Starting phenix.real_space_refine on Sun Nov 17 12:03:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzy_41774/11_2024/8tzy_41774.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzy_41774/11_2024/8tzy_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzy_41774/11_2024/8tzy_41774.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzy_41774/11_2024/8tzy_41774.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzy_41774/11_2024/8tzy_41774.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzy_41774/11_2024/8tzy_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-5513/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: 6.90, per 1000 atoms: 0.50 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: 3.45 Conformation dependent library (CDL) restraints added in 1.2 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: 1.21 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: 4.85 Time building geometry restraints manager: 4.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6593 1.03 - 1.23: 34 1.23 - 1.43: 3065 1.43 - 1.62: 4151 1.62 - 1.82: 45 Bond restraints: 13888 Sorted by residual: bond pdb=" N CYS C 452 " pdb=" CA CYS C 452 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" N VAL B 3 " pdb=" CA VAL B 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N SER E 2 " pdb=" CA SER E 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" N GLN A 1 " pdb=" CA GLN A 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.84e+00 bond pdb=" N SER D 7 " pdb=" CA SER D 7 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.73e+00 ... (remaining 13883 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 24470 1.57 - 3.13: 415 3.13 - 4.70: 62 4.70 - 6.26: 5 6.26 - 7.83: 4 Bond angle restraints: 24956 Sorted by residual: angle pdb=" CA LYS E 103 " pdb=" CB LYS E 103 " pdb=" CG LYS E 103 " ideal model delta sigma weight residual 114.10 121.93 -7.83 2.00e+00 2.50e-01 1.53e+01 angle pdb=" N VAL D 119 " pdb=" CA VAL D 119 " pdb=" C VAL D 119 " ideal model delta sigma weight residual 109.34 102.85 6.49 2.08e+00 2.31e-01 9.72e+00 angle pdb=" CA PRO E 45 " pdb=" N PRO E 45 " pdb=" CD PRO E 45 " ideal model delta sigma weight residual 112.00 107.65 4.35 1.40e+00 5.10e-01 9.66e+00 angle pdb=" N LYS E 103 " pdb=" CA LYS E 103 " pdb=" CB LYS E 103 " ideal model delta sigma weight residual 111.66 107.01 4.65 1.56e+00 4.11e-01 8.90e+00 angle pdb=" C LYS E 103 " pdb=" CA LYS E 103 " pdb=" CB LYS E 103 " ideal model delta sigma weight residual 110.75 116.30 -5.55 1.99e+00 2.53e-01 7.77e+00 ... (remaining 24951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 5898 16.90 - 33.80: 624 33.80 - 50.70: 207 50.70 - 67.60: 61 67.60 - 84.50: 7 Dihedral angle restraints: 6797 sinusoidal: 3539 harmonic: 3258 Sorted by residual: dihedral pdb=" CB CYS C 494 " pdb=" SG CYS C 494 " pdb=" SG CYS C 564 " pdb=" CB CYS C 564 " ideal model delta sinusoidal sigma weight residual 93.00 150.01 -57.01 1 1.00e+01 1.00e-02 4.37e+01 dihedral pdb=" CB CYS C 508 " pdb=" SG CYS C 508 " pdb=" SG CYS C 552 " pdb=" CB CYS C 552 " ideal model delta sinusoidal sigma weight residual 93.00 42.14 50.86 1 1.00e+01 1.00e-02 3.54e+01 dihedral pdb=" CB CYS C 581 " pdb=" SG CYS C 581 " pdb=" SG CYS C 585 " pdb=" CB CYS C 585 " ideal model delta sinusoidal sigma weight residual 93.00 138.63 -45.63 1 1.00e+01 1.00e-02 2.89e+01 ... (remaining 6794 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 719 0.035 - 0.070: 268 0.070 - 0.106: 81 0.106 - 0.141: 57 0.141 - 0.176: 1 Chirality restraints: 1126 Sorted by residual: chirality pdb=" CA VAL D 119 " pdb=" N VAL D 119 " pdb=" C VAL D 119 " pdb=" CB VAL D 119 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.75e-01 chirality pdb=" CA VAL D 93 " pdb=" N VAL D 93 " pdb=" C VAL D 93 " pdb=" CB VAL D 93 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CA VAL B 132 " pdb=" N VAL B 132 " pdb=" C VAL B 132 " pdb=" CB VAL B 132 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 1123 not shown) Planarity restraints: 2182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 103 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.50e+00 pdb=" C LYS E 103 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS E 103 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL E 104 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 118 " 0.009 2.00e-02 2.50e+03 1.69e-02 2.86e+00 pdb=" C PHE B 118 " -0.029 2.00e-02 2.50e+03 pdb=" O PHE B 118 " 0.011 2.00e-02 2.50e+03 pdb=" N PRO B 119 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA E 44 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO E 45 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO E 45 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 45 " 0.020 5.00e-02 4.00e+02 ... (remaining 2179 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.24: 1802 2.24 - 2.83: 28213 2.83 - 3.42: 32006 3.42 - 4.01: 44316 4.01 - 4.60: 65758 Nonbonded interactions: 172095 Sorted by model distance: nonbonded pdb=" OG SER A 133 " pdb=" HZ2 LYS A 224 " model vdw 1.645 2.450 nonbonded pdb=" HG SER D 192 " pdb=" OH TYR D 200 " model vdw 1.662 2.450 nonbonded pdb=" O GLY E 66 " pdb=" H THR E 73 " model vdw 1.672 2.450 nonbonded pdb=" HZ2 LYS A 220 " pdb=" OD1 ASP E 122 " model vdw 1.693 2.450 nonbonded pdb=" O ILE B 117 " pdb=" HG1 THR D 225 " model vdw 1.698 2.450 ... (remaining 172090 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 22 or (resid 23 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 24 or resid 33 through 53 \ or resid 59 through 61 or (resid 62 through 63 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 64 or (resid 65 through 6 \ 6 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 67 through 72 or resid 78 through 97 or (resid 98 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 99 through 101 \ or (resid 102 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 103 through 114 or (resid 115 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 116 through 132 or re \ sid 140 through 150 or (resid 151 through 152 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 153 through 166 or (resid 1 \ 67 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 168 through 180 or (resid 181 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 182 through 194 or (resid 195 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 196 through 209 or (resid 210 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 211 or (resid 212 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 213 or (resid \ 214 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 215 through 225)) selection = (chain 'D' and (resid 7 through 193 or (resid 194 through 195 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 196 or (res \ id 197 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 198 through 202 or (resid 203 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 204 through 217 or (resid 218 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 219 through 220 or (resid 221 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 222 through 225)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.500 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.470 ------------------------------------------------------------------------------- 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 7290 Z= 0.193 Angle : 0.603 7.829 9948 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 *********************** 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 : 1.148 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: 0.4158 time to fit residues: 44.1052 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 : 1.085 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 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 7290 Z= 0.176 Angle : 0.571 5.379 9948 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 *********************** 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 : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.7905 (m-80) cc_final: 0.7163 (m-10) outliers start: 17 outliers final: 13 residues processed: 84 average time/residue: 0.3603 time to fit residues: 42.3904 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 : 1.122 ------------------------------------------------------------------------------- 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 47 optimal weight: 0.0030 chunk 26 optimal weight: 0.8980 chunk 71 optimal weight: 0.3980 chunk 58 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 76 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 29 optimal weight: 0.0060 chunk 69 optimal weight: 0.3980 overall best weight: 0.2606 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7290 Z= 0.149 Angle : 0.541 6.866 9948 Z= 0.277 Chirality : 0.045 0.143 1126 Planarity : 0.004 0.036 1286 Dihedral : 4.336 22.334 1035 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 2.30 % Allowed : 24.39 % Favored : 73.31 % 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: -2.62 (0.27), residues: 942 helix: -1.05 (0.93), residues: 32 sheet: -0.40 (0.32), residues: 292 loop : -2.64 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.000 TRP A 47 HIS 0.004 0.001 HIS B 198 PHE 0.009 0.001 PHE C 509 TYR 0.009 0.001 TYR B 50 ARG 0.002 0.000 ARG C 492 *********************** 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 89 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.7844 (m-80) cc_final: 0.7151 (m-10) REVERT: E 36 TRP cc_start: 0.6628 (m100) cc_final: 0.6375 (m100) outliers start: 17 outliers final: 13 residues processed: 83 average time/residue: 0.3850 time to fit residues: 43.7987 Evaluate side-chains 78 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASN 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 615 LEU 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 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 85 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 58 optimal weight: 0.3980 chunk 86 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 chunk 24 optimal weight: 0.0020 overall best weight: 0.8190 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7290 Z= 0.188 Angle : 0.544 5.151 9948 Z= 0.280 Chirality : 0.045 0.139 1126 Planarity : 0.004 0.039 1286 Dihedral : 4.359 21.322 1034 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % Rotamer: Outliers : 2.85 % Allowed : 24.80 % Favored : 72.36 % 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: -2.63 (0.27), residues: 942 helix: -1.17 (0.88), residues: 32 sheet: -0.44 (0.32), residues: 297 loop : -2.64 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 47 HIS 0.003 0.001 HIS D 206 PHE 0.010 0.001 PHE E 139 TYR 0.013 0.001 TYR B 50 ARG 0.004 0.000 ARG C 492 *********************** 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: 21 poor density : 71 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.6832 (mt0) REVERT: B 37 TYR cc_start: 0.7942 (m-80) cc_final: 0.7300 (m-10) REVERT: D 147 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6454 (tt) REVERT: E 36 TRP cc_start: 0.6661 (m100) cc_final: 0.6420 (m100) outliers start: 21 outliers final: 16 residues processed: 83 average time/residue: 0.3517 time to fit residues: 40.9333 Evaluate side-chains 87 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLN 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 37 optimal weight: 0.0980 chunk 78 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 198 GLN ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7290 Z= 0.167 Angle : 0.539 5.696 9948 Z= 0.276 Chirality : 0.045 0.141 1126 Planarity : 0.004 0.039 1286 Dihedral : 4.320 21.861 1034 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.40 % Favored : 89.60 % Rotamer: Outliers : 3.12 % Allowed : 25.07 % 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: -2.67 (0.27), residues: 942 helix: -1.06 (0.89), residues: 32 sheet: -0.45 (0.32), residues: 294 loop : -2.68 (0.24), residues: 616 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 0.008 0.001 PHE E 139 TYR 0.011 0.001 TYR B 50 ARG 0.003 0.000 ARG C 492 *********************** 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 94 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.7934 (m-80) cc_final: 0.7377 (m-10) REVERT: D 147 LEU cc_start: 0.6668 (OUTLIER) cc_final: 0.6443 (tt) REVERT: D 218 GLU cc_start: 0.7033 (pm20) cc_final: 0.5205 (mt-10) REVERT: E 36 TRP cc_start: 0.6619 (m100) cc_final: 0.6401 (m100) outliers start: 23 outliers final: 18 residues processed: 84 average time/residue: 0.3468 time to fit residues: 41.1428 Evaluate side-chains 86 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 30 optimal weight: 2.9990 chunk 82 optimal weight: 0.0020 chunk 18 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7290 Z= 0.176 Angle : 0.539 6.197 9948 Z= 0.276 Chirality : 0.045 0.140 1126 Planarity : 0.004 0.039 1286 Dihedral : 4.297 21.224 1034 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.57 % Favored : 88.43 % 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: -2.65 (0.27), residues: 942 helix: -1.05 (0.88), residues: 32 sheet: -0.43 (0.32), residues: 297 loop : -2.68 (0.24), residues: 613 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 0.009 0.001 PHE E 139 TYR 0.012 0.001 TYR B 50 ARG 0.003 0.000 ARG C 492 *********************** 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 97 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 69 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7780 (mp0) REVERT: B 37 TYR cc_start: 0.7952 (m-80) cc_final: 0.7388 (m-10) REVERT: B 156 SER cc_start: 0.9337 (p) cc_final: 0.9034 (m) REVERT: D 147 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6512 (tt) REVERT: D 218 GLU cc_start: 0.7048 (pm20) cc_final: 0.5234 (mt-10) REVERT: D 224 LYS cc_start: 0.5857 (tptt) cc_final: 0.5630 (tptp) outliers start: 28 outliers final: 20 residues processed: 89 average time/residue: 0.3412 time to fit residues: 42.8285 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 : 1.002 ------------------------------------------------------------------------------- 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7290 Z= 0.177 Angle : 0.543 6.300 9948 Z= 0.278 Chirality : 0.045 0.141 1126 Planarity : 0.004 0.039 1286 Dihedral : 4.305 21.689 1034 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.57 % Favored : 88.43 % Rotamer: Outliers : 3.39 % Allowed : 24.25 % Favored : 72.36 % 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: -1.02 (0.88), residues: 32 sheet: -0.50 (0.31), residues: 301 loop : -2.67 (0.24), residues: 609 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 0.003 0.000 ARG C 492 *********************** 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 95 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.7968 (m-80) cc_final: 0.7407 (m-10) REVERT: B 156 SER cc_start: 0.9321 (p) cc_final: 0.9008 (m) REVERT: D 147 LEU cc_start: 0.6584 (OUTLIER) cc_final: 0.6324 (tt) REVERT: D 218 GLU cc_start: 0.7033 (pm20) cc_final: 0.5203 (mt-10) REVERT: D 224 LYS cc_start: 0.5900 (tptt) cc_final: 0.5636 (tptp) outliers start: 25 outliers final: 23 residues processed: 87 average time/residue: 0.3521 time to fit residues: 43.5522 Evaluate side-chains 92 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 488 HIS 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 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 54 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 17 optimal weight: 0.0270 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7290 Z= 0.154 Angle : 0.528 6.533 9948 Z= 0.269 Chirality : 0.044 0.139 1126 Planarity : 0.004 0.037 1286 Dihedral : 4.166 21.493 1034 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.93 % Favored : 89.07 % Rotamer: Outliers : 3.52 % Allowed : 23.85 % Favored : 72.63 % 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: -2.62 (0.27), residues: 942 helix: -0.22 (1.03), residues: 26 sheet: -0.44 (0.32), residues: 294 loop : -2.66 (0.24), residues: 622 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 0.008 0.001 PHE C 509 TYR 0.011 0.001 TYR B 50 ARG 0.003 0.000 ARG C 492 *********************** 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 97 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: A 43 GLN cc_start: 0.6497 (tm-30) cc_final: 0.6147 (tm-30) REVERT: B 37 TYR cc_start: 0.7882 (m-80) cc_final: 0.7242 (m-10) REVERT: B 156 SER cc_start: 0.9320 (p) cc_final: 0.9018 (m) REVERT: D 218 GLU cc_start: 0.7012 (pm20) cc_final: 0.5194 (mt-10) REVERT: D 224 LYS cc_start: 0.5830 (tptt) cc_final: 0.5579 (tptp) outliers start: 26 outliers final: 24 residues processed: 91 average time/residue: 0.3832 time to fit residues: 48.4402 Evaluate side-chains 95 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 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 488 HIS 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 217 VAL Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 206 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.1980 chunk 87 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 26 optimal weight: 0.3980 chunk 77 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7290 Z= 0.190 Angle : 0.546 6.535 9948 Z= 0.280 Chirality : 0.045 0.138 1126 Planarity : 0.004 0.036 1286 Dihedral : 4.291 21.484 1034 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.10 % Favored : 87.90 % Rotamer: Outliers : 3.52 % Allowed : 24.12 % Favored : 72.36 % 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: -0.32 (1.01), residues: 26 sheet: -0.67 (0.31), residues: 307 loop : -2.65 (0.24), residues: 609 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 0.011 0.001 PHE E 139 TYR 0.012 0.001 TYR B 50 ARG 0.002 0.000 ARG C 492 *********************** 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 96 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 70 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: A 43 GLN cc_start: 0.6789 (tm-30) cc_final: 0.6562 (tm-30) REVERT: A 189 THR cc_start: 0.7001 (OUTLIER) cc_final: 0.6713 (t) REVERT: B 156 SER cc_start: 0.9324 (p) cc_final: 0.9014 (m) outliers start: 26 outliers final: 24 residues processed: 90 average time/residue: 0.3456 time to fit residues: 44.4731 Evaluate side-chains 96 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 70 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 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 488 HIS 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 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 42 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7290 Z= 0.235 Angle : 0.583 6.585 9948 Z= 0.302 Chirality : 0.046 0.141 1126 Planarity : 0.004 0.038 1286 Dihedral : 4.601 20.751 1034 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.21 % Allowed : 13.27 % Favored : 86.52 % Rotamer: Outliers : 3.66 % Allowed : 23.98 % Favored : 72.36 % 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: -2.98 (0.26), residues: 942 helix: -1.66 (0.87), residues: 26 sheet: -0.89 (0.30), residues: 304 loop : -2.75 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 113 HIS 0.002 0.001 HIS C 488 PHE 0.013 0.001 PHE E 139 TYR 0.013 0.001 TYR B 50 ARG 0.002 0.000 ARG B 62 ********************** 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: 27 poor density : 73 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7386 (tt0) REVERT: A 10 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7655 (mp0) REVERT: A 43 GLN cc_start: 0.6898 (tm-30) cc_final: 0.6652 (tm-30) REVERT: A 189 THR cc_start: 0.7140 (OUTLIER) cc_final: 0.6869 (t) outliers start: 27 outliers final: 23 residues processed: 94 average time/residue: 0.3289 time to fit residues: 43.7751 Evaluate side-chains 96 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 70 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN 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 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 488 HIS 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 175 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 202 CYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 206 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 0.0170 chunk 75 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 = 0.4564 r_free = 0.4564 target = 0.207864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.174508 restraints weight = 30975.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.174233 restraints weight = 31433.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.177266 restraints weight = 26640.703| |-----------------------------------------------------------------------------| r_work (final): 0.4305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.235 7290 Z= 0.273 Angle : 0.945 59.049 9948 Z= 0.557 Chirality : 0.047 0.444 1126 Planarity : 0.004 0.038 1286 Dihedral : 4.595 21.088 1034 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.21 % Allowed : 13.38 % Favored : 86.41 % Rotamer: Outliers : 3.66 % Allowed : 23.98 % Favored : 72.36 % 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: -3.01 (0.26), residues: 942 helix: -1.69 (0.86), residues: 26 sheet: -0.98 (0.30), residues: 311 loop : -2.74 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 113 HIS 0.002 0.001 HIS A 170 PHE 0.012 0.001 PHE E 139 TYR 0.013 0.001 TYR B 50 ARG 0.002 0.000 ARG B 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3114.08 seconds wall clock time: 56 minutes 35.33 seconds (3395.33 seconds total)