Starting phenix.real_space_refine on Thu May 15 22:10:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tzy_41774/05_2025/8tzy_41774.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tzy_41774/05_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_41774/05_2025/8tzy_41774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tzy_41774/05_2025/8tzy_41774.map" model { file = "/net/cci-nas-00/data/ceres_data/8tzy_41774/05_2025/8tzy_41774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tzy_41774/05_2025/8tzy_41774.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP: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: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} 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: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'ARG:plan': 2} 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, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 51 Time building chain proxies: 6.68, per 1000 atoms: 0.49 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: 3.33 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.14 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: 4.52 Time building geometry restraints manager: 4.04 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: 1.100 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: 0.250 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 30.270 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.860 ------------------------------------------------------------------------------- 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 : 8.90 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (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 TRP 0.005 0.001 TRP B 36 HIS 0.003 0.001 HIS C 488 PHE 0.010 0.001 PHE E 139 TYR 0.009 0.001 TYR B 50 ARG 0.005 0.000 ARG C 492 Details of bonding type rmsd hydrogen bonds : bond 0.22494 ( 180) hydrogen bonds : angle 9.73304 ( 444) SS BOND : bond 0.00332 ( 15) SS BOND : angle 0.65705 ( 30) covalent geometry : bond 0.00290 ( 7290) covalent geometry : angle 0.60293 ( 9948) *********************** 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 : 1.036 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: 0.4079 time to fit residues: 42.9319 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 : 1.005 ------------------------------------------------------------------------------- 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 80 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 chunk 38 optimal weight: 0.0870 chunk 74 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.4626 r_free = 0.4626 target = 0.212604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.183539 restraints weight = 29993.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.180616 restraints weight = 25292.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.183930 restraints weight = 22964.795| |-----------------------------------------------------------------------------| r_work (final): 0.4368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.0722 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= 0.113 Angle : 0.571 5.379 9978 Z= 0.294 Chirality : 0.046 0.152 1126 Planarity : 0.004 0.033 1286 Dihedral : 4.547 21.914 1035 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.93 % Favored : 89.07 % Rotamer: Outliers : 2.30 % Allowed : 24.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.27), residues: 942 helix: -1.23 (0.93), residues: 30 sheet: -0.59 (0.31), residues: 311 loop : -2.60 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.003 0.001 HIS B 198 PHE 0.010 0.001 PHE E 139 TYR 0.014 0.001 TYR B 50 ARG 0.003 0.000 ARG C 492 Details of bonding type rmsd hydrogen bonds : bond 0.03622 ( 180) hydrogen bonds : angle 7.32967 ( 444) SS BOND : bond 0.00310 ( 15) SS BOND : angle 0.59430 ( 30) covalent geometry : bond 0.00264 ( 7290) covalent geometry : angle 0.57112 ( 9948) *********************** 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 91 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.7757 (m-80) cc_final: 0.6950 (m-10) outliers start: 17 outliers final: 13 residues processed: 84 average time/residue: 0.3560 time to fit residues: 41.5186 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 : 1.101 ------------------------------------------------------------------------------- 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 68 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 79 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- 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 = 0.212000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.175202 restraints weight = 30777.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.177517 restraints weight = 21263.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.180690 restraints weight = 16553.653| |-----------------------------------------------------------------------------| r_work (final): 0.4287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7305 Z= 0.169 Angle : 0.602 7.059 9978 Z= 0.313 Chirality : 0.046 0.144 1126 Planarity : 0.004 0.041 1286 Dihedral : 4.762 21.547 1035 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.80 % Favored : 86.20 % Rotamer: Outliers : 3.39 % Allowed : 24.12 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.26), residues: 942 helix: -1.35 (0.89), residues: 30 sheet: -0.82 (0.31), residues: 304 loop : -2.77 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 47 HIS 0.003 0.001 HIS D 170 PHE 0.014 0.001 PHE E 139 TYR 0.015 0.001 TYR B 50 ARG 0.002 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03860 ( 180) hydrogen bonds : angle 7.20461 ( 444) SS BOND : bond 0.00444 ( 15) SS BOND : angle 0.80459 ( 30) covalent geometry : bond 0.00399 ( 7290) covalent geometry : angle 0.60096 ( 9948) *********************** 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 98 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 TRP cc_start: 0.6678 (m100) cc_final: 0.6455 (m100) outliers start: 25 outliers final: 22 residues processed: 88 average time/residue: 0.3762 time to fit residues: 45.8303 Evaluate side-chains 90 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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 136 LEU 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 16 SER Chi-restraints excluded: chain D residue 17 SER 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 202 CYS 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 90 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 6 optimal weight: 0.2980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4609 r_free = 0.4609 target = 0.214213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.177584 restraints weight = 30672.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.180691 restraints weight = 20312.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.182648 restraints weight = 15922.673| |-----------------------------------------------------------------------------| r_work (final): 0.4308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.1198 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= 0.120 Angle : 0.561 6.158 9978 Z= 0.289 Chirality : 0.045 0.141 1126 Planarity : 0.004 0.041 1286 Dihedral : 4.578 22.020 1034 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % Rotamer: Outliers : 3.79 % Allowed : 24.25 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.27), residues: 942 helix: -1.33 (0.87), residues: 32 sheet: -0.67 (0.32), residues: 299 loop : -2.81 (0.23), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 47 HIS 0.004 0.001 HIS B 198 PHE 0.010 0.001 PHE E 139 TYR 0.013 0.001 TYR B 50 ARG 0.005 0.000 ARG C 492 Details of bonding type rmsd hydrogen bonds : bond 0.03148 ( 180) hydrogen bonds : angle 6.76767 ( 444) SS BOND : bond 0.00344 ( 15) SS BOND : angle 0.58559 ( 30) covalent geometry : bond 0.00283 ( 7290) covalent geometry : angle 0.56109 ( 9948) *********************** 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 92 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 64 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8123 (mp0) REVERT: D 147 LEU cc_start: 0.6645 (OUTLIER) cc_final: 0.6432 (tt) outliers start: 28 outliers final: 19 residues processed: 83 average time/residue: 0.3448 time to fit residues: 40.3049 Evaluate side-chains 83 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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 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 615 LEU Chi-restraints excluded: chain D residue 16 SER 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 13 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 chunk 19 optimal weight: 0.3980 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 = 0.4610 r_free = 0.4610 target = 0.214097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.176834 restraints weight = 30703.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.179823 restraints weight = 21346.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.182117 restraints weight = 15862.612| |-----------------------------------------------------------------------------| r_work (final): 0.4306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.1352 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= 0.121 Angle : 0.556 5.832 9978 Z= 0.286 Chirality : 0.045 0.141 1126 Planarity : 0.004 0.041 1286 Dihedral : 4.537 21.948 1034 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.53 % Favored : 87.47 % Rotamer: Outliers : 4.20 % Allowed : 23.98 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.27), residues: 942 helix: -1.25 (0.87), residues: 32 sheet: -0.70 (0.31), residues: 299 loop : -2.80 (0.23), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 47 HIS 0.003 0.001 HIS B 198 PHE 0.011 0.001 PHE E 139 TYR 0.012 0.001 TYR B 50 ARG 0.003 0.000 ARG C 492 Details of bonding type rmsd hydrogen bonds : bond 0.03087 ( 180) hydrogen bonds : angle 6.59237 ( 444) SS BOND : bond 0.00359 ( 15) SS BOND : angle 0.66514 ( 30) covalent geometry : bond 0.00289 ( 7290) covalent geometry : angle 0.55596 ( 9948) *********************** 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 98 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 67 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8105 (mp0) REVERT: A 189 THR cc_start: 0.7120 (OUTLIER) cc_final: 0.6833 (t) REVERT: B 156 SER cc_start: 0.9365 (p) cc_final: 0.9025 (m) REVERT: D 147 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6481 (tt) outliers start: 31 outliers final: 27 residues processed: 88 average time/residue: 0.3506 time to fit residues: 42.8417 Evaluate side-chains 97 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 67 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 39 GLN 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 189 THR 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 143 GLU 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 66 optimal weight: 0.6980 chunk 80 optimal weight: 0.2980 chunk 84 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 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 = 0.4616 r_free = 0.4616 target = 0.214618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.177086 restraints weight = 30792.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.180258 restraints weight = 21251.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.182282 restraints weight = 16210.907| |-----------------------------------------------------------------------------| r_work (final): 0.4309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.1448 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= 0.116 Angle : 0.548 5.841 9978 Z= 0.281 Chirality : 0.045 0.141 1126 Planarity : 0.004 0.040 1286 Dihedral : 4.484 21.878 1034 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.89 % Favored : 88.11 % Rotamer: Outliers : 4.47 % Allowed : 24.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.27), residues: 942 helix: -1.22 (0.87), residues: 32 sheet: -0.64 (0.32), residues: 297 loop : -2.79 (0.23), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 47 HIS 0.003 0.001 HIS D 206 PHE 0.010 0.001 PHE E 139 TYR 0.012 0.001 TYR B 50 ARG 0.003 0.000 ARG A 23 Details of bonding type rmsd hydrogen bonds : bond 0.02963 ( 180) hydrogen bonds : angle 6.46139 ( 444) SS BOND : bond 0.00338 ( 15) SS BOND : angle 0.64908 ( 30) covalent geometry : bond 0.00273 ( 7290) covalent geometry : angle 0.54786 ( 9948) *********************** 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 102 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 69 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8089 (mp0) REVERT: B 156 SER cc_start: 0.9363 (p) cc_final: 0.9028 (m) REVERT: D 147 LEU cc_start: 0.6682 (OUTLIER) cc_final: 0.6460 (tt) outliers start: 33 outliers final: 28 residues processed: 91 average time/residue: 0.3250 time to fit residues: 41.8571 Evaluate side-chains 95 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 39 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 120 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 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 16 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 17 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 63 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 53 optimal weight: 0.0270 chunk 2 optimal weight: 0.0570 chunk 18 optimal weight: 0.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- 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 = 0.4642 r_free = 0.4642 target = 0.216483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.179081 restraints weight = 30457.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.183318 restraints weight = 20146.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.185767 restraints weight = 15066.264| |-----------------------------------------------------------------------------| r_work (final): 0.4352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7305 Z= 0.095 Angle : 0.531 6.291 9978 Z= 0.271 Chirality : 0.045 0.139 1126 Planarity : 0.004 0.039 1286 Dihedral : 4.275 22.143 1034 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 4.20 % Allowed : 24.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.27), residues: 942 helix: -1.07 (0.89), residues: 32 sheet: -0.61 (0.31), residues: 302 loop : -2.71 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 47 HIS 0.004 0.001 HIS B 198 PHE 0.009 0.001 PHE C 509 TYR 0.010 0.001 TYR B 50 ARG 0.003 0.000 ARG C 492 Details of bonding type rmsd hydrogen bonds : bond 0.02644 ( 180) hydrogen bonds : angle 6.08037 ( 444) SS BOND : bond 0.00255 ( 15) SS BOND : angle 0.54435 ( 30) covalent geometry : bond 0.00228 ( 7290) covalent geometry : angle 0.53117 ( 9948) *********************** 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 104 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 73 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8096 (mp0) REVERT: A 189 THR cc_start: 0.6978 (OUTLIER) cc_final: 0.6645 (t) REVERT: B 37 TYR cc_start: 0.7888 (m-80) cc_final: 0.7239 (m-10) REVERT: B 156 SER cc_start: 0.9338 (p) cc_final: 0.9029 (m) REVERT: D 147 LEU cc_start: 0.6478 (OUTLIER) cc_final: 0.6210 (tt) outliers start: 31 outliers final: 26 residues processed: 94 average time/residue: 0.3309 time to fit residues: 44.6260 Evaluate side-chains 99 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 39 GLN 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 120 THR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 195 LEU 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 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 16 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 57 optimal weight: 2.9990 chunk 78 optimal weight: 0.0870 chunk 61 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.4642 r_free = 0.4642 target = 0.216384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.185713 restraints weight = 30464.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.184913 restraints weight = 26859.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.186798 restraints weight = 24643.670| |-----------------------------------------------------------------------------| r_work (final): 0.4360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7305 Z= 0.100 Angle : 0.531 6.244 9978 Z= 0.271 Chirality : 0.044 0.140 1126 Planarity : 0.004 0.039 1286 Dihedral : 4.263 21.862 1034 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.93 % Favored : 89.07 % Rotamer: Outliers : 4.34 % Allowed : 24.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.27), residues: 942 helix: -0.97 (0.89), residues: 32 sheet: -0.57 (0.31), residues: 307 loop : -2.69 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 47 HIS 0.004 0.001 HIS B 198 PHE 0.008 0.001 PHE C 509 TYR 0.010 0.001 TYR B 50 ARG 0.002 0.000 ARG C 492 Details of bonding type rmsd hydrogen bonds : bond 0.02662 ( 180) hydrogen bonds : angle 6.01855 ( 444) SS BOND : bond 0.00266 ( 15) SS BOND : angle 0.53301 ( 30) covalent geometry : bond 0.00239 ( 7290) covalent geometry : angle 0.53137 ( 9948) *********************** 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 102 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 70 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8067 (mp0) REVERT: A 189 THR cc_start: 0.6990 (OUTLIER) cc_final: 0.6673 (t) REVERT: B 37 TYR cc_start: 0.7768 (m-80) cc_final: 0.7070 (m-10) REVERT: B 156 SER cc_start: 0.9229 (p) cc_final: 0.8956 (m) outliers start: 32 outliers final: 28 residues processed: 93 average time/residue: 0.3267 time to fit residues: 43.5023 Evaluate side-chains 100 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 70 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 39 GLN 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 120 THR 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 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 16 SER Chi-restraints excluded: chain D residue 17 SER 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 67 optimal weight: 4.9990 chunk 85 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 17 optimal weight: 0.0370 chunk 73 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.216414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.179958 restraints weight = 30505.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.183554 restraints weight = 20535.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.185747 restraints weight = 15091.070| |-----------------------------------------------------------------------------| r_work (final): 0.4337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7305 Z= 0.096 Angle : 0.530 6.323 9978 Z= 0.270 Chirality : 0.044 0.140 1126 Planarity : 0.004 0.038 1286 Dihedral : 4.263 21.768 1034 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.27), residues: 942 helix: -0.22 (1.03), residues: 26 sheet: -0.62 (0.31), residues: 315 loop : -2.66 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 47 HIS 0.003 0.001 HIS B 198 PHE 0.008 0.001 PHE C 509 TYR 0.010 0.001 TYR B 50 ARG 0.002 0.000 ARG C 492 Details of bonding type rmsd hydrogen bonds : bond 0.02612 ( 180) hydrogen bonds : angle 5.95559 ( 444) SS BOND : bond 0.00268 ( 15) SS BOND : angle 0.46972 ( 30) covalent geometry : bond 0.00231 ( 7290) covalent geometry : angle 0.53048 ( 9948) *********************** 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 101 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 70 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8031 (mp0) REVERT: A 189 THR cc_start: 0.7056 (OUTLIER) cc_final: 0.6689 (t) REVERT: B 37 TYR cc_start: 0.7925 (m-80) cc_final: 0.7281 (m-10) REVERT: B 156 SER cc_start: 0.9348 (p) cc_final: 0.9031 (m) outliers start: 31 outliers final: 29 residues processed: 93 average time/residue: 0.3421 time to fit residues: 45.3345 Evaluate side-chains 101 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 70 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 39 GLN 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 120 THR 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 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 16 SER Chi-restraints excluded: chain D residue 17 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 33 optimal weight: 0.5980 chunk 36 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.210111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.173057 restraints weight = 30924.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.176569 restraints weight = 21344.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.179170 restraints weight = 16143.378| |-----------------------------------------------------------------------------| r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.1809 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= 0.126 Angle : 0.548 6.432 9978 Z= 0.280 Chirality : 0.045 0.139 1126 Planarity : 0.004 0.039 1286 Dihedral : 4.363 22.162 1034 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer: Outliers : 4.07 % Allowed : 24.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.27), residues: 942 helix: -1.02 (0.87), residues: 32 sheet: -0.70 (0.31), residues: 306 loop : -2.69 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 47 HIS 0.002 0.001 HIS B 198 PHE 0.010 0.001 PHE E 139 TYR 0.012 0.001 TYR B 50 ARG 0.002 0.000 ARG C 492 Details of bonding type rmsd hydrogen bonds : bond 0.02818 ( 180) hydrogen bonds : angle 6.02930 ( 444) SS BOND : bond 0.00357 ( 15) SS BOND : angle 0.62180 ( 30) covalent geometry : bond 0.00298 ( 7290) covalent geometry : angle 0.54794 ( 9948) ********************** 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 100 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 70 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8024 (mp0) REVERT: A 189 THR cc_start: 0.7113 (OUTLIER) cc_final: 0.6727 (t) REVERT: B 156 SER cc_start: 0.9362 (p) cc_final: 0.9040 (m) outliers start: 30 outliers final: 27 residues processed: 92 average time/residue: 0.3260 time to fit residues: 42.6308 Evaluate side-chains 99 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 39 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 120 THR Chi-restraints excluded: chain A residue 189 THR 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 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 16 SER Chi-restraints excluded: chain D residue 17 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 60 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.215449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.184010 restraints weight = 30751.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.183635 restraints weight = 27585.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.185610 restraints weight = 24716.970| |-----------------------------------------------------------------------------| r_work (final): 0.4350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.1908 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= 0.107 Angle : 0.536 6.397 9978 Z= 0.273 Chirality : 0.044 0.139 1126 Planarity : 0.004 0.038 1286 Dihedral : 4.295 21.832 1034 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % Rotamer: Outliers : 4.34 % Allowed : 24.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.27), residues: 942 helix: -0.18 (1.02), residues: 26 sheet: -0.64 (0.31), residues: 308 loop : -2.67 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 47 HIS 0.002 0.001 HIS C 488 PHE 0.009 0.001 PHE E 139 TYR 0.012 0.001 TYR B 50 ARG 0.002 0.000 ARG C 492 Details of bonding type rmsd hydrogen bonds : bond 0.02664 ( 180) hydrogen bonds : angle 5.93528 ( 444) SS BOND : bond 0.00329 ( 15) SS BOND : angle 0.58616 ( 30) covalent geometry : bond 0.00257 ( 7290) covalent geometry : angle 0.53582 ( 9948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4374.32 seconds wall clock time: 76 minutes 6.73 seconds (4566.73 seconds total)