR cc_start: 0.7668 (t80) cc_final: 0.7039 (t80) REVERT: J 151 PHE cc_start: 0.9154 (m-80) cc_final: 0.8559 (m-80) REVERT: K 83 MET cc_start: 0.8941 (ppp) cc_final: 0.8596 (tpt) REVERT: K 85 MET cc_start: 0.9266 (mmp) cc_final: 0.8726 (mmp) REVERT: K 105 MET cc_start: 0.8352 (ptp) cc_final: 0.7772 (ppp) REVERT: K 114 MET cc_start: 0.9081 (pmm) cc_final: 0.8685 (pmm) REVERT: K 144 GLU cc_start: 0.9085 (mp0) cc_final: 0.7948 (tp30) REVERT: K 148 ASP cc_start: 0.9136 (m-30) cc_final: 0.8225 (m-30) REVERT: L 108 MET cc_start: 0.8912 (mpp) cc_final: 0.8540 (mpp) REVERT: L 128 MET cc_start: 0.8967 (mmm) cc_final: 0.8694 (mmt) REVERT: L 144 LEU cc_start: 0.7945 (tp) cc_final: 0.7596 (pp) REVERT: N 108 LEU cc_start: 0.8878 (tp) cc_final: 0.8522 (tt) outliers start: 3 outliers final: 3 residues processed: 166 average time/residue: 0.2153 time to fit residues: 50.8319 Evaluate side-chains 142 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 139 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 20.0000 chunk 14 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 chunk 80 optimal weight: 0.0670 chunk 78 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.6787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10036 Z= 0.166 Angle : 0.637 12.433 13644 Z= 0.311 Chirality : 0.045 0.145 1563 Planarity : 0.005 0.063 1745 Dihedral : 4.920 24.753 1452 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.24), residues: 1214 helix: -0.17 (0.25), residues: 462 sheet: -2.90 (0.40), residues: 109 loop : -2.65 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 171 HIS 0.007 0.001 HIS J 70 PHE 0.019 0.001 PHE K 115 TYR 0.015 0.001 TYR J 57 ARG 0.004 0.000 ARG I 17 *********************** 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 172 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 169 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.8534 (tpt) cc_final: 0.8101 (tpp) REVERT: H 154 MET cc_start: 0.6201 (mtt) cc_final: 0.5423 (mtt) REVERT: H 208 ILE cc_start: 0.9130 (pt) cc_final: 0.8728 (mm) REVERT: H 262 LEU cc_start: 0.9777 (mm) cc_final: 0.9472 (pp) REVERT: H 340 PHE cc_start: 0.8705 (t80) cc_final: 0.8354 (t80) REVERT: H 390 GLU cc_start: 0.9379 (pt0) cc_final: 0.9085 (pt0) REVERT: I 100 ASP cc_start: 0.9010 (t0) cc_final: 0.8485 (t70) REVERT: I 103 ILE cc_start: 0.9625 (mm) cc_final: 0.9397 (mm) REVERT: I 137 TYR cc_start: 0.8440 (m-80) cc_final: 0.7879 (m-80) REVERT: J 50 TYR cc_start: 0.7279 (t80) cc_final: 0.6802 (t80) REVERT: J 133 MET cc_start: 0.8752 (mmm) cc_final: 0.8405 (mmm) REVERT: J 151 PHE cc_start: 0.9104 (m-80) cc_final: 0.8649 (m-80) REVERT: K 85 MET cc_start: 0.9213 (mmp) cc_final: 0.8723 (mmp) REVERT: K 105 MET cc_start: 0.8230 (ptp) cc_final: 0.7735 (ppp) REVERT: K 114 MET cc_start: 0.9107 (pmm) cc_final: 0.8792 (pmm) REVERT: K 115 PHE cc_start: 0.9097 (m-10) cc_final: 0.8885 (m-10) REVERT: K 136 LEU cc_start: 0.8440 (tt) cc_final: 0.8230 (tt) REVERT: K 144 GLU cc_start: 0.9108 (mp0) cc_final: 0.8059 (tp30) REVERT: K 148 ASP cc_start: 0.9042 (m-30) cc_final: 0.8136 (m-30) REVERT: L 108 MET cc_start: 0.8894 (mpp) cc_final: 0.8469 (mpp) REVERT: L 128 MET cc_start: 0.8887 (mmm) cc_final: 0.8601 (mmt) REVERT: L 144 LEU cc_start: 0.7951 (tp) cc_final: 0.7683 (pp) REVERT: M 100 TYR cc_start: 0.8428 (m-80) cc_final: 0.7972 (m-80) REVERT: N 108 LEU cc_start: 0.8846 (tp) cc_final: 0.8542 (tt) outliers start: 3 outliers final: 3 residues processed: 170 average time/residue: 0.2138 time to fit residues: 52.0259 Evaluate side-chains 146 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 143 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 38 optimal weight: 0.0570 chunk 25 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 11 optimal weight: 0.0270 chunk 100 optimal weight: 2.9990 overall best weight: 1.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.6980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10036 Z= 0.180 Angle : 0.634 12.243 13644 Z= 0.315 Chirality : 0.045 0.172 1563 Planarity : 0.005 0.062 1745 Dihedral : 4.835 25.012 1452 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.96 % Favored : 88.96 % Rotamer: Outliers : 0.36 % Allowed : 1.44 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.25), residues: 1214 helix: -0.13 (0.25), residues: 469 sheet: -2.66 (0.43), residues: 103 loop : -2.54 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 217 HIS 0.006 0.001 HIS H 114 PHE 0.022 0.001 PHE L 134 TYR 0.015 0.001 TYR K 93 ARG 0.005 0.000 ARG I 54 *********************** 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 167 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 164 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.8656 (tpt) cc_final: 0.8303 (tpp) REVERT: H 79 GLU cc_start: 0.8973 (tt0) cc_final: 0.8110 (mm-30) REVERT: H 156 ASN cc_start: 0.9238 (t0) cc_final: 0.9020 (t0) REVERT: H 208 ILE cc_start: 0.9131 (pt) cc_final: 0.8726 (mm) REVERT: H 340 PHE cc_start: 0.8767 (t80) cc_final: 0.8357 (t80) REVERT: H 390 GLU cc_start: 0.9399 (pt0) cc_final: 0.9028 (pt0) REVERT: I 85 LEU cc_start: 0.8884 (mt) cc_final: 0.8291 (tp) REVERT: I 100 ASP cc_start: 0.8986 (t0) cc_final: 0.8472 (t70) REVERT: I 103 ILE cc_start: 0.9619 (mm) cc_final: 0.9411 (mm) REVERT: I 137 TYR cc_start: 0.8536 (m-80) cc_final: 0.7941 (m-80) REVERT: J 151 PHE cc_start: 0.9129 (m-80) cc_final: 0.8671 (m-80) REVERT: K 85 MET cc_start: 0.9212 (mmp) cc_final: 0.8675 (mmp) REVERT: K 105 MET cc_start: 0.8288 (ptp) cc_final: 0.7795 (ppp) REVERT: K 114 MET cc_start: 0.9057 (pmm) cc_final: 0.8818 (pmm) REVERT: K 115 PHE cc_start: 0.9129 (m-10) cc_final: 0.8803 (m-10) REVERT: K 136 LEU cc_start: 0.8564 (tt) cc_final: 0.8337 (tt) REVERT: K 144 GLU cc_start: 0.9090 (mp0) cc_final: 0.7974 (tp30) REVERT: K 148 ASP cc_start: 0.9057 (m-30) cc_final: 0.7946 (m-30) REVERT: L 128 MET cc_start: 0.8858 (mmm) cc_final: 0.8547 (mmt) REVERT: L 144 LEU cc_start: 0.7924 (tp) cc_final: 0.7657 (pp) REVERT: M 100 TYR cc_start: 0.8478 (m-80) cc_final: 0.8089 (m-80) REVERT: N 108 LEU cc_start: 0.8881 (tp) cc_final: 0.8580 (tt) outliers start: 3 outliers final: 3 residues processed: 166 average time/residue: 0.2058 time to fit residues: 49.2625 Evaluate side-chains 146 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 143 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 71 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 78 optimal weight: 0.0040 chunk 126 optimal weight: 20.0000 overall best weight: 2.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.7526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10036 Z= 0.241 Angle : 0.681 11.912 13644 Z= 0.344 Chirality : 0.046 0.141 1563 Planarity : 0.005 0.063 1745 Dihedral : 5.177 23.681 1452 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.18 % Favored : 86.74 % Rotamer: Outliers : 0.36 % Allowed : 1.08 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.24), residues: 1214 helix: -0.30 (0.24), residues: 473 sheet: -2.64 (0.44), residues: 103 loop : -2.61 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 171 HIS 0.009 0.002 HIS H 114 PHE 0.015 0.001 PHE K 115 TYR 0.019 0.002 TYR K 93 ARG 0.006 0.001 ARG H 69 *********************** 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 163 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 160 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.8708 (tpt) cc_final: 0.8309 (tpp) REVERT: H 79 GLU cc_start: 0.9083 (tt0) cc_final: 0.8281 (tm-30) REVERT: H 208 ILE cc_start: 0.9220 (pt) cc_final: 0.8852 (mm) REVERT: H 340 PHE cc_start: 0.8867 (t80) cc_final: 0.8422 (t80) REVERT: H 390 GLU cc_start: 0.9410 (pt0) cc_final: 0.9149 (pt0) REVERT: I 100 ASP cc_start: 0.9018 (t0) cc_final: 0.8553 (t70) REVERT: I 103 ILE cc_start: 0.9627 (mm) cc_final: 0.9422 (mm) REVERT: I 137 TYR cc_start: 0.8503 (m-80) cc_final: 0.7960 (m-10) REVERT: J 133 MET cc_start: 0.8767 (mmm) cc_final: 0.8473 (mmm) REVERT: J 151 PHE cc_start: 0.9152 (m-80) cc_final: 0.8821 (m-80) REVERT: K 85 MET cc_start: 0.9261 (mmp) cc_final: 0.8697 (mmp) REVERT: K 103 ILE cc_start: 0.8817 (mm) cc_final: 0.8585 (mm) REVERT: K 105 MET cc_start: 0.8451 (ptp) cc_final: 0.7828 (ppp) REVERT: K 136 LEU cc_start: 0.8752 (tt) cc_final: 0.8469 (tt) REVERT: K 144 GLU cc_start: 0.9065 (mp0) cc_final: 0.8005 (tp30) REVERT: K 148 ASP cc_start: 0.8928 (m-30) cc_final: 0.8503 (m-30) REVERT: L 128 MET cc_start: 0.8888 (mmm) cc_final: 0.8639 (mmt) REVERT: L 144 LEU cc_start: 0.8116 (tp) cc_final: 0.7856 (pp) REVERT: M 100 TYR cc_start: 0.8665 (m-80) cc_final: 0.8272 (m-80) REVERT: N 108 LEU cc_start: 0.9023 (tp) cc_final: 0.8721 (tt) outliers start: 3 outliers final: 3 residues processed: 161 average time/residue: 0.2005 time to fit residues: 47.1074 Evaluate side-chains 138 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 135 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 0.8980 chunk 59 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 105 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 112 optimal weight: 9.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.7551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10036 Z= 0.194 Angle : 0.654 11.971 13644 Z= 0.322 Chirality : 0.045 0.183 1563 Planarity : 0.005 0.064 1745 Dihedral : 4.976 24.110 1452 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.04 % Favored : 88.88 % Rotamer: Outliers : 0.36 % Allowed : 0.72 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.24), residues: 1214 helix: -0.17 (0.25), residues: 470 sheet: -2.66 (0.43), residues: 98 loop : -2.57 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 171 HIS 0.006 0.001 HIS H 114 PHE 0.020 0.001 PHE L 134 TYR 0.019 0.001 TYR J 69 ARG 0.009 0.001 ARG M 95 ********************** 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 164 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 161 time to evaluate : 1.247 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: 0.8608 (tpt) cc_final: 0.8178 (tpp) REVERT: H 76 MET cc_start: 0.9148 (ttt) cc_final: 0.8590 (ttt) REVERT: H 79 GLU cc_start: 0.9079 (tt0) cc_final: 0.8157 (mm-30) REVERT: H 208 ILE cc_start: 0.9184 (pt) cc_final: 0.8798 (mm) REVERT: H 340 PHE cc_start: 0.8829 (t80) cc_final: 0.8417 (t80) REVERT: H 390 GLU cc_start: 0.9368 (pt0) cc_final: 0.9076 (pt0) REVERT: I 100 ASP cc_start: 0.9011 (t0) cc_final: 0.8400 (t0) REVERT: I 103 ILE cc_start: 0.9594 (mm) cc_final: 0.9318 (mm) REVERT: I 137 TYR cc_start: 0.8511 (m-80) cc_final: 0.8007 (m-10) REVERT: J 133 MET cc_start: 0.8786 (mmm) cc_final: 0.8400 (mmm) REVERT: J 151 PHE cc_start: 0.9166 (m-80) cc_final: 0.8901 (m-80) REVERT: K 85 MET cc_start: 0.9200 (mmp) cc_final: 0.8615 (mmp) REVERT: K 103 ILE cc_start: 0.8689 (mm) cc_final: 0.8470 (mm) REVERT: K 105 MET cc_start: 0.8373 (ptp) cc_final: 0.7895 (ppp) REVERT: K 144 GLU cc_start: 0.9126 (mp0) cc_final: 0.8035 (tp30) REVERT: K 148 ASP cc_start: 0.9180 (m-30) cc_final: 0.8781 (m-30) REVERT: L 128 MET cc_start: 0.8911 (mmm) cc_final: 0.8584 (mmt) REVERT: L 144 LEU cc_start: 0.8041 (tp) cc_final: 0.7811 (pp) REVERT: M 100 TYR cc_start: 0.8664 (m-80) cc_final: 0.7249 (t80) REVERT: N 108 LEU cc_start: 0.9102 (tp) cc_final: 0.8795 (tt) outliers start: 3 outliers final: 3 residues processed: 162 average time/residue: 0.2160 time to fit residues: 51.6972 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 : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 105 optimal weight: 0.0270 chunk 44 optimal weight: 3.9990 chunk 108 optimal weight: 0.0050 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 6 optimal weight: 0.0670 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.049357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.043298 restraints weight = 109573.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.044050 restraints weight = 79069.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.044514 restraints weight = 60903.947| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.7388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10036 Z= 0.162 Angle : 0.680 16.664 13644 Z= 0.323 Chirality : 0.046 0.291 1563 Planarity : 0.005 0.058 1745 Dihedral : 4.701 28.162 1452 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.30 % Favored : 89.62 % Rotamer: Outliers : 0.36 % Allowed : 0.72 % Favored : 98.92 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.25), residues: 1214 helix: -0.08 (0.25), residues: 466 sheet: -2.47 (0.45), residues: 106 loop : -2.52 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP H 171 HIS 0.005 0.001 HIS H 114 PHE 0.023 0.001 PHE H 77 TYR 0.015 0.001 TYR K 93 ARG 0.006 0.001 ARG I 17 =============================================================================== Job complete usr+sys time: 2202.39 seconds wall clock time: 40 minutes 48.13 seconds (2448.13 seconds total)