Starting phenix.real_space_refine on Sat Aug 23 17:33:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tzy_41774/08_2025/8tzy_41774.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tzy_41774/08_2025/8tzy_41774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tzy_41774/08_2025/8tzy_41774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tzy_41774/08_2025/8tzy_41774.map" model { file = "/net/cci-nas-00/data/ceres_data/8tzy_41774/08_2025/8tzy_41774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tzy_41774/08_2025/8tzy_41774.cif" } resolution = 3.8 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 40 5.16 5 C 4488 2.51 5 N 1208 2.21 5 O 1384 1.98 5 H 6598 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13718 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3241 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 13, 'TRANS': 211} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 3006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3006 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 12, 'TRANS': 199} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2307 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 148} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'TRP:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 72 Chain: "D" Number of atoms: 2682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2682 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain breaks: 4 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 44 Chain: "E" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 2482 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 10, 'TRANS': 168} Chain breaks: 7 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 51 Time building chain proxies: 3.09, per 1000 atoms: 0.23 Number of scatterers: 13718 At special positions: 0 Unit cell: (75.04, 109.76, 165.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 O 1384 8.00 N 1208 7.00 C 4488 6.00 H 6598 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.04 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.04 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 452 " - pdb=" SG CYS C 620 " distance=2.03 Simple disulfide: pdb=" SG CYS C 459 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 494 " - pdb=" SG CYS C 564 " distance=2.03 Simple disulfide: pdb=" SG CYS C 508 " - pdb=" SG CYS C 552 " distance=2.03 Simple disulfide: pdb=" SG CYS C 569 " - pdb=" SG CYS C 597 " distance=2.03 Simple disulfide: pdb=" SG CYS C 581 " - pdb=" SG CYS C 585 " distance=2.03 Simple disulfide: pdb=" SG CYS C 607 " - pdb=" SG CYS C 644 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 146 " - pdb=" SG CYS D 202 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 339.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1780 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 21 sheets defined 4.7% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.939A pdb=" N GLN A 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.858A pdb=" N THR A 91 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 removed outlier: 3.708A pdb=" N GLU B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 547 Processing helix chain 'C' and resid 593 through 598 Processing helix chain 'C' and resid 613 through 618 Processing helix chain 'E' and resid 121 through 128 removed outlier: 4.019A pdb=" N LYS E 126 " --> pdb=" O ASP E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 4.160A pdb=" N ILE A 2 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR A 78 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 4.106A pdb=" N THR A 117 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 92 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLY A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 11 through 12 removed outlier: 4.106A pdb=" N THR A 117 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 92 " --> pdb=" O VAL A 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 130 removed outlier: 3.656A pdb=" N LEU A 130 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY A 145 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 204 through 206 removed outlier: 3.602A pdb=" N THR A 211 " --> pdb=" O HIS A 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.759A pdb=" N THR B 5 " --> pdb=" O ARG B 24 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 55 removed outlier: 3.667A pdb=" N ILE B 54 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN B 39 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 91 " --> pdb=" O PHE B 97 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 114 through 118 removed outlier: 6.489A pdb=" N TYR B 173 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 144 through 147 removed outlier: 4.072A pdb=" N LYS B 207 " --> pdb=" O CYS B 194 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 502 through 503 removed outlier: 4.301A pdb=" N MET C 555 " --> pdb=" O CYS C 503 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 508 through 509 Processing sheet with id=AB3, first strand: chain 'C' and resid 607 through 609 Processing sheet with id=AB4, first strand: chain 'D' and resid 18 through 22 removed outlier: 3.738A pdb=" N VAL D 20 " --> pdb=" O MET D 81 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET D 81 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA D 79 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 46 through 51 removed outlier: 5.120A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL D 37 " --> pdb=" O TYR D 95 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N SER D 112 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 129 through 130 removed outlier: 3.942A pdb=" N GLY D 145 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR D 182 " --> pdb=" O ASP D 150 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 157 through 160 removed outlier: 3.778A pdb=" N CYS D 202 " --> pdb=" O LYS D 215 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS D 215 " --> pdb=" O CYS D 202 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 21 through 22 Processing sheet with id=AB9, first strand: chain 'E' and resid 46 through 50 removed outlier: 6.097A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN E 39 " --> pdb=" O VAL E 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 114 through 118 removed outlier: 3.882A pdb=" N ASN E 138 " --> pdb=" O TYR E 173 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 144 through 145 Processing sheet with id=AC3, first strand: chain 'E' and resid 153 through 154 185 hydrogen bonds defined for protein. 444 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: 2.12 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6593 1.03 - 1.23: 34 1.23 - 1.43: 3065 1.43 - 1.62: 4151 1.62 - 1.82: 45 Bond restraints: 13888 Sorted by residual: bond pdb=" N CYS C 452 " pdb=" CA CYS C 452 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" N VAL B 3 " pdb=" CA VAL B 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N SER E 2 " pdb=" CA SER E 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" N GLN A 1 " pdb=" CA GLN A 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.84e+00 bond pdb=" N SER D 7 " pdb=" CA SER D 7 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.73e+00 ... (remaining 13883 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 24470 1.57 - 3.13: 415 3.13 - 4.70: 62 4.70 - 6.26: 5 6.26 - 7.83: 4 Bond angle restraints: 24956 Sorted by residual: angle pdb=" CA LYS E 103 " pdb=" CB LYS E 103 " pdb=" CG LYS E 103 " ideal model delta sigma weight residual 114.10 121.93 -7.83 2.00e+00 2.50e-01 1.53e+01 angle pdb=" N VAL D 119 " pdb=" CA VAL D 119 " pdb=" C VAL D 119 " ideal model delta sigma weight residual 109.34 102.85 6.49 2.08e+00 2.31e-01 9.72e+00 angle pdb=" CA PRO E 45 " pdb=" N PRO E 45 " pdb=" CD PRO E 45 " ideal model delta sigma weight residual 112.00 107.65 4.35 1.40e+00 5.10e-01 9.66e+00 angle pdb=" N LYS E 103 " pdb=" CA LYS E 103 " pdb=" CB LYS E 103 " ideal model delta sigma weight residual 111.66 107.01 4.65 1.56e+00 4.11e-01 8.90e+00 angle pdb=" C LYS E 103 " pdb=" CA LYS E 103 " pdb=" CB LYS E 103 " ideal model delta sigma weight residual 110.75 116.30 -5.55 1.99e+00 2.53e-01 7.77e+00 ... (remaining 24951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 5898 16.90 - 33.80: 624 33.80 - 50.70: 207 50.70 - 67.60: 61 67.60 - 84.50: 7 Dihedral angle restraints: 6797 sinusoidal: 3539 harmonic: 3258 Sorted by residual: dihedral pdb=" CB CYS C 494 " pdb=" SG CYS C 494 " pdb=" SG CYS C 564 " pdb=" CB CYS C 564 " ideal model delta sinusoidal sigma weight residual 93.00 150.01 -57.01 1 1.00e+01 1.00e-02 4.37e+01 dihedral pdb=" CB CYS C 508 " pdb=" SG CYS C 508 " pdb=" SG CYS C 552 " pdb=" CB CYS C 552 " ideal model delta sinusoidal sigma weight residual 93.00 42.14 50.86 1 1.00e+01 1.00e-02 3.54e+01 dihedral pdb=" CB CYS C 581 " pdb=" SG CYS C 581 " pdb=" SG CYS C 585 " pdb=" CB CYS C 585 " ideal model delta sinusoidal sigma weight residual 93.00 138.63 -45.63 1 1.00e+01 1.00e-02 2.89e+01 ... (remaining 6794 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 719 0.035 - 0.070: 268 0.070 - 0.106: 81 0.106 - 0.141: 57 0.141 - 0.176: 1 Chirality restraints: 1126 Sorted by residual: chirality pdb=" CA VAL D 119 " pdb=" N VAL D 119 " pdb=" C VAL D 119 " pdb=" CB VAL D 119 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.75e-01 chirality pdb=" CA VAL D 93 " pdb=" N VAL D 93 " pdb=" C VAL D 93 " pdb=" CB VAL D 93 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CA VAL B 132 " pdb=" N VAL B 132 " pdb=" C VAL B 132 " pdb=" CB VAL B 132 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 1123 not shown) Planarity restraints: 2182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 103 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.50e+00 pdb=" C LYS E 103 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS E 103 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL E 104 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 118 " 0.009 2.00e-02 2.50e+03 1.69e-02 2.86e+00 pdb=" C PHE B 118 " -0.029 2.00e-02 2.50e+03 pdb=" O PHE B 118 " 0.011 2.00e-02 2.50e+03 pdb=" N PRO B 119 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA E 44 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO E 45 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO E 45 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 45 " 0.020 5.00e-02 4.00e+02 ... (remaining 2179 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.24: 1802 2.24 - 2.83: 28213 2.83 - 3.42: 32006 3.42 - 4.01: 44316 4.01 - 4.60: 65758 Nonbonded interactions: 172095 Sorted by model distance: nonbonded pdb=" OG SER A 133 " pdb=" HZ2 LYS A 224 " model vdw 1.645 2.450 nonbonded pdb=" HG SER D 192 " pdb=" OH TYR D 200 " model vdw 1.662 2.450 nonbonded pdb=" O GLY E 66 " pdb=" H THR E 73 " model vdw 1.672 2.450 nonbonded pdb=" HZ2 LYS A 220 " pdb=" OD1 ASP E 122 " model vdw 1.693 2.450 nonbonded pdb=" O ILE B 117 " pdb=" HG1 THR D 225 " model vdw 1.698 2.450 ... (remaining 172090 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 22 or (resid 23 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 24 or resid 33 through 53 \ or resid 59 through 61 or (resid 62 through 63 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 64 or (resid 65 through 6 \ 6 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 67 through 72 or resid 78 through 97 or (resid 98 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 99 through 101 \ or (resid 102 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 103 through 114 or (resid 115 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 116 through 132 or re \ sid 140 through 150 or (resid 151 through 152 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 153 through 166 or (resid 1 \ 67 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 168 through 180 or (resid 181 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 182 through 194 or (resid 195 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 196 through 209 or (resid 210 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 211 or (resid 212 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 213 or (resid \ 214 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 215 through 225)) selection = (chain 'D' and (resid 7 through 193 or (resid 194 through 195 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 196 or (res \ id 197 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 198 through 202 or (resid 203 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 204 through 217 or (resid 218 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 219 through 220 or (resid 221 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 222 through 225)) } 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: 0.950 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: 0.060 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.380 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 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 : 0.003 0.038 7305 Z= 0.129 Angle : 0.603 7.829 9978 Z= 0.311 Chirality : 0.046 0.176 1126 Planarity : 0.004 0.040 1286 Dihedral : 15.906 84.500 2492 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer: Outliers : 0.41 % Allowed : 26.15 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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 aren not related in a simple way. whole: -2.74 (0.27), residues: 942 helix: -1.94 (0.88), residues: 24 sheet: -0.67 (0.30), residues: 319 loop : -2.63 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 492 TYR 0.009 0.001 TYR B 50 PHE 0.010 0.001 PHE E 139 TRP 0.005 0.001 TRP B 36 HIS 0.003 0.001 HIS C 488 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 7290) covalent geometry : angle 0.60293 ( 9948) SS BOND : bond 0.00332 ( 15) SS BOND : angle 0.65705 ( 30) hydrogen bonds : bond 0.22494 ( 180) hydrogen bonds : angle 9.73304 ( 444) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 135 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue THR 197 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue VAL 191 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue SER 203 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue THR 473 is missing expected H atoms. Skipping. Residue SER 480 is missing expected H atoms. Skipping. Residue TYR 485 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue TYR 507 is missing expected H atoms. Skipping. Residue LYS 562 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue TYR 151 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue LYS 212 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue SER 203 is missing expected H atoms. Skipping. Evaluate side-chains 78 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 78 average time/residue: 0.1487 time to fit residues: 15.4738 Evaluate side-chains 72 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 204 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.0070 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 124 GLN ** 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 = 0.4622 r_free = 0.4622 target = 0.212257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.177164 restraints weight = 30203.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.180464 restraints weight = 20706.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.182632 restraints weight = 15637.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.186515 restraints weight = 13048.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.186667 restraints weight = 10099.813| |-----------------------------------------------------------------------------| r_work (final): 0.4385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.0699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7305 Z= 0.116 Angle : 0.573 5.383 9978 Z= 0.295 Chirality : 0.045 0.150 1126 Planarity : 0.004 0.033 1286 Dihedral : 4.557 21.892 1035 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Rotamer: Outliers : 2.17 % Allowed : 24.25 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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 aren not related in a simple way. whole: -2.66 (0.27), residues: 942 helix: -1.29 (0.91), residues: 30 sheet: -0.56 (0.30), residues: 321 loop : -2.66 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 492 TYR 0.014 0.001 TYR B 50 PHE 0.010 0.001 PHE E 139 TRP 0.007 0.001 TRP A 47 HIS 0.003 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 7290) covalent geometry : angle 0.57240 ( 9948) SS BOND : bond 0.00354 ( 15) SS BOND : angle 0.63210 ( 30) hydrogen bonds : bond 0.03993 ( 180) hydrogen bonds : angle 7.39477 ( 444) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 135 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue THR 197 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue VAL 191 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue SER 203 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue THR 473 is missing expected H atoms. Skipping. Residue SER 480 is missing expected H atoms. Skipping. Residue TYR 485 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue TYR 507 is missing expected H atoms. Skipping. Residue LYS 562 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue TYR 151 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue LYS 212 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue SER 203 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.7904 (m-80) cc_final: 0.7143 (m-10) REVERT: E 36 TRP cc_start: 0.6600 (m100) cc_final: 0.6364 (m100) outliers start: 16 outliers final: 13 residues processed: 82 average time/residue: 0.1222 time to fit residues: 14.2973 Evaluate side-chains 81 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 202 CYS Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 206 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 15 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 6 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN ** B 124 GLN ** 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 = 0.4576 r_free = 0.4576 target = 0.210274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.172298 restraints weight = 30846.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.176407 restraints weight = 22052.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.178352 restraints weight = 16582.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.180926 restraints weight = 13418.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.181183 restraints weight = 11456.058| |-----------------------------------------------------------------------------| r_work (final): 0.4294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7305 Z= 0.188 Angle : 0.630 6.901 9978 Z= 0.327 Chirality : 0.046 0.146 1126 Planarity : 0.004 0.041 1286 Dihedral : 4.927 21.350 1035 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.97 % Favored : 85.03 % Rotamer: Outliers : 3.79 % Allowed : 24.12 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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 aren not related in a simple way. whole: -3.07 (0.26), residues: 942 helix: -1.51 (0.85), residues: 30 sheet: -1.00 (0.30), residues: 309 loop : -2.81 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 62 TYR 0.016 0.001 TYR B 50 PHE 0.017 0.002 PHE E 139 TRP 0.009 0.001 TRP A 47 HIS 0.003 0.001 HIS D 170 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 7290) covalent geometry : angle 0.62936 ( 9948) SS BOND : bond 0.00481 ( 15) SS BOND : angle 0.90954 ( 30) hydrogen bonds : bond 0.04114 ( 180) hydrogen bonds : angle 7.29282 ( 444) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 135 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue THR 197 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue VAL 191 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue SER 203 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue THR 473 is missing expected H atoms. Skipping. Residue SER 480 is missing expected H atoms. Skipping. Residue TYR 485 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue TYR 507 is missing expected H atoms. Skipping. Residue LYS 562 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue TYR 151 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue LYS 212 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue SER 203 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 147 LEU cc_start: 0.6847 (OUTLIER) cc_final: 0.6606 (tt) outliers start: 28 outliers final: 22 residues processed: 91 average time/residue: 0.1586 time to fit residues: 19.6729 Evaluate side-chains 93 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 637 GLU Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 202 CYS Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 206 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 47 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN ** B 124 GLN ** 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 = 0.4591 r_free = 0.4591 target = 0.211749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.173967 restraints weight = 30817.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.177203 restraints weight = 21715.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.179039 restraints weight = 16528.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.182431 restraints weight = 14049.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.182616 restraints weight = 11835.824| |-----------------------------------------------------------------------------| r_work (final): 0.4312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7305 Z= 0.145 Angle : 0.581 5.503 9978 Z= 0.301 Chirality : 0.046 0.163 1126 Planarity : 0.004 0.040 1286 Dihedral : 4.814 22.034 1035 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.53 % Favored : 87.47 % Rotamer: Outliers : 4.74 % Allowed : 24.25 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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 aren not related in a simple way. whole: -3.08 (0.26), residues: 942 helix: -1.39 (0.86), residues: 30 sheet: -0.88 (0.31), residues: 297 loop : -2.89 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 492 TYR 0.014 0.001 TYR B 50 PHE 0.013 0.001 PHE E 139 TRP 0.007 0.001 TRP A 47 HIS 0.003 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 7290) covalent geometry : angle 0.58106 ( 9948) SS BOND : bond 0.00400 ( 15) SS BOND : angle 0.67103 ( 30) hydrogen bonds : bond 0.03384 ( 180) hydrogen bonds : angle 6.90391 ( 444) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 135 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue THR 197 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue VAL 191 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue SER 203 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue THR 473 is missing expected H atoms. Skipping. Residue SER 480 is missing expected H atoms. Skipping. Residue TYR 485 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue TYR 507 is missing expected H atoms. Skipping. Residue LYS 562 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue TYR 151 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue LYS 212 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue SER 203 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 71 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.8009 (mp0) REVERT: B 156 SER cc_start: 0.9379 (p) cc_final: 0.9034 (m) REVERT: D 147 LEU cc_start: 0.6682 (OUTLIER) cc_final: 0.6473 (tt) outliers start: 35 outliers final: 24 residues processed: 95 average time/residue: 0.1310 time to fit residues: 17.3896 Evaluate side-chains 92 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 488 HIS Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 637 GLU Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 202 CYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 209 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 36 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN ** B 124 GLN ** 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 = 0.4603 r_free = 0.4603 target = 0.213267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.176047 restraints weight = 30840.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.179411 restraints weight = 20403.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.181370 restraints weight = 16495.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.184977 restraints weight = 13213.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.184556 restraints weight = 10999.935| |-----------------------------------------------------------------------------| r_work (final): 0.4338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7305 Z= 0.121 Angle : 0.567 5.727 9978 Z= 0.292 Chirality : 0.045 0.146 1126 Planarity : 0.004 0.039 1286 Dihedral : 4.678 22.251 1034 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.31 % Favored : 87.58 % Rotamer: Outliers : 3.93 % Allowed : 24.66 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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 aren not related in a simple way. whole: -3.05 (0.26), residues: 942 helix: -1.37 (0.84), residues: 32 sheet: -0.83 (0.31), residues: 299 loop : -2.89 (0.23), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 492 TYR 0.012 0.001 TYR B 50 PHE 0.011 0.001 PHE E 139 TRP 0.005 0.001 TRP A 47 HIS 0.004 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 7290) covalent geometry : angle 0.56596 ( 9948) SS BOND : bond 0.00392 ( 15) SS BOND : angle 0.83312 ( 30) hydrogen bonds : bond 0.03149 ( 180) hydrogen bonds : angle 6.67730 ( 444) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 135 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue THR 197 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue VAL 191 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue SER 203 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue THR 473 is missing expected H atoms. Skipping. Residue SER 480 is missing expected H atoms. Skipping. Residue TYR 485 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue TYR 507 is missing expected H atoms. Skipping. Residue LYS 562 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue TYR 151 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue LYS 212 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue SER 203 is missing expected H atoms. Skipping. Evaluate side-chains 95 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7916 (mp0) REVERT: A 189 THR cc_start: 0.7101 (OUTLIER) cc_final: 0.6791 (t) REVERT: B 156 SER cc_start: 0.9368 (p) cc_final: 0.9027 (m) REVERT: D 147 LEU cc_start: 0.6675 (OUTLIER) cc_final: 0.6441 (tt) outliers start: 29 outliers final: 24 residues processed: 84 average time/residue: 0.1248 time to fit residues: 15.3637 Evaluate side-chains 92 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 65 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 488 HIS Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 637 GLU Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 202 CYS Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 206 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 4 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN ** B 124 GLN ** 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 = 0.4575 r_free = 0.4575 target = 0.209343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.172779 restraints weight = 30502.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.175373 restraints weight = 22472.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.177603 restraints weight = 17718.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.180858 restraints weight = 14516.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.181245 restraints weight = 12051.409| |-----------------------------------------------------------------------------| r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7305 Z= 0.191 Angle : 0.624 5.229 9978 Z= 0.327 Chirality : 0.046 0.149 1126 Planarity : 0.005 0.042 1286 Dihedral : 5.020 21.279 1034 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 15.50 % Favored : 84.39 % Rotamer: Outliers : 5.56 % Allowed : 23.44 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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 aren not related in a simple way. whole: -3.39 (0.26), residues: 942 helix: -1.59 (0.80), residues: 30 sheet: -1.30 (0.30), residues: 306 loop : -2.99 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 492 TYR 0.016 0.002 TYR B 50 PHE 0.020 0.002 PHE E 139 TRP 0.007 0.001 TRP D 36 HIS 0.002 0.001 HIS C 488 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 7290) covalent geometry : angle 0.62267 ( 9948) SS BOND : bond 0.00554 ( 15) SS BOND : angle 1.06852 ( 30) hydrogen bonds : bond 0.03691 ( 180) hydrogen bonds : angle 6.91973 ( 444) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 135 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue THR 197 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue VAL 191 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue SER 203 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue THR 473 is missing expected H atoms. Skipping. Residue SER 480 is missing expected H atoms. Skipping. Residue TYR 485 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue TYR 507 is missing expected H atoms. Skipping. Residue LYS 562 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue TYR 151 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue LYS 212 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue SER 203 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 70 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7463 (tt0) REVERT: A 189 THR cc_start: 0.7317 (OUTLIER) cc_final: 0.6946 (t) outliers start: 41 outliers final: 31 residues processed: 102 average time/residue: 0.1418 time to fit residues: 20.6447 Evaluate side-chains 101 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 68 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 488 HIS Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 637 GLU Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 202 CYS Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 209 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 63 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 9 optimal weight: 0.5980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN ** B 124 GLN ** 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 = 0.4549 r_free = 0.4549 target = 0.206214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.169114 restraints weight = 30920.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.172678 restraints weight = 22035.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.175086 restraints weight = 16781.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.176914 restraints weight = 13692.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.177524 restraints weight = 12322.067| |-----------------------------------------------------------------------------| r_work (final): 0.4294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7305 Z= 0.147 Angle : 0.591 6.791 9978 Z= 0.305 Chirality : 0.046 0.148 1126 Planarity : 0.004 0.041 1286 Dihedral : 4.922 23.918 1034 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.63 % Favored : 87.15 % Rotamer: Outliers : 4.61 % Allowed : 24.12 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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 aren not related in a simple way. whole: -3.32 (0.26), residues: 942 helix: -1.47 (0.83), residues: 30 sheet: -1.13 (0.31), residues: 295 loop : -3.00 (0.23), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 18 TYR 0.014 0.001 TYR B 50 PHE 0.013 0.001 PHE E 139 TRP 0.006 0.001 TRP A 47 HIS 0.003 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 7290) covalent geometry : angle 0.59065 ( 9948) SS BOND : bond 0.00409 ( 15) SS BOND : angle 0.75576 ( 30) hydrogen bonds : bond 0.03329 ( 180) hydrogen bonds : angle 6.74704 ( 444) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 135 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue THR 197 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue VAL 191 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue SER 203 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue THR 473 is missing expected H atoms. Skipping. Residue SER 480 is missing expected H atoms. Skipping. Residue TYR 485 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue TYR 507 is missing expected H atoms. Skipping. Residue LYS 562 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue TYR 151 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue LYS 212 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue SER 203 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 72 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7450 (mp0) REVERT: B 156 SER cc_start: 0.9369 (p) cc_final: 0.9051 (m) REVERT: D 147 LEU cc_start: 0.6702 (OUTLIER) cc_final: 0.6486 (tt) outliers start: 34 outliers final: 30 residues processed: 96 average time/residue: 0.1124 time to fit residues: 15.3901 Evaluate side-chains 100 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 68 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 488 HIS Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 637 GLU Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 202 CYS Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 209 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 88 optimal weight: 0.3980 chunk 48 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 51 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN ** B 124 GLN ** 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 = 0.4607 r_free = 0.4607 target = 0.210305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.174741 restraints weight = 30042.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.177536 restraints weight = 22974.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.179128 restraints weight = 17553.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.180571 restraints weight = 14559.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.181165 restraints weight = 13838.505| |-----------------------------------------------------------------------------| r_work (final): 0.4315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7305 Z= 0.111 Angle : 0.559 6.152 9978 Z= 0.286 Chirality : 0.045 0.143 1126 Planarity : 0.004 0.039 1286 Dihedral : 4.612 22.906 1034 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.57 % Favored : 88.22 % Rotamer: Outliers : 4.47 % Allowed : 24.53 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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 aren not related in a simple way. whole: -3.18 (0.26), residues: 942 helix: -1.33 (0.83), residues: 32 sheet: -0.95 (0.32), residues: 287 loop : -2.93 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 492 TYR 0.012 0.001 TYR B 50 PHE 0.009 0.001 PHE E 139 TRP 0.005 0.001 TRP D 160 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 7290) covalent geometry : angle 0.55870 ( 9948) SS BOND : bond 0.00308 ( 15) SS BOND : angle 0.59279 ( 30) hydrogen bonds : bond 0.02921 ( 180) hydrogen bonds : angle 6.40612 ( 444) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 135 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue THR 197 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue VAL 191 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue SER 203 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue THR 473 is missing expected H atoms. Skipping. Residue SER 480 is missing expected H atoms. Skipping. Residue TYR 485 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue TYR 507 is missing expected H atoms. Skipping. Residue LYS 562 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue TYR 151 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue LYS 212 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue SER 203 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 73 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 THR cc_start: 0.6744 (OUTLIER) cc_final: 0.6295 (m) REVERT: B 156 SER cc_start: 0.9341 (p) cc_final: 0.9053 (m) REVERT: D 10 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6809 (mp0) REVERT: D 224 LYS cc_start: 0.5989 (tptt) cc_final: 0.5755 (tptp) outliers start: 33 outliers final: 28 residues processed: 98 average time/residue: 0.1255 time to fit residues: 17.7561 Evaluate side-chains 102 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 72 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 488 HIS Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 202 CYS Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 206 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 94 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN ** B 124 GLN ** 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 = 0.4586 r_free = 0.4586 target = 0.211178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.174240 restraints weight = 30747.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.177149 restraints weight = 22122.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.179013 restraints weight = 16906.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.181954 restraints weight = 14156.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.182019 restraints weight = 11750.142| |-----------------------------------------------------------------------------| r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7305 Z= 0.147 Angle : 0.581 6.079 9978 Z= 0.299 Chirality : 0.045 0.147 1126 Planarity : 0.004 0.040 1286 Dihedral : 4.722 21.916 1034 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 13.27 % Favored : 86.52 % Rotamer: Outliers : 4.74 % Allowed : 24.39 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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 aren not related in a simple way. whole: -3.23 (0.26), residues: 942 helix: -1.42 (0.80), residues: 32 sheet: -1.01 (0.31), residues: 295 loop : -2.97 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 492 TYR 0.014 0.001 TYR B 50 PHE 0.014 0.001 PHE E 139 TRP 0.005 0.001 TRP A 47 HIS 0.003 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 7290) covalent geometry : angle 0.58018 ( 9948) SS BOND : bond 0.00406 ( 15) SS BOND : angle 0.68868 ( 30) hydrogen bonds : bond 0.03197 ( 180) hydrogen bonds : angle 6.46101 ( 444) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 135 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue THR 197 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue VAL 191 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue SER 203 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue THR 473 is missing expected H atoms. Skipping. Residue SER 480 is missing expected H atoms. Skipping. Residue TYR 485 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue TYR 507 is missing expected H atoms. Skipping. Residue LYS 562 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue TYR 151 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue LYS 212 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue SER 203 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 73 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 THR cc_start: 0.6818 (OUTLIER) cc_final: 0.6384 (m) REVERT: B 156 SER cc_start: 0.9349 (p) cc_final: 0.9057 (m) REVERT: D 10 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6752 (mp0) outliers start: 35 outliers final: 31 residues processed: 100 average time/residue: 0.1249 time to fit residues: 17.9899 Evaluate side-chains 102 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 69 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 488 HIS Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 202 CYS Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 206 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 40 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN ** B 124 GLN ** 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 = 0.4591 r_free = 0.4591 target = 0.211681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.182009 restraints weight = 30635.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.180979 restraints weight = 28345.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.182004 restraints weight = 24714.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.183194 restraints weight = 21351.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.183956 restraints weight = 16644.142| |-----------------------------------------------------------------------------| r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.149 7305 Z= 0.151 Angle : 0.945 59.199 9978 Z= 0.539 Chirality : 0.046 0.176 1126 Planarity : 0.004 0.039 1286 Dihedral : 4.712 22.341 1034 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.21 % Allowed : 13.38 % Favored : 86.41 % Rotamer: Outliers : 4.61 % Allowed : 24.39 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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 aren not related in a simple way. whole: -3.23 (0.26), residues: 942 helix: -1.77 (0.84), residues: 26 sheet: -1.15 (0.30), residues: 309 loop : -2.89 (0.23), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 492 TYR 0.013 0.001 TYR B 50 PHE 0.012 0.001 PHE E 139 TRP 0.005 0.001 TRP A 47 HIS 0.003 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7290) covalent geometry : angle 0.94533 ( 9948) SS BOND : bond 0.00391 ( 15) SS BOND : angle 0.63831 ( 30) hydrogen bonds : bond 0.03080 ( 180) hydrogen bonds : angle 6.44599 ( 444) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 135 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue THR 197 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue LYS 126 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LYS 149 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue VAL 191 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue SER 203 is missing expected H atoms. Skipping. Residue THR 206 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue THR 473 is missing expected H atoms. Skipping. Residue SER 480 is missing expected H atoms. Skipping. Residue TYR 485 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue TYR 507 is missing expected H atoms. Skipping. Residue LYS 562 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue ILE 102 is missing expected H atoms. Skipping. Residue TYR 151 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 207 is missing expected H atoms. Skipping. Residue LYS 212 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue SER 203 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 70 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 THR cc_start: 0.6793 (OUTLIER) cc_final: 0.6353 (m) REVERT: B 156 SER cc_start: 0.9242 (p) cc_final: 0.8975 (m) REVERT: D 10 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6889 (mp0) outliers start: 34 outliers final: 29 residues processed: 96 average time/residue: 0.1272 time to fit residues: 17.3971 Evaluate side-chains 100 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 69 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 202 CYS Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 206 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 83 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 69 optimal weight: 0.1980 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 0.0980 chunk 78 optimal weight: 0.0670 chunk 72 optimal weight: 3.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** 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 = 0.4587 r_free = 0.4587 target = 0.211427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.174627 restraints weight = 30948.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.177439 restraints weight = 21545.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.179794 restraints weight = 16301.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.184047 restraints weight = 13225.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.184102 restraints weight = 10477.962| |-----------------------------------------------------------------------------| r_work (final): 0.4321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.149 7305 Z= 0.151 Angle : 0.945 59.199 9978 Z= 0.539 Chirality : 0.046 0.176 1126 Planarity : 0.004 0.039 1286 Dihedral : 4.712 22.341 1034 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.21 % Allowed : 13.38 % Favored : 86.41 % Rotamer: Outliers : 4.20 % Allowed : 24.66 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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 aren not related in a simple way. whole: -3.23 (0.26), residues: 942 helix: -1.77 (0.84), residues: 26 sheet: -1.15 (0.30), residues: 309 loop : -2.89 (0.23), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 492 TYR 0.013 0.001 TYR B 50 PHE 0.012 0.001 PHE E 139 TRP 0.005 0.001 TRP A 47 HIS 0.003 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7290) covalent geometry : angle 0.94533 ( 9948) SS BOND : bond 0.00391 ( 15) SS BOND : angle 0.63831 ( 30) hydrogen bonds : bond 0.03080 ( 180) hydrogen bonds : angle 6.44599 ( 444) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2156.05 seconds wall clock time: 37 minutes 21.00 seconds (2241.00 seconds total)