Starting phenix.real_space_refine on Thu Mar 14 21:33:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wfg_32465/03_2024/7wfg_32465_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wfg_32465/03_2024/7wfg_32465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wfg_32465/03_2024/7wfg_32465.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wfg_32465/03_2024/7wfg_32465.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wfg_32465/03_2024/7wfg_32465_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wfg_32465/03_2024/7wfg_32465_updated.pdb" } resolution = 4.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 12 7.16 5 S 64 5.16 5 C 6304 2.51 5 N 1677 2.21 5 O 1779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H ARG 225": "NH1" <-> "NH2" Residue "H ARG 329": "NH1" <-> "NH2" Residue "H ARG 351": "NH1" <-> "NH2" Residue "I ARG 35": "NH1" <-> "NH2" Residue "I ARG 56": "NH1" <-> "NH2" Residue "I ARG 72": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "K ARG 66": "NH1" <-> "NH2" Residue "K ARG 70": "NH1" <-> "NH2" Residue "K ARG 91": "NH1" <-> "NH2" Residue "K ARG 124": "NH1" <-> "NH2" Residue "K ARG 167": "NH1" <-> "NH2" Residue "L ARG 156": "NH1" <-> "NH2" Residue "M ARG 172": "NH1" <-> "NH2" Residue "N ARG 88": "NH1" <-> "NH2" Residue "N ARG 92": "NH1" <-> "NH2" Residue "O ARG 120": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9836 Number of models: 1 Model: "" Number of chains: 11 Chain: "H" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2812 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 20, 'TRANS': 335} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'TRP:plan': 1, 'PHE:plan': 5, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 86 Chain: "I" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1236 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 152} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "J" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1120 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 146} Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 118 Chain: "K" Number of atoms: 1199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1199 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 12, 'TRANS': 154} Chain breaks: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 66 Chain: "L" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 646 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 70} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'PHE:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "M" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 767 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain breaks: 1 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 110 Chain: "N" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 909 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 13, 'TRANS': 132} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 290 Unresolved non-hydrogen angles: 396 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 5, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 7, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 183 Chain: "O" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 520 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain breaks: 2 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "T" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 603 Classifications: {'peptide': 122} Incomplete info: {'backbone_only': 7, 'truncation_to_alanine': 115} Link IDs: {'TRANS': 121} Unresolved non-hydrogen bonds: 251 Unresolved non-hydrogen angles: 380 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'UNK:plan-1': 122} Unresolved non-hydrogen planarities: 122 Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3592 SG CYS I 110 39.258 36.676 84.998 1.00144.09 S ATOM 5818 SG CYS K 108 52.007 42.309 71.485 1.00166.07 S Time building chain proxies: 5.65, per 1000 atoms: 0.57 Number of scatterers: 9836 At special positions: 0 Unit cell: (113.36, 119.6, 121.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 12 26.01 S 64 16.00 O 1779 8.00 N 1677 7.00 C 6304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.46 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 I 201 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 110 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 104 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 74 " pdb=" SF4 I 202 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 114 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 67 " pdb=" SF4 K 301 " pdb="FE4 SF4 K 301 " - pdb=" SG CYS K 108 " Number of angles added : 18 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2568 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 8 sheets defined 35.9% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'H' and resid 51 through 57 Processing helix chain 'H' and resid 60 through 63 No H-bonds generated for 'chain 'H' and resid 60 through 63' Processing helix chain 'H' and resid 75 through 90 removed outlier: 3.691A pdb=" N GLU H 79 " --> pdb=" O THR H 75 " (cutoff:3.500A) Proline residue: H 86 - end of helix Processing helix chain 'H' and resid 96 through 124 Proline residue: H 120 - end of helix Processing helix chain 'H' and resid 135 through 148 removed outlier: 4.614A pdb=" N PHE H 140 " --> pdb=" O ARG H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 195 removed outlier: 4.180A pdb=" N CYS H 179 " --> pdb=" O CYS H 175 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASP H 180 " --> pdb=" O LEU H 176 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N THR H 184 " --> pdb=" O ASP H 180 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLU H 185 " --> pdb=" O TYR H 181 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS H 191 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU H 192 " --> pdb=" O GLU H 188 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ILE H 193 " --> pdb=" O TYR H 189 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N THR H 194 " --> pdb=" O GLN H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 214 No H-bonds generated for 'chain 'H' and resid 211 through 214' Processing helix chain 'H' and resid 222 through 227 removed outlier: 4.756A pdb=" N SER H 227 " --> pdb=" O MET H 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 236 No H-bonds generated for 'chain 'H' and resid 233 through 236' Processing helix chain 'H' and resid 257 through 277 Processing helix chain 'H' and resid 357 through 364 removed outlier: 4.044A pdb=" N GLN H 363 " --> pdb=" O PHE H 359 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE H 364 " --> pdb=" O ILE H 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 374 through 383 removed outlier: 4.367A pdb=" N MET H 378 " --> pdb=" O LEU H 374 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N THR H 379 " --> pdb=" O ALA H 375 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 34 removed outlier: 3.871A pdb=" N ASN I 34 " --> pdb=" O LEU I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 143 No H-bonds generated for 'chain 'I' and resid 141 through 143' Processing helix chain 'I' and resid 149 through 151 No H-bonds generated for 'chain 'I' and resid 149 through 151' Processing helix chain 'J' and resid 37 through 44 Processing helix chain 'J' and resid 108 through 117 Processing helix chain 'J' and resid 152 through 154 No H-bonds generated for 'chain 'J' and resid 152 through 154' Processing helix chain 'K' and resid 17 through 30 Processing helix chain 'K' and resid 43 through 47 removed outlier: 3.824A pdb=" N ILE K 46 " --> pdb=" O CYS K 43 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU K 47 " --> pdb=" O CYS K 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 43 through 47' Processing helix chain 'K' and resid 83 through 96 Proline residue: K 87 - end of helix Processing helix chain 'K' and resid 113 through 115 No H-bonds generated for 'chain 'K' and resid 113 through 115' Processing helix chain 'K' and resid 126 through 128 No H-bonds generated for 'chain 'K' and resid 126 through 128' Processing helix chain 'K' and resid 143 through 159 removed outlier: 4.071A pdb=" N ILE K 147 " --> pdb=" O PRO K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 162 through 165 Processing helix chain 'L' and resid 98 through 118 removed outlier: 4.048A pdb=" N MET L 108 " --> pdb=" O TYR L 104 " (cutoff:3.500A) Proline residue: L 109 - end of helix Processing helix chain 'L' and resid 125 through 137 Processing helix chain 'L' and resid 140 through 143 removed outlier: 3.849A pdb=" N LEU L 143 " --> pdb=" O PRO L 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 140 through 143' Processing helix chain 'M' and resid 133 through 149 Processing helix chain 'M' and resid 157 through 176 Processing helix chain 'N' and resid 64 through 71 Processing helix chain 'N' and resid 87 through 95 Processing helix chain 'N' and resid 111 through 115 Processing helix chain 'N' and resid 140 through 144 Processing helix chain 'N' and resid 167 through 179 Proline residue: N 176 - end of helix Processing helix chain 'T' and resid 3 through 5 No H-bonds generated for 'chain 'T' and resid 3 through 5' Processing helix chain 'T' and resid 14 through 17 No H-bonds generated for 'chain 'T' and resid 14 through 17' Processing helix chain 'T' and resid 26 through 38 Processing helix chain 'T' and resid 45 through 61 Processing helix chain 'T' and resid 63 through 72 Processing helix chain 'T' and resid 99 through 120 Processing sheet with id= A, first strand: chain 'H' and resid 27 through 30 removed outlier: 3.521A pdb=" N ARG H 27 " --> pdb=" O ILE H 43 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE H 29 " --> pdb=" O GLU H 41 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 325 through 330 Processing sheet with id= C, first strand: chain 'J' and resid 28 through 31 removed outlier: 6.737A pdb=" N CYS J 85 " --> pdb=" O LEU J 29 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE J 31 " --> pdb=" O CYS J 85 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LYS J 87 " --> pdb=" O ILE J 31 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'J' and resid 64 through 66 Processing sheet with id= E, first strand: chain 'J' and resid 96 through 98 removed outlier: 5.833A pdb=" N THR J 121 " --> pdb=" O ILE J 97 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'N' and resid 75 through 78 Processing sheet with id= G, first strand: chain 'N' and resid 99 through 103 Processing sheet with id= H, first strand: chain 'O' and resid 140 through 143 removed outlier: 3.926A pdb=" N ASP O 118 " --> pdb=" O LEU O 129 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLY O 131 " --> pdb=" O VAL O 116 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N VAL O 116 " --> pdb=" O GLY O 131 " (cutoff:3.500A) 290 hydrogen bonds defined for protein. 852 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.42: 3991 1.42 - 1.64: 5927 1.64 - 1.86: 82 1.86 - 2.09: 0 2.09 - 2.31: 36 Bond restraints: 10036 Sorted by residual: bond pdb=" C ARG L 152 " pdb=" N LYS L 153 " ideal model delta sigma weight residual 1.332 1.201 0.132 1.40e-02 5.10e+03 8.86e+01 bond pdb=" C GLU I 68 " pdb=" N VAL I 69 " ideal model delta sigma weight residual 1.334 1.265 0.068 1.28e-02 6.10e+03 2.86e+01 bond pdb=" C PRO N 148 " pdb=" N PRO N 149 " ideal model delta sigma weight residual 1.326 1.392 -0.065 1.44e-02 4.82e+03 2.07e+01 bond pdb=" N ARG N 179 " pdb=" CA ARG N 179 " ideal model delta sigma weight residual 1.462 1.493 -0.031 7.70e-03 1.69e+04 1.62e+01 bond pdb=" N LEU N 175 " pdb=" CA LEU N 175 " ideal model delta sigma weight residual 1.463 1.490 -0.027 6.90e-03 2.10e+04 1.51e+01 ... (remaining 10031 not shown) Histogram of bond angle deviations from ideal: 72.25 - 84.75: 36 84.75 - 97.25: 0 97.25 - 109.75: 1332 109.75 - 122.25: 10465 122.25 - 134.75: 1811 Bond angle restraints: 13644 Sorted by residual: angle pdb=" N PRO K 140 " pdb=" CA PRO K 140 " pdb=" C PRO K 140 " ideal model delta sigma weight residual 110.70 120.21 -9.51 1.22e+00 6.72e-01 6.08e+01 angle pdb=" N SER N 177 " pdb=" CA SER N 177 " pdb=" C SER N 177 " ideal model delta sigma weight residual 113.23 104.14 9.09 1.24e+00 6.50e-01 5.37e+01 angle pdb=" N LEU K 37 " pdb=" CA LEU K 37 " pdb=" C LEU K 37 " ideal model delta sigma weight residual 113.02 106.16 6.86 1.20e+00 6.94e-01 3.27e+01 angle pdb=" N PRO L 109 " pdb=" CA PRO L 109 " pdb=" C PRO L 109 " ideal model delta sigma weight residual 110.70 117.06 -6.36 1.22e+00 6.72e-01 2.72e+01 angle pdb=" N ASN N 181 " pdb=" CA ASN N 181 " pdb=" C ASN N 181 " ideal model delta sigma weight residual 114.39 107.58 6.81 1.45e+00 4.76e-01 2.21e+01 ... (remaining 13639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.90: 5624 14.90 - 29.80: 312 29.80 - 44.70: 96 44.70 - 59.60: 26 59.60 - 74.51: 2 Dihedral angle restraints: 6060 sinusoidal: 2097 harmonic: 3963 Sorted by residual: dihedral pdb=" CA THR K 117 " pdb=" C THR K 117 " pdb=" N ASP K 118 " pdb=" CA ASP K 118 " ideal model delta harmonic sigma weight residual -180.00 -153.96 -26.04 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA GLY H 218 " pdb=" C GLY H 218 " pdb=" N LEU H 219 " pdb=" CA LEU H 219 " ideal model delta harmonic sigma weight residual 180.00 -154.68 -25.32 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA ARG L 152 " pdb=" C ARG L 152 " pdb=" N LYS L 153 " pdb=" CA LYS L 153 " ideal model delta harmonic sigma weight residual 180.00 155.93 24.07 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 6057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1231 0.070 - 0.139: 265 0.139 - 0.209: 52 0.209 - 0.278: 14 0.278 - 0.348: 1 Chirality restraints: 1563 Sorted by residual: chirality pdb=" CA LEU H 32 " pdb=" N LEU H 32 " pdb=" C LEU H 32 " pdb=" CB LEU H 32 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CA ARG M 161 " pdb=" N ARG M 161 " pdb=" C ARG M 161 " pdb=" CB ARG M 161 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB ILE I 65 " pdb=" CA ILE I 65 " pdb=" CG1 ILE I 65 " pdb=" CG2 ILE I 65 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1560 not shown) Planarity restraints: 1745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU K 136 " -0.042 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO K 137 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO K 137 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO K 137 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 64 " 0.041 5.00e-02 4.00e+02 6.15e-02 6.06e+00 pdb=" N PRO H 65 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO H 65 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 65 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP J 140 " 0.040 5.00e-02 4.00e+02 6.01e-02 5.79e+00 pdb=" N PRO J 141 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO J 141 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO J 141 " 0.033 5.00e-02 4.00e+02 ... (remaining 1742 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 841 2.74 - 3.28: 9665 3.28 - 3.82: 16362 3.82 - 4.36: 18461 4.36 - 4.90: 30580 Nonbonded interactions: 75909 Sorted by model distance: nonbonded pdb=" OE2 GLU H 146 " pdb=" N SER I 50 " model vdw 2.204 2.520 nonbonded pdb=" CB ALA H 165 " pdb=" NH1 ARG I 52 " model vdw 2.248 3.540 nonbonded pdb=" NZ LYS N 128 " pdb=" O PRO O 136 " model vdw 2.257 2.520 nonbonded pdb=" O VAL H 203 " pdb=" OG SER H 257 " model vdw 2.301 2.440 nonbonded pdb=" NH2 ARG H 136 " pdb=" O HIS I 32 " model vdw 2.304 2.520 ... (remaining 75904 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 13.740 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 29.310 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.132 10036 Z= 0.365 Angle : 1.008 9.753 13644 Z= 0.593 Chirality : 0.063 0.348 1563 Planarity : 0.007 0.064 1745 Dihedral : 11.464 74.505 3492 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.27 % Favored : 87.48 % Rotamer: Outliers : 1.08 % Allowed : 3.11 % Favored : 95.81 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.06 (0.18), residues: 1214 helix: -3.16 (0.16), residues: 405 sheet: -2.66 (0.48), residues: 93 loop : -3.76 (0.19), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 117 HIS 0.008 0.001 HIS M 169 PHE 0.016 0.002 PHE H 182 TYR 0.016 0.002 TYR J 57 ARG 0.015 0.001 ARG H 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 262 time to evaluate : 1.180 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE H 132 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.7825 (tpt) cc_final: 0.7336 (tpp) REVERT: H 47 LEU cc_start: 0.9296 (tp) cc_final: 0.8851 (tp) REVERT: H 49 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7844 (mpp80) REVERT: H 105 MET cc_start: 0.9533 (ptp) cc_final: 0.9057 (ptt) REVERT: H 156 ASN cc_start: 0.9382 (t0) cc_final: 0.9130 (t0) REVERT: H 171 TRP cc_start: 0.9322 (t60) cc_final: 0.9042 (t60) REVERT: H 261 TYR cc_start: 0.8837 (t80) cc_final: 0.8626 (t80) REVERT: H 262 LEU cc_start: 0.9547 (mt) cc_final: 0.9286 (pp) REVERT: H 378 MET cc_start: 0.9076 (mmp) cc_final: 0.8669 (mmp) REVERT: H 381 LEU cc_start: 0.9450 (pp) cc_final: 0.8455 (pp) REVERT: H 384 ILE cc_start: 0.9671 (mm) cc_final: 0.9321 (tp) REVERT: H 390 GLU cc_start: 0.9130 (pt0) cc_final: 0.8798 (pt0) REVERT: I 85 LEU cc_start: 0.8474 (mt) cc_final: 0.7835 (tp) REVERT: I 100 ASP cc_start: 0.8560 (t0) cc_final: 0.7633 (t70) REVERT: I 101 PHE cc_start: 0.9240 (m-10) cc_final: 0.8995 (m-80) REVERT: I 103 ILE cc_start: 0.9528 (mm) cc_final: 0.9170 (mm) REVERT: I 134 GLU cc_start: 0.8639 (tt0) cc_final: 0.8424 (tm-30) REVERT: I 137 TYR cc_start: 0.7528 (m-10) cc_final: 0.6809 (m-10) REVERT: J 51 LEU cc_start: 0.8577 (tp) cc_final: 0.8373 (tp) REVERT: J 71 LEU cc_start: 0.8562 (tp) cc_final: 0.8171 (tp) REVERT: J 111 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8535 (mm-30) REVERT: J 128 LEU cc_start: 0.8978 (tp) cc_final: 0.8569 (mt) REVERT: K 103 ILE cc_start: 0.9291 (mm) cc_final: 0.8892 (mp) REVERT: K 144 GLU cc_start: 0.8132 (mp0) cc_final: 0.7815 (tp30) REVERT: L 128 MET cc_start: 0.8939 (mmm) cc_final: 0.8601 (mmt) REVERT: L 142 LEU cc_start: 0.8682 (mm) cc_final: 0.8471 (mm) REVERT: L 144 LEU cc_start: 0.8174 (pt) cc_final: 0.7949 (pt) REVERT: L 160 MET cc_start: 0.7307 (mpp) cc_final: 0.6776 (tpp) REVERT: N 140 VAL cc_start: 0.9093 (m) cc_final: 0.8871 (p) outliers start: 9 outliers final: 3 residues processed: 268 average time/residue: 0.2346 time to fit residues: 84.7160 Evaluate side-chains 176 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 172 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 9.9990 chunk 100 optimal weight: 0.0070 chunk 55 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 77 optimal weight: 0.3980 chunk 120 optimal weight: 0.0020 overall best weight: 0.8810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 18 HIS H 23 HIS H 363 GLN I 10 ASN ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 54 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10036 Z= 0.165 Angle : 0.626 11.994 13644 Z= 0.311 Chirality : 0.044 0.147 1563 Planarity : 0.005 0.060 1745 Dihedral : 5.036 30.839 1452 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 0.36 % Allowed : 4.55 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.67 (0.21), residues: 1214 helix: -1.48 (0.22), residues: 418 sheet: -1.85 (0.52), residues: 91 loop : -3.29 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 117 HIS 0.009 0.002 HIS M 96 PHE 0.021 0.001 PHE H 182 TYR 0.019 0.001 TYR M 100 ARG 0.006 0.000 ARG I 17 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 200 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.7546 (tpt) cc_final: 0.7175 (tpp) REVERT: H 47 LEU cc_start: 0.9261 (tp) cc_final: 0.8967 (tp) REVERT: H 76 MET cc_start: 0.8946 (mtt) cc_final: 0.8580 (mtm) REVERT: H 122 MET cc_start: 0.7832 (tpt) cc_final: 0.7144 (tmm) REVERT: H 171 TRP cc_start: 0.9353 (t60) cc_final: 0.9050 (t60) REVERT: H 261 TYR cc_start: 0.8924 (t80) cc_final: 0.8667 (t80) REVERT: H 262 LEU cc_start: 0.9566 (mt) cc_final: 0.9292 (tt) REVERT: H 381 LEU cc_start: 0.8939 (pp) cc_final: 0.8657 (pp) REVERT: I 9 MET cc_start: 0.1611 (tmm) cc_final: 0.1264 (tmm) REVERT: I 101 PHE cc_start: 0.9230 (m-10) cc_final: 0.8369 (m-80) REVERT: I 137 TYR cc_start: 0.7727 (m-10) cc_final: 0.7415 (m-10) REVERT: J 128 LEU cc_start: 0.9038 (tp) cc_final: 0.8797 (tp) REVERT: J 133 MET cc_start: 0.8133 (mmm) cc_final: 0.7763 (mmt) REVERT: K 114 MET cc_start: 0.8895 (pmm) cc_final: 0.8454 (pmm) REVERT: K 144 GLU cc_start: 0.8544 (mp0) cc_final: 0.8018 (tp30) REVERT: L 128 MET cc_start: 0.8957 (mmm) cc_final: 0.8623 (mmt) REVERT: L 144 LEU cc_start: 0.8462 (pt) cc_final: 0.8063 (tt) REVERT: M 100 TYR cc_start: 0.8159 (m-80) cc_final: 0.7954 (m-80) outliers start: 3 outliers final: 3 residues processed: 201 average time/residue: 0.1967 time to fit residues: 56.6278 Evaluate side-chains 158 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 155 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 82 optimal weight: 0.4980 chunk 33 optimal weight: 0.1980 chunk 120 optimal weight: 10.0000 chunk 130 optimal weight: 20.0000 chunk 107 optimal weight: 0.0870 chunk 119 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10036 Z= 0.173 Angle : 0.608 10.054 13644 Z= 0.301 Chirality : 0.043 0.146 1563 Planarity : 0.005 0.066 1745 Dihedral : 4.762 27.761 1452 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.38 % Favored : 89.54 % Rotamer: Outliers : 0.36 % Allowed : 2.75 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.23), residues: 1214 helix: -0.64 (0.24), residues: 426 sheet: -1.92 (0.50), residues: 92 loop : -3.05 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 83 HIS 0.007 0.001 HIS H 155 PHE 0.016 0.001 PHE K 45 TYR 0.012 0.001 TYR M 100 ARG 0.006 0.000 ARG M 161 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 184 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.7675 (tpt) cc_final: 0.7214 (tpp) REVERT: H 76 MET cc_start: 0.9010 (mtt) cc_final: 0.8757 (ttm) REVERT: H 79 GLU cc_start: 0.8647 (tt0) cc_final: 0.7872 (mm-30) REVERT: H 261 TYR cc_start: 0.9051 (t80) cc_final: 0.8800 (t80) REVERT: H 262 LEU cc_start: 0.9594 (mt) cc_final: 0.9313 (pp) REVERT: H 378 MET cc_start: 0.9166 (mmp) cc_final: 0.8883 (mmp) REVERT: I 9 MET cc_start: 0.2154 (tmm) cc_final: 0.1799 (tmm) REVERT: I 100 ASP cc_start: 0.8476 (t0) cc_final: 0.8244 (t70) REVERT: I 101 PHE cc_start: 0.9176 (m-10) cc_final: 0.8190 (m-80) REVERT: J 69 TYR cc_start: 0.7399 (m-10) cc_final: 0.6430 (m-10) REVERT: J 128 LEU cc_start: 0.9037 (tp) cc_final: 0.8802 (tp) REVERT: K 114 MET cc_start: 0.8980 (pmm) cc_final: 0.8263 (pmm) REVERT: K 144 GLU cc_start: 0.8625 (mp0) cc_final: 0.8027 (tp30) REVERT: L 128 MET cc_start: 0.8914 (mmm) cc_final: 0.8648 (mmt) REVERT: L 144 LEU cc_start: 0.8563 (pt) cc_final: 0.8173 (pt) REVERT: M 100 TYR cc_start: 0.8206 (m-80) cc_final: 0.7990 (m-80) outliers start: 3 outliers final: 3 residues processed: 185 average time/residue: 0.2034 time to fit residues: 53.8419 Evaluate side-chains 149 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 146 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 48 HIS H 93 GLN H 361 ASN J 110 GLN M 169 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.6153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 10036 Z= 0.364 Angle : 0.823 11.217 13644 Z= 0.421 Chirality : 0.049 0.228 1563 Planarity : 0.007 0.080 1745 Dihedral : 5.992 24.549 1452 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 30.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.77 % Favored : 87.15 % Rotamer: Outliers : 0.36 % Allowed : 4.90 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.24), residues: 1214 helix: -0.54 (0.25), residues: 424 sheet: -2.10 (0.50), residues: 94 loop : -2.86 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP I 83 HIS 0.012 0.003 HIS J 70 PHE 0.019 0.002 PHE K 115 TYR 0.025 0.002 TYR M 158 ARG 0.010 0.001 ARG H 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 158 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.8639 (tpt) cc_final: 0.8108 (tpp) REVERT: H 76 MET cc_start: 0.9164 (mtt) cc_final: 0.8801 (mtm) REVERT: H 223 MET cc_start: 0.9221 (mpp) cc_final: 0.8880 (mpp) REVERT: H 262 LEU cc_start: 0.9717 (mt) cc_final: 0.9463 (pp) REVERT: H 352 TRP cc_start: 0.9032 (t-100) cc_final: 0.8711 (t-100) REVERT: H 390 GLU cc_start: 0.9277 (pt0) cc_final: 0.8978 (pt0) REVERT: I 9 MET cc_start: 0.1660 (tmm) cc_final: 0.1380 (tmm) REVERT: I 100 ASP cc_start: 0.8658 (t0) cc_final: 0.7949 (t70) REVERT: I 101 PHE cc_start: 0.9084 (m-10) cc_final: 0.8809 (m-10) REVERT: I 103 ILE cc_start: 0.9488 (mm) cc_final: 0.9201 (mm) REVERT: I 113 TYR cc_start: 0.9539 (m-80) cc_final: 0.9181 (m-10) REVERT: J 70 HIS cc_start: 0.7172 (m90) cc_final: 0.6911 (m90) REVERT: J 133 MET cc_start: 0.8820 (mmm) cc_final: 0.8382 (mmm) REVERT: K 85 MET cc_start: 0.9411 (mmp) cc_final: 0.8902 (mmp) REVERT: K 114 MET cc_start: 0.9235 (pmm) cc_final: 0.8542 (pmm) REVERT: K 133 ASP cc_start: 0.8914 (m-30) cc_final: 0.8680 (m-30) REVERT: K 144 GLU cc_start: 0.9015 (mp0) cc_final: 0.8076 (tp30) REVERT: K 148 ASP cc_start: 0.9273 (m-30) cc_final: 0.8547 (m-30) REVERT: L 108 MET cc_start: 0.8679 (mpp) cc_final: 0.8437 (mpp) REVERT: L 138 PHE cc_start: 0.9022 (m-80) cc_final: 0.8794 (m-80) REVERT: L 144 LEU cc_start: 0.8555 (pt) cc_final: 0.8319 (tp) outliers start: 3 outliers final: 3 residues processed: 161 average time/residue: 0.1665 time to fit residues: 40.2433 Evaluate side-chains 134 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 131 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 95 optimal weight: 0.0030 chunk 53 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 chunk 88 optimal weight: 0.0770 chunk 0 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.5350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 18 HIS H 361 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.5746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10036 Z= 0.161 Angle : 0.649 10.570 13644 Z= 0.316 Chirality : 0.045 0.142 1563 Planarity : 0.005 0.067 1745 Dihedral : 5.050 24.375 1452 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 0.36 % Allowed : 1.91 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.24), residues: 1214 helix: -0.14 (0.26), residues: 437 sheet: -2.12 (0.47), residues: 100 loop : -2.85 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 217 HIS 0.008 0.001 HIS H 155 PHE 0.020 0.001 PHE K 115 TYR 0.016 0.001 TYR L 129 ARG 0.004 0.000 ARG I 17 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 176 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.8515 (tpt) cc_final: 0.7986 (tpp) REVERT: H 76 MET cc_start: 0.8812 (mtt) cc_final: 0.8482 (mtm) REVERT: H 79 GLU cc_start: 0.8943 (tt0) cc_final: 0.8021 (tm-30) REVERT: H 154 MET cc_start: 0.6769 (mtt) cc_final: 0.6531 (mtt) REVERT: H 262 LEU cc_start: 0.9734 (mt) cc_final: 0.9436 (pp) REVERT: H 390 GLU cc_start: 0.9300 (pt0) cc_final: 0.8938 (pt0) REVERT: I 113 TYR cc_start: 0.9233 (m-80) cc_final: 0.8896 (m-80) REVERT: I 137 TYR cc_start: 0.7881 (m-80) cc_final: 0.7438 (m-10) REVERT: J 120 ILE cc_start: 0.9580 (mt) cc_final: 0.9330 (mm) REVERT: J 133 MET cc_start: 0.8857 (mmm) cc_final: 0.8458 (mmm) REVERT: K 37 LEU cc_start: 0.7329 (tp) cc_final: 0.6992 (tp) REVERT: K 85 MET cc_start: 0.9347 (mmp) cc_final: 0.8793 (mmp) REVERT: K 114 MET cc_start: 0.9169 (pmm) cc_final: 0.8636 (pmm) REVERT: K 144 GLU cc_start: 0.9073 (mp0) cc_final: 0.8136 (tp30) REVERT: K 148 ASP cc_start: 0.9381 (m-30) cc_final: 0.8686 (m-30) REVERT: K 153 LEU cc_start: 0.9649 (mm) cc_final: 0.9443 (mm) REVERT: L 108 MET cc_start: 0.8645 (mpp) cc_final: 0.8371 (mpp) REVERT: L 142 LEU cc_start: 0.8912 (mm) cc_final: 0.8712 (mm) REVERT: L 144 LEU cc_start: 0.8370 (pt) cc_final: 0.7772 (pt) REVERT: M 100 TYR cc_start: 0.8439 (m-80) cc_final: 0.8048 (m-80) outliers start: 3 outliers final: 3 residues processed: 178 average time/residue: 0.2053 time to fit residues: 54.4663 Evaluate side-chains 143 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 140 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 361 ASN I 24 GLN ** J 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.7686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 10036 Z= 0.429 Angle : 0.869 11.561 13644 Z= 0.448 Chirality : 0.051 0.207 1563 Planarity : 0.006 0.059 1745 Dihedral : 6.310 25.887 1452 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 34.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.00 % Favored : 85.83 % Rotamer: Outliers : 0.36 % Allowed : 3.47 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.02 (0.23), residues: 1214 helix: -0.86 (0.24), residues: 447 sheet: -2.46 (0.50), residues: 89 loop : -2.86 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP H 352 HIS 0.008 0.002 HIS H 155 PHE 0.021 0.002 PHE H 340 TYR 0.023 0.002 TYR M 158 ARG 0.017 0.001 ARG H 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 150 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.8847 (tpt) cc_final: 0.8359 (tpp) REVERT: H 47 LEU cc_start: 0.9365 (tp) cc_final: 0.9120 (tp) REVERT: H 76 MET cc_start: 0.9200 (mtt) cc_final: 0.8792 (ttm) REVERT: H 105 MET cc_start: 0.9296 (ptt) cc_final: 0.8965 (ptt) REVERT: H 154 MET cc_start: 0.7163 (mtt) cc_final: 0.6914 (mtt) REVERT: H 223 MET cc_start: 0.9139 (mpp) cc_final: 0.8860 (mpp) REVERT: H 340 PHE cc_start: 0.8736 (t80) cc_final: 0.8509 (t80) REVERT: H 352 TRP cc_start: 0.8925 (t-100) cc_final: 0.8302 (t-100) REVERT: H 388 MET cc_start: 0.8809 (ptm) cc_final: 0.8078 (tmm) REVERT: I 100 ASP cc_start: 0.8761 (t0) cc_final: 0.8232 (t70) REVERT: I 103 ILE cc_start: 0.9541 (mm) cc_final: 0.9308 (mm) REVERT: I 113 TYR cc_start: 0.9598 (m-80) cc_final: 0.9288 (m-10) REVERT: I 137 TYR cc_start: 0.8004 (m-80) cc_final: 0.7534 (m-10) REVERT: J 50 TYR cc_start: 0.7963 (t80) cc_final: 0.7287 (t80) REVERT: J 133 MET cc_start: 0.8934 (mmm) cc_final: 0.8703 (mmm) REVERT: K 85 MET cc_start: 0.9170 (mmp) cc_final: 0.8539 (mmp) REVERT: K 114 MET cc_start: 0.8955 (pmm) cc_final: 0.8751 (pmm) REVERT: K 115 PHE cc_start: 0.9290 (m-10) cc_final: 0.8860 (m-10) REVERT: K 133 ASP cc_start: 0.8924 (m-30) cc_final: 0.8635 (m-30) REVERT: K 180 LYS cc_start: 0.8043 (mmmm) cc_final: 0.7722 (mmtt) REVERT: L 108 MET cc_start: 0.8993 (mpp) cc_final: 0.8753 (mpp) REVERT: L 128 MET cc_start: 0.9025 (mmm) cc_final: 0.8698 (mmt) outliers start: 3 outliers final: 3 residues processed: 152 average time/residue: 0.1734 time to fit residues: 39.6635 Evaluate side-chains 119 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 116 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 20.0000 chunk 14 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 80 optimal weight: 0.3980 chunk 78 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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: 0.7506 moved from start: 0.7316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10036 Z= 0.184 Angle : 0.648 11.556 13644 Z= 0.323 Chirality : 0.045 0.146 1563 Planarity : 0.004 0.056 1745 Dihedral : 5.385 23.366 1452 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.13 % Favored : 89.79 % Rotamer: Outliers : 0.36 % Allowed : 1.32 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.24), residues: 1214 helix: -0.36 (0.25), residues: 448 sheet: -2.41 (0.46), residues: 99 loop : -2.74 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 352 HIS 0.006 0.001 HIS H 155 PHE 0.016 0.001 PHE K 115 TYR 0.016 0.001 TYR J 57 ARG 0.004 0.000 ARG H 138 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 159 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.8765 (tpt) cc_final: 0.8406 (tpp) REVERT: H 76 MET cc_start: 0.8868 (mtt) cc_final: 0.8518 (ttm) REVERT: H 105 MET cc_start: 0.9187 (ptt) cc_final: 0.8869 (ptt) REVERT: H 208 ILE cc_start: 0.9249 (pt) cc_final: 0.8862 (mm) REVERT: H 340 PHE cc_start: 0.8564 (t80) cc_final: 0.8254 (t80) REVERT: H 352 TRP cc_start: 0.8671 (t-100) cc_final: 0.7948 (t-100) REVERT: I 100 ASP cc_start: 0.8828 (t0) cc_final: 0.8610 (t70) REVERT: I 137 TYR cc_start: 0.7709 (m-80) cc_final: 0.7186 (m-10) REVERT: J 50 TYR cc_start: 0.7567 (t80) cc_final: 0.7247 (t80) REVERT: J 133 MET cc_start: 0.9063 (mmm) cc_final: 0.8657 (mmm) REVERT: K 85 MET cc_start: 0.9239 (mmp) cc_final: 0.8558 (mmp) REVERT: K 103 ILE cc_start: 0.8622 (mm) cc_final: 0.8394 (mm) REVERT: K 114 MET cc_start: 0.8881 (pmm) cc_final: 0.8674 (pmm) REVERT: K 115 PHE cc_start: 0.9152 (m-10) cc_final: 0.8618 (m-10) REVERT: K 144 GLU cc_start: 0.9343 (mp0) cc_final: 0.8022 (tp30) REVERT: K 148 ASP cc_start: 0.9581 (m-30) cc_final: 0.9278 (m-30) REVERT: K 152 LYS cc_start: 0.9458 (mtmm) cc_final: 0.9145 (mttp) REVERT: K 180 LYS cc_start: 0.7597 (mmmm) cc_final: 0.7383 (mmtt) REVERT: L 108 MET cc_start: 0.8999 (mpp) cc_final: 0.8742 (mpp) REVERT: L 128 MET cc_start: 0.8961 (mmm) cc_final: 0.8686 (mmt) outliers start: 3 outliers final: 3 residues processed: 161 average time/residue: 0.1857 time to fit residues: 43.9420 Evaluate side-chains 140 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 137 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 0.9980 chunk 51 optimal weight: 0.0370 chunk 76 optimal weight: 6.9990 chunk 38 optimal weight: 0.4980 chunk 25 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 63 optimal weight: 0.0570 chunk 11 optimal weight: 3.9990 chunk 100 optimal weight: 0.0970 overall best weight: 0.3374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.7057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10036 Z= 0.152 Angle : 0.647 12.106 13644 Z= 0.311 Chirality : 0.045 0.157 1563 Planarity : 0.004 0.053 1745 Dihedral : 4.824 24.422 1452 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.38 % Favored : 89.54 % Rotamer: Outliers : 0.36 % Allowed : 1.32 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.24), residues: 1214 helix: 0.02 (0.26), residues: 440 sheet: -2.06 (0.47), residues: 99 loop : -2.65 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 171 HIS 0.005 0.001 HIS H 155 PHE 0.020 0.001 PHE K 115 TYR 0.019 0.001 TYR M 100 ARG 0.005 0.000 ARG I 17 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 169 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.8601 (tpt) cc_final: 0.8334 (tpp) REVERT: H 105 MET cc_start: 0.9123 (ptt) cc_final: 0.8916 (ptt) REVERT: H 208 ILE cc_start: 0.9237 (pt) cc_final: 0.8862 (mm) REVERT: H 340 PHE cc_start: 0.8503 (t80) cc_final: 0.8243 (t80) REVERT: H 352 TRP cc_start: 0.8650 (t-100) cc_final: 0.8229 (t-100) REVERT: I 137 TYR cc_start: 0.7758 (m-80) cc_final: 0.7155 (m-80) REVERT: J 50 TYR cc_start: 0.7220 (t80) cc_final: 0.6996 (t80) REVERT: J 133 MET cc_start: 0.8842 (mmm) cc_final: 0.8483 (mmm) REVERT: K 85 MET cc_start: 0.9086 (mmp) cc_final: 0.8468 (mmp) REVERT: K 114 MET cc_start: 0.8682 (pmm) cc_final: 0.8432 (pmm) REVERT: K 115 PHE cc_start: 0.9221 (m-10) cc_final: 0.8653 (m-10) REVERT: K 144 GLU cc_start: 0.9293 (mp0) cc_final: 0.8096 (tp30) REVERT: K 148 ASP cc_start: 0.9549 (m-30) cc_final: 0.8973 (m-30) REVERT: K 152 LYS cc_start: 0.9454 (mtmm) cc_final: 0.9155 (mttp) REVERT: K 180 LYS cc_start: 0.7710 (mmmm) cc_final: 0.7394 (mmtt) REVERT: L 128 MET cc_start: 0.8919 (mmm) cc_final: 0.8660 (mmt) REVERT: L 144 LEU cc_start: 0.7929 (tp) cc_final: 0.7595 (pp) REVERT: M 100 TYR cc_start: 0.8514 (m-80) cc_final: 0.8220 (m-80) outliers start: 3 outliers final: 3 residues processed: 170 average time/residue: 0.1834 time to fit residues: 46.1114 Evaluate side-chains 144 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 141 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 9.9990 chunk 122 optimal weight: 20.0000 chunk 112 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 52 optimal weight: 0.0770 chunk 93 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 361 ASN ** J 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.7942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10036 Z= 0.308 Angle : 0.741 10.076 13644 Z= 0.374 Chirality : 0.047 0.141 1563 Planarity : 0.005 0.055 1745 Dihedral : 5.520 22.866 1452 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 27.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.34 % Favored : 86.49 % Rotamer: Outliers : 0.36 % Allowed : 1.20 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.46 (0.24), residues: 1214 helix: -0.28 (0.24), residues: 450 sheet: -2.49 (0.48), residues: 88 loop : -2.58 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP H 247 HIS 0.008 0.002 HIS H 114 PHE 0.015 0.001 PHE J 89 TYR 0.015 0.002 TYR J 122 ARG 0.007 0.001 ARG H 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 157 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 47 LEU cc_start: 0.9355 (tp) cc_final: 0.8994 (tp) REVERT: H 79 GLU cc_start: 0.9353 (tt0) cc_final: 0.9104 (tt0) REVERT: H 208 ILE cc_start: 0.9312 (pt) cc_final: 0.8975 (mm) REVERT: H 329 ARG cc_start: 0.9373 (pmt170) cc_final: 0.9047 (ptp90) REVERT: H 340 PHE cc_start: 0.8642 (t80) cc_final: 0.8368 (t80) REVERT: H 352 TRP cc_start: 0.8998 (t-100) cc_final: 0.8242 (t-100) REVERT: H 372 MET cc_start: 0.7910 (mpp) cc_final: 0.7705 (mpp) REVERT: H 388 MET cc_start: 0.8864 (ptm) cc_final: 0.8535 (ppp) REVERT: I 137 TYR cc_start: 0.8005 (m-80) cc_final: 0.7666 (m-10) REVERT: J 50 TYR cc_start: 0.7838 (t80) cc_final: 0.7334 (t80) REVERT: J 133 MET cc_start: 0.9008 (mmm) cc_final: 0.8585 (mmm) REVERT: K 85 MET cc_start: 0.9371 (mmp) cc_final: 0.8774 (mmm) REVERT: K 152 LYS cc_start: 0.9415 (mtmm) cc_final: 0.9109 (mtmm) REVERT: K 180 LYS cc_start: 0.7946 (mmmm) cc_final: 0.7554 (mmpt) REVERT: L 128 MET cc_start: 0.8955 (mmm) cc_final: 0.8729 (mmt) REVERT: L 144 LEU cc_start: 0.7872 (tp) cc_final: 0.7556 (pp) REVERT: M 100 TYR cc_start: 0.8783 (m-80) cc_final: 0.8407 (m-80) outliers start: 3 outliers final: 3 residues processed: 159 average time/residue: 0.1813 time to fit residues: 42.8981 Evaluate side-chains 134 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 131 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 81 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 83 optimal weight: 8.9990 chunk 112 optimal weight: 7.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.8768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 10036 Z= 0.370 Angle : 0.824 12.668 13644 Z= 0.415 Chirality : 0.049 0.220 1563 Planarity : 0.006 0.052 1745 Dihedral : 6.164 25.404 1452 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 31.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.09 % Favored : 85.83 % Rotamer: Outliers : 0.36 % Allowed : 0.96 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.23), residues: 1214 helix: -0.70 (0.24), residues: 444 sheet: -2.90 (0.50), residues: 79 loop : -2.72 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP H 247 HIS 0.009 0.002 HIS H 114 PHE 0.018 0.002 PHE K 115 TYR 0.018 0.002 TYR K 93 ARG 0.012 0.001 ARG I 17 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 151 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.9023 (tpt) cc_final: 0.8729 (tpp) REVERT: H 79 GLU cc_start: 0.9419 (tt0) cc_final: 0.8748 (tt0) REVERT: H 340 PHE cc_start: 0.8736 (t80) cc_final: 0.8424 (t80) REVERT: H 352 TRP cc_start: 0.9015 (t-100) cc_final: 0.8197 (t-100) REVERT: I 100 ASP cc_start: 0.9226 (t0) cc_final: 0.8981 (t70) REVERT: I 137 TYR cc_start: 0.7926 (m-80) cc_final: 0.7710 (m-10) REVERT: J 50 TYR cc_start: 0.7898 (t80) cc_final: 0.7185 (t80) REVERT: J 133 MET cc_start: 0.9150 (mmm) cc_final: 0.8617 (mmm) REVERT: K 85 MET cc_start: 0.9175 (mmp) cc_final: 0.8663 (mmm) REVERT: K 92 LEU cc_start: 0.9057 (pp) cc_final: 0.8708 (pp) REVERT: K 95 GLN cc_start: 0.8760 (mt0) cc_final: 0.8396 (mt0) REVERT: K 103 ILE cc_start: 0.8598 (mm) cc_final: 0.8353 (mm) REVERT: K 133 ASP cc_start: 0.8717 (m-30) cc_final: 0.8383 (m-30) REVERT: K 135 TYR cc_start: 0.8921 (m-80) cc_final: 0.8602 (m-80) REVERT: K 152 LYS cc_start: 0.9470 (mtmm) cc_final: 0.9105 (mtmm) REVERT: K 180 LYS cc_start: 0.8096 (mmmm) cc_final: 0.7759 (mmpt) REVERT: L 108 MET cc_start: 0.9217 (mpp) cc_final: 0.8865 (mpp) REVERT: M 143 PHE cc_start: 0.8704 (t80) cc_final: 0.8454 (t80) outliers start: 3 outliers final: 3 residues processed: 153 average time/residue: 0.1792 time to fit residues: 40.7832 Evaluate side-chains 126 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 123 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 105 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 108 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 361 ASN ** J 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.047957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.042494 restraints weight = 115829.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.043218 restraints weight = 82105.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.043746 restraints weight = 62406.152| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.8428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10036 Z= 0.194 Angle : 0.679 13.563 13644 Z= 0.331 Chirality : 0.046 0.171 1563 Planarity : 0.005 0.111 1745 Dihedral : 5.442 23.817 1452 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 21.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.87 % Favored : 89.04 % Rotamer: Outliers : 0.36 % Allowed : 0.84 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.24), residues: 1214 helix: -0.38 (0.25), residues: 455 sheet: -2.68 (0.46), residues: 94 loop : -2.67 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 247 HIS 0.004 0.001 HIS H 114 PHE 0.013 0.001 PHE H 182 TYR 0.015 0.001 TYR J 57 ARG 0.006 0.001 ARG I 17 =============================================================================== Job complete usr+sys time: 2101.24 seconds wall clock time: 38 minutes 31.82 seconds (2311.82 seconds total)