Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 22:18:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ran_24378/04_2023/7ran_24378_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ran_24378/04_2023/7ran_24378.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ran_24378/04_2023/7ran_24378_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ran_24378/04_2023/7ran_24378_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ran_24378/04_2023/7ran_24378_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ran_24378/04_2023/7ran_24378.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ran_24378/04_2023/7ran_24378.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ran_24378/04_2023/7ran_24378_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ran_24378/04_2023/7ran_24378_updated.pdb" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 5425 2.51 5 N 1449 2.21 5 O 1594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 172": "OD1" <-> "OD2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B ASP 124": "OD1" <-> "OD2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B GLU 196": "OE1" <-> "OE2" Residue "B TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 38": "OD1" <-> "OD2" Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 138": "OE1" <-> "OE2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 323": "OD1" <-> "OD2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 62": "OD1" <-> "OD2" Residue "E PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 74": "OD1" <-> "OD2" Residue "E ASP 109": "OD1" <-> "OD2" Residue "E PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8523 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2023 Classifications: {'peptide': 269} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 9, 'TRANS': 259} Chain breaks: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1837 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 40 Chain: "C" Number of atoms: 2556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2556 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 376 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1715 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 217} Chain breaks: 2 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'3IQ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.92, per 1000 atoms: 0.58 Number of scatterers: 8523 At special positions: 0 Unit cell: (103.104, 106.513, 125.259, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 1594 8.00 N 1449 7.00 C 5425 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 227 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 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: 3.24 Conformation dependent library (CDL) restraints added in 1.5 seconds 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2098 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 15 sheets defined 33.8% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 80 through 101 removed outlier: 3.603A pdb=" N VAL A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 137 removed outlier: 4.250A pdb=" N MET A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Proline residue: A 129 - end of helix Processing helix chain 'A' and resid 149 through 178 Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 191 through 216 Proline residue: A 209 - end of helix removed outlier: 4.320A pdb=" N VAL A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE A 213 " --> pdb=" O PRO A 209 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 221 No H-bonds generated for 'chain 'A' and resid 218 through 221' Processing helix chain 'A' and resid 232 through 265 removed outlier: 4.121A pdb=" N ILE A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 314 through 348 removed outlier: 3.719A pdb=" N CYS A 337 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Proline residue: A 338 - end of helix removed outlier: 4.007A pdb=" N ILE A 344 " --> pdb=" O PHE A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 382 removed outlier: 3.863A pdb=" N ASN A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TRP A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Proline residue: A 377 - end of helix removed outlier: 3.636A pdb=" N TYR A 380 " --> pdb=" O ASN A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 396 Processing helix chain 'B' and resid 7 through 32 removed outlier: 3.948A pdb=" N ARG B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 118 through 129 Processing helix chain 'B' and resid 146 through 155 Processing helix chain 'B' and resid 165 through 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 184 through 203 removed outlier: 3.567A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 242 removed outlier: 4.196A pdb=" N ASP B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 24 Processing helix chain 'C' and resid 30 through 33 No H-bonds generated for 'chain 'C' and resid 30 through 33' Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'D' and resid 11 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing sheet with id= A, first strand: chain 'B' and resid 211 through 215 removed outlier: 7.756A pdb=" N VAL B 139 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N HIS B 214 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU B 141 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 37 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B 109 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 7.004A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU C 70 " --> pdb=" O TRP C 82 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.928A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.646A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 220 through 222 removed outlier: 3.675A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 229 through 234 removed outlier: 7.150A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 294 through 298 removed outlier: 3.659A pdb=" N ASN C 295 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER C 277 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.964A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 33 through 35 Processing sheet with id= K, first strand: chain 'E' and resid 49 through 51 Processing sheet with id= L, first strand: chain 'E' and resid 92 through 94 Processing sheet with id= M, first strand: chain 'E' and resid 134 through 136 removed outlier: 7.041A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'E' and resid 143 through 148 Processing sheet with id= O, first strand: chain 'E' and resid 214 through 219 removed outlier: 3.561A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) 373 hydrogen bonds defined for protein. 1068 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: 2.99 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2771 1.35 - 1.46: 2106 1.46 - 1.58: 3741 1.58 - 1.70: 0 1.70 - 1.82: 80 Bond restraints: 8698 Sorted by residual: bond pdb=" C7 3IQ A 501 " pdb=" C8 3IQ A 501 " ideal model delta sigma weight residual 1.557 1.333 0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C10 3IQ A 501 " pdb=" C9 3IQ A 501 " ideal model delta sigma weight residual 1.684 1.529 0.155 2.00e-02 2.50e+03 5.98e+01 bond pdb=" C10 3IQ A 501 " pdb=" N2 3IQ A 501 " ideal model delta sigma weight residual 1.360 1.490 -0.130 2.00e-02 2.50e+03 4.22e+01 bond pdb=" C11 3IQ A 501 " pdb=" C7 3IQ A 501 " ideal model delta sigma weight residual 1.387 1.503 -0.116 2.00e-02 2.50e+03 3.35e+01 bond pdb=" C8 3IQ A 501 " pdb=" C9 3IQ A 501 " ideal model delta sigma weight residual 1.405 1.497 -0.092 2.00e-02 2.50e+03 2.11e+01 ... (remaining 8693 not shown) Histogram of bond angle deviations from ideal: 100.02 - 107.39: 246 107.39 - 114.76: 5132 114.76 - 122.13: 4859 122.13 - 129.51: 1526 129.51 - 136.88: 61 Bond angle restraints: 11824 Sorted by residual: angle pdb=" C6 3IQ A 501 " pdb=" C5 3IQ A 501 " pdb=" C7 3IQ A 501 " ideal model delta sigma weight residual 102.42 125.45 -23.03 3.00e+00 1.11e-01 5.89e+01 angle pdb=" C1 3IQ A 501 " pdb=" C5 3IQ A 501 " pdb=" C7 3IQ A 501 " ideal model delta sigma weight residual 149.47 128.40 21.07 3.00e+00 1.11e-01 4.93e+01 angle pdb=" C ARG C 129 " pdb=" N GLU C 130 " pdb=" CA GLU C 130 " ideal model delta sigma weight residual 121.54 128.51 -6.97 1.91e+00 2.74e-01 1.33e+01 angle pdb=" N GLU C 130 " pdb=" CA GLU C 130 " pdb=" CB GLU C 130 " ideal model delta sigma weight residual 110.49 116.36 -5.87 1.69e+00 3.50e-01 1.20e+01 angle pdb=" CA GLU C 130 " pdb=" CB GLU C 130 " pdb=" CG GLU C 130 " ideal model delta sigma weight residual 114.10 120.68 -6.58 2.00e+00 2.50e-01 1.08e+01 ... (remaining 11819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 4731 17.82 - 35.64: 329 35.64 - 53.46: 59 53.46 - 71.28: 8 71.28 - 89.09: 3 Dihedral angle restraints: 5130 sinusoidal: 1884 harmonic: 3246 Sorted by residual: dihedral pdb=" CB CYS A 148 " pdb=" SG CYS A 148 " pdb=" SG CYS A 227 " pdb=" CB CYS A 227 " ideal model delta sinusoidal sigma weight residual -86.00 -175.09 89.09 1 1.00e+01 1.00e-02 9.45e+01 dihedral pdb=" CA PRO A 209 " pdb=" C PRO A 209 " pdb=" N ILE A 210 " pdb=" CA ILE A 210 " ideal model delta harmonic sigma weight residual -180.00 -160.59 -19.41 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA TYR E 101 " pdb=" C TYR E 101 " pdb=" N TYR E 102 " pdb=" CA TYR E 102 " ideal model delta harmonic sigma weight residual 180.00 162.62 17.38 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 5127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1073 0.050 - 0.101: 230 0.101 - 0.151: 54 0.151 - 0.201: 10 0.201 - 0.252: 4 Chirality restraints: 1371 Sorted by residual: chirality pdb=" C9 3IQ A 501 " pdb=" C10 3IQ A 501 " pdb=" C12 3IQ A 501 " pdb=" C8 3IQ A 501 " both_signs ideal model delta sigma weight residual False 2.79 2.54 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA GLU C 130 " pdb=" N GLU C 130 " pdb=" C GLU C 130 " pdb=" CB GLU C 130 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA THR A 88 " pdb=" N THR A 88 " pdb=" C THR A 88 " pdb=" CB THR A 88 " both_signs ideal model delta sigma weight residual False 2.53 2.73 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1368 not shown) Planarity restraints: 1501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 208 " -0.058 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO A 209 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 209 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 209 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 128 " 0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO A 129 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 129 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 129 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 342 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.76e+00 pdb=" C THR A 342 " -0.023 2.00e-02 2.50e+03 pdb=" O THR A 342 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN A 343 " 0.008 2.00e-02 2.50e+03 ... (remaining 1498 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 76 2.65 - 3.21: 7648 3.21 - 3.78: 11859 3.78 - 4.34: 15633 4.34 - 4.90: 27304 Nonbonded interactions: 62520 Sorted by model distance: nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.091 2.440 nonbonded pdb=" OD1 ASN A 110 " pdb=" OH TYR A 387 " model vdw 2.150 2.440 nonbonded pdb=" OG SER E 192 " pdb=" OG1 THR E 203 " model vdw 2.215 2.440 nonbonded pdb=" OG SER C 281 " pdb=" O HIS D 44 " model vdw 2.317 2.440 nonbonded pdb=" O GLY E 9 " pdb=" NH1 ARG E 18 " model vdw 2.319 2.520 ... (remaining 62515 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 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: 0.000 Extract box with map and model: 7.600 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 25.960 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 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 : 0.005 0.224 8698 Z= 0.300 Angle : 0.704 23.033 11824 Z= 0.397 Chirality : 0.047 0.252 1371 Planarity : 0.004 0.088 1501 Dihedral : 12.512 79.829 3023 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.61 (0.25), residues: 1100 helix: 2.65 (0.26), residues: 380 sheet: -0.07 (0.32), residues: 259 loop : -1.29 (0.25), residues: 461 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.991 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1975 time to fit residues: 40.2110 Evaluate side-chains 118 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.099 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 85 optimal weight: 0.0770 chunk 33 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 8698 Z= 0.187 Angle : 0.521 6.671 11824 Z= 0.278 Chirality : 0.042 0.146 1371 Planarity : 0.004 0.065 1501 Dihedral : 4.471 58.565 1207 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.58 (0.25), residues: 1100 helix: 2.57 (0.26), residues: 380 sheet: -0.05 (0.32), residues: 259 loop : -1.27 (0.25), residues: 461 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 0.964 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 126 average time/residue: 0.1911 time to fit residues: 34.3800 Evaluate side-chains 120 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 109 time to evaluate : 0.958 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0781 time to fit residues: 2.8768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 179 ASN A 343 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 8698 Z= 0.235 Angle : 0.550 7.363 11824 Z= 0.294 Chirality : 0.042 0.144 1371 Planarity : 0.004 0.056 1501 Dihedral : 4.547 56.414 1207 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.46 (0.25), residues: 1100 helix: 2.35 (0.26), residues: 383 sheet: -0.06 (0.32), residues: 268 loop : -1.31 (0.26), residues: 449 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 1.150 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 111 average time/residue: 0.2098 time to fit residues: 33.0199 Evaluate side-chains 100 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 1.086 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0836 time to fit residues: 2.0871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 363 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 8698 Z= 0.228 Angle : 0.540 6.960 11824 Z= 0.289 Chirality : 0.042 0.138 1371 Planarity : 0.004 0.055 1501 Dihedral : 4.546 54.665 1207 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.43 (0.25), residues: 1100 helix: 2.29 (0.26), residues: 383 sheet: -0.01 (0.32), residues: 266 loop : -1.33 (0.26), residues: 451 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 0.998 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 109 average time/residue: 0.2019 time to fit residues: 31.5865 Evaluate side-chains 107 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 1.109 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0828 time to fit residues: 2.6315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 0.1980 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 8698 Z= 0.199 Angle : 0.523 6.521 11824 Z= 0.281 Chirality : 0.041 0.142 1371 Planarity : 0.003 0.051 1501 Dihedral : 4.457 54.217 1207 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.40 (0.25), residues: 1100 helix: 2.26 (0.26), residues: 387 sheet: 0.01 (0.33), residues: 259 loop : -1.40 (0.25), residues: 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 0.904 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 106 average time/residue: 0.2017 time to fit residues: 30.1532 Evaluate side-chains 98 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 1.045 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0831 time to fit residues: 1.5729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 105 optimal weight: 0.0170 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 8698 Z= 0.155 Angle : 0.491 6.530 11824 Z= 0.264 Chirality : 0.040 0.138 1371 Planarity : 0.003 0.050 1501 Dihedral : 4.284 53.001 1207 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.57 (0.25), residues: 1100 helix: 2.47 (0.26), residues: 379 sheet: 0.04 (0.33), residues: 260 loop : -1.26 (0.26), residues: 461 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 1.130 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 106 average time/residue: 0.2140 time to fit residues: 32.2017 Evaluate side-chains 105 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 1.033 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0915 time to fit residues: 1.7316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 8698 Z= 0.179 Angle : 0.512 6.562 11824 Z= 0.273 Chirality : 0.041 0.146 1371 Planarity : 0.003 0.049 1501 Dihedral : 4.298 53.010 1207 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.56 (0.25), residues: 1100 helix: 2.44 (0.26), residues: 379 sheet: 0.05 (0.33), residues: 258 loop : -1.25 (0.26), residues: 463 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 1.034 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 106 average time/residue: 0.2084 time to fit residues: 31.1335 Evaluate side-chains 104 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 0.998 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0809 time to fit residues: 2.1519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 51 optimal weight: 0.0870 chunk 9 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 91 optimal weight: 0.0980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 8698 Z= 0.143 Angle : 0.487 6.674 11824 Z= 0.260 Chirality : 0.040 0.155 1371 Planarity : 0.003 0.049 1501 Dihedral : 4.146 51.792 1207 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.70 (0.25), residues: 1100 helix: 2.59 (0.27), residues: 379 sheet: 0.07 (0.33), residues: 260 loop : -1.16 (0.26), residues: 461 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 105 time to evaluate : 1.059 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 108 average time/residue: 0.2082 time to fit residues: 31.8416 Evaluate side-chains 105 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 1.046 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0806 time to fit residues: 1.8723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.4980 chunk 100 optimal weight: 0.1980 chunk 58 optimal weight: 0.0670 chunk 42 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 8698 Z= 0.149 Angle : 0.491 6.601 11824 Z= 0.261 Chirality : 0.040 0.154 1371 Planarity : 0.003 0.048 1501 Dihedral : 4.115 51.700 1207 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.72 (0.25), residues: 1100 helix: 2.61 (0.27), residues: 379 sheet: 0.06 (0.33), residues: 262 loop : -1.13 (0.26), residues: 459 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 0.995 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 108 average time/residue: 0.2277 time to fit residues: 33.9496 Evaluate side-chains 100 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.019 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 108 optimal weight: 0.4980 chunk 99 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 92 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 8698 Z= 0.162 Angle : 0.504 6.878 11824 Z= 0.268 Chirality : 0.041 0.157 1371 Planarity : 0.003 0.048 1501 Dihedral : 4.152 51.917 1207 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.72 (0.25), residues: 1100 helix: 2.58 (0.27), residues: 379 sheet: 0.12 (0.33), residues: 260 loop : -1.14 (0.26), residues: 461 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.118 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.2397 time to fit residues: 34.0511 Evaluate side-chains 103 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.014 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.148191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.119707 restraints weight = 12444.848| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.43 r_work: 0.3203 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 8698 Z= 0.182 Angle : 0.522 7.598 11824 Z= 0.276 Chirality : 0.041 0.165 1371 Planarity : 0.003 0.047 1501 Dihedral : 4.229 52.509 1207 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.68 (0.25), residues: 1100 helix: 2.54 (0.27), residues: 379 sheet: 0.10 (0.33), residues: 260 loop : -1.17 (0.26), residues: 461 =============================================================================== Job complete usr+sys time: 1799.35 seconds wall clock time: 33 minutes 23.12 seconds (2003.12 seconds total)